Starting phenix.real_space_refine on Thu Mar 6 00:45:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lyy_30019/03_2025/6lyy_30019.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lyy_30019/03_2025/6lyy_30019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lyy_30019/03_2025/6lyy_30019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lyy_30019/03_2025/6lyy_30019.map" model { file = "/net/cci-nas-00/data/ceres_data/6lyy_30019/03_2025/6lyy_30019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lyy_30019/03_2025/6lyy_30019.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.120 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: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 2670 2.51 5 N 694 2.21 5 O 711 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 4104 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2902 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain breaks: 1 Chain: "B" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1167 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 681 Unresolved non-hydrogen dihedrals: 443 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 277 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'EY0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.08, per 1000 atoms: 0.75 Number of scatterers: 4104 At special positions: 0 Unit cell: (104.736, 62.187, 120.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 F 3 9.00 O 711 8.00 N 694 7.00 C 2670 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 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 553.9 milliseconds 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1068 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 64.0% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 16 through 35 removed outlier: 4.495A pdb=" N ILE A 24 " --> pdb=" O TRP A 20 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 55 through 83 removed outlier: 4.844A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 85 through 104 Processing helix chain 'A' and resid 108 through 139 Proline residue: A 130 - end of helix removed outlier: 3.505A pdb=" N PHE A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.564A pdb=" N ALA A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N SER A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Proline residue: A 155 - end of helix removed outlier: 4.301A pdb=" N ALA A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 173 through 194 removed outlier: 4.028A pdb=" N GLY A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N CYS A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 260 through 274 removed outlier: 4.315A pdb=" N GLY A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ILE A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 294 through 322 removed outlier: 3.777A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Proline residue: A 314 - end of helix removed outlier: 3.657A pdb=" N THR A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 347 removed outlier: 4.227A pdb=" N SER A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 383 removed outlier: 4.608A pdb=" N TYR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 398 through 405 removed outlier: 3.870A pdb=" N VAL A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.807A pdb=" N LEU A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 440 removed outlier: 4.164A pdb=" N TYR A 423 " --> pdb=" O TYR A 419 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 428 " --> pdb=" O TRP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 447 removed outlier: 4.280A pdb=" N ASN A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 153 through 156 Processing helix chain 'B' and resid 205 through 234 Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 235 through 238 Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 32 Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.066A pdb=" N GLY B 95 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.501A pdb=" N ARG B 166 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 115 removed outlier: 3.766A pdb=" N GLY B 192 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP B 139 " --> pdb=" O LEU B 150 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 864 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 643 1.31 - 1.43: 1151 1.43 - 1.56: 2349 1.56 - 1.68: 13 1.68 - 1.81: 40 Bond restraints: 4196 Sorted by residual: bond pdb=" C30 EY0 A 601 " pdb=" C31 EY0 A 601 " ideal model delta sigma weight residual 1.532 1.323 0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C30 EY0 A 601 " pdb=" O29 EY0 A 601 " ideal model delta sigma weight residual 1.418 1.610 -0.192 2.00e-02 2.50e+03 9.22e+01 bond pdb=" C4 EY0 A 601 " pdb=" O10 EY0 A 601 " ideal model delta sigma weight residual 1.218 1.407 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C27 EY0 A 601 " pdb=" N28 EY0 A 601 " ideal model delta sigma weight residual 1.334 1.481 -0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C32 EY0 A 601 " pdb=" N28 EY0 A 601 " ideal model delta sigma weight residual 1.450 1.557 -0.107 2.00e-02 2.50e+03 2.85e+01 ... (remaining 4191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 5297 2.07 - 4.14: 349 4.14 - 6.20: 73 6.20 - 8.27: 12 8.27 - 10.34: 5 Bond angle restraints: 5736 Sorted by residual: angle pdb=" OG1 THR A 108 " pdb=" CB THR A 108 " pdb=" CG2 THR A 108 " ideal model delta sigma weight residual 109.30 119.64 -10.34 2.00e+00 2.50e-01 2.67e+01 angle pdb=" N ILE B 142 " pdb=" CA ILE B 142 " pdb=" C ILE B 142 " ideal model delta sigma weight residual 108.12 114.98 -6.86 1.34e+00 5.57e-01 2.62e+01 angle pdb=" C THR B 28 " pdb=" CA THR B 28 " pdb=" CB THR B 28 " ideal model delta sigma weight residual 109.51 117.99 -8.48 1.71e+00 3.42e-01 2.46e+01 angle pdb=" CA THR A 108 " pdb=" CB THR A 108 " pdb=" CG2 THR A 108 " ideal model delta sigma weight residual 110.50 118.78 -8.28 1.70e+00 3.46e-01 2.37e+01 angle pdb=" C GLY B 58 " pdb=" N GLY B 59 " pdb=" CA GLY B 59 " ideal model delta sigma weight residual 122.47 126.79 -4.32 8.90e-01 1.26e+00 2.36e+01 ... (remaining 5731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.71: 2116 14.71 - 29.42: 192 29.42 - 44.13: 56 44.13 - 58.84: 10 58.84 - 73.55: 5 Dihedral angle restraints: 2379 sinusoidal: 698 harmonic: 1681 Sorted by residual: dihedral pdb=" C VAL B 50 " pdb=" N VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual -122.00 -139.08 17.08 0 2.50e+00 1.60e-01 4.67e+01 dihedral pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual 123.40 139.14 -15.74 0 2.50e+00 1.60e-01 3.97e+01 dihedral pdb=" C VAL B 61 " pdb=" N VAL B 61 " pdb=" CA VAL B 61 " pdb=" CB VAL B 61 " ideal model delta harmonic sigma weight residual -122.00 -136.20 14.20 0 2.50e+00 1.60e-01 3.22e+01 ... (remaining 2376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.260: 655 0.260 - 0.520: 14 0.520 - 0.781: 2 0.781 - 1.041: 0 1.041 - 1.301: 1 Chirality restraints: 672 Sorted by residual: chirality pdb=" CB THR A 108 " pdb=" CA THR A 108 " pdb=" OG1 THR A 108 " pdb=" CG2 THR A 108 " both_signs ideal model delta sigma weight residual False 2.55 1.25 1.30 2.00e-01 2.50e+01 4.23e+01 chirality pdb=" CA VAL B 50 " pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CB VAL B 50 " both_signs ideal model delta sigma weight residual False 2.44 1.88 0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" CA GLU B 172 " pdb=" N GLU B 172 " pdb=" C GLU B 172 " pdb=" CB GLU B 172 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.73e+00 ... (remaining 669 not shown) Planarity restraints: 727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 103 " 0.013 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C GLY B 103 " -0.042 2.00e-02 2.50e+03 pdb=" O GLY B 103 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO B 104 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 55 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C TRP B 55 " 0.042 2.00e-02 2.50e+03 pdb=" O TRP B 55 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 56 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 323 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO A 324 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " -0.029 5.00e-02 4.00e+02 ... (remaining 724 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 122 2.70 - 3.25: 4397 3.25 - 3.80: 6262 3.80 - 4.35: 7509 4.35 - 4.90: 12310 Nonbonded interactions: 30600 Sorted by model distance: nonbonded pdb=" O THR A 351 " pdb=" OG1 THR A 352 " model vdw 2.152 3.040 nonbonded pdb=" ND1 HIS B 115 " pdb=" NH2 ARG B 203 " model vdw 2.217 3.200 nonbonded pdb=" CD2 LEU A 281 " pdb=" F24 EY0 A 601 " model vdw 2.269 3.410 nonbonded pdb=" O GLY A 173 " pdb=" OG SER A 177 " model vdw 2.333 3.040 nonbonded pdb=" O GLY A 73 " pdb=" OG SER A 76 " model vdw 2.335 3.040 ... (remaining 30595 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.290 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4893 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 : 0.010 0.209 4196 Z= 0.749 Angle : 1.163 10.338 5736 Z= 0.739 Chirality : 0.100 1.301 672 Planarity : 0.005 0.052 727 Dihedral : 13.413 73.546 1311 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.90 % Allowed : 5.39 % Favored : 93.71 % Cbeta Deviations : 1.69 % Peptide Plane: Cis-proline : 7.41 % 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: -3.75 (0.30), residues: 591 helix: -2.37 (0.23), residues: 348 sheet: -0.47 (0.50), residues: 104 loop : -3.81 (0.39), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 174 HIS 0.001 0.001 HIS A 344 PHE 0.024 0.002 PHE A 27 TYR 0.012 0.002 TYR A 140 ARG 0.004 0.001 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.429 Fit side-chains REVERT: A 95 LEU cc_start: 0.6292 (tp) cc_final: 0.6014 (tp) REVERT: A 318 LEU cc_start: 0.8498 (tp) cc_final: 0.8236 (tt) REVERT: A 418 ASP cc_start: 0.8128 (t70) cc_final: 0.7438 (t70) outliers start: 3 outliers final: 0 residues processed: 72 average time/residue: 0.1823 time to fit residues: 16.2219 Evaluate side-chains 53 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 270 ASN A 340 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.235397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.202970 restraints weight = 6574.049| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 2.94 r_work: 0.4212 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4196 Z= 0.243 Angle : 0.707 6.291 5736 Z= 0.364 Chirality : 0.045 0.162 672 Planarity : 0.004 0.039 727 Dihedral : 4.987 43.690 641 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.89 % Allowed : 12.57 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.35), residues: 591 helix: -0.55 (0.28), residues: 349 sheet: 0.18 (0.51), residues: 110 loop : -2.65 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 174 HIS 0.004 0.001 HIS A 344 PHE 0.017 0.002 PHE A 27 TYR 0.011 0.002 TYR A 113 ARG 0.004 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.382 Fit side-chains REVERT: A 47 ILE cc_start: 0.8594 (mm) cc_final: 0.8294 (mm) REVERT: A 95 LEU cc_start: 0.7318 (tp) cc_final: 0.7029 (tp) REVERT: A 138 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7370 (m-80) REVERT: A 187 ASN cc_start: 0.8226 (t0) cc_final: 0.7979 (t0) REVERT: A 196 ARG cc_start: 0.7692 (mtm180) cc_final: 0.7412 (mtm180) REVERT: A 274 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7433 (t80) REVERT: A 282 VAL cc_start: 0.9018 (p) cc_final: 0.8590 (m) REVERT: A 418 ASP cc_start: 0.7837 (t70) cc_final: 0.7232 (t70) outliers start: 13 outliers final: 6 residues processed: 88 average time/residue: 0.1239 time to fit residues: 14.3703 Evaluate side-chains 78 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 322 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 40 optimal weight: 40.0000 chunk 6 optimal weight: 0.0070 chunk 5 optimal weight: 0.1980 chunk 55 optimal weight: 9.9990 chunk 44 optimal weight: 0.0060 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 344 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.237295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.206320 restraints weight = 6157.388| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 2.85 r_work: 0.4238 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4196 Z= 0.174 Angle : 0.620 8.010 5736 Z= 0.313 Chirality : 0.042 0.142 672 Planarity : 0.004 0.040 727 Dihedral : 4.670 41.723 641 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.09 % Allowed : 14.67 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.44 (0.36), residues: 591 helix: 0.21 (0.29), residues: 349 sheet: 0.53 (0.50), residues: 112 loop : -2.17 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 174 HIS 0.003 0.001 HIS A 344 PHE 0.037 0.002 PHE A 332 TYR 0.012 0.001 TYR A 113 ARG 0.001 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.430 Fit side-chains REVERT: A 138 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7196 (m-80) REVERT: A 272 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7789 (mp) REVERT: A 282 VAL cc_start: 0.9008 (p) cc_final: 0.8538 (m) outliers start: 17 outliers final: 9 residues processed: 83 average time/residue: 0.1260 time to fit residues: 13.9785 Evaluate side-chains 78 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 322 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.0050 chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 50.0000 chunk 5 optimal weight: 0.3980 chunk 50 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** 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 = 0.4625 r_free = 0.4625 target = 0.232135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.200613 restraints weight = 6477.070| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 2.97 r_work: 0.4201 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4196 Z= 0.206 Angle : 0.641 8.118 5736 Z= 0.322 Chirality : 0.043 0.147 672 Planarity : 0.004 0.043 727 Dihedral : 4.551 36.391 641 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.79 % Allowed : 16.77 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.36), residues: 591 helix: 0.38 (0.29), residues: 351 sheet: 1.09 (0.53), residues: 98 loop : -2.15 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 174 HIS 0.003 0.001 HIS A 344 PHE 0.024 0.002 PHE A 274 TYR 0.015 0.001 TYR A 287 ARG 0.004 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.412 Fit side-chains REVERT: A 138 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: A 332 PHE cc_start: 0.8002 (t80) cc_final: 0.7763 (t80) REVERT: A 438 PHE cc_start: 0.7260 (t80) cc_final: 0.7038 (t80) outliers start: 16 outliers final: 8 residues processed: 93 average time/residue: 0.1069 time to fit residues: 13.7190 Evaluate side-chains 82 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 391 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 18 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 42 optimal weight: 0.0980 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.231262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.201528 restraints weight = 6256.695| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 2.86 r_work: 0.4225 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4196 Z= 0.174 Angle : 0.606 7.603 5736 Z= 0.302 Chirality : 0.042 0.139 672 Planarity : 0.004 0.042 727 Dihedral : 4.336 24.916 641 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 6.59 % Allowed : 18.56 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.14 (0.37), residues: 591 helix: 0.64 (0.29), residues: 352 sheet: 1.16 (0.53), residues: 98 loop : -1.98 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 174 HIS 0.002 0.001 HIS A 344 PHE 0.021 0.001 PHE A 27 TYR 0.009 0.001 TYR A 113 ARG 0.002 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.422 Fit side-chains REVERT: A 48 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5250 (mp0) REVERT: A 138 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7222 (m-80) REVERT: A 282 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8907 (m) REVERT: A 412 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6498 (mp) outliers start: 22 outliers final: 8 residues processed: 94 average time/residue: 0.1160 time to fit residues: 15.2161 Evaluate side-chains 84 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 218 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** 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 = 0.4629 r_free = 0.4629 target = 0.232229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.200215 restraints weight = 6393.424| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 2.94 r_work: 0.4179 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4196 Z= 0.185 Angle : 0.602 7.322 5736 Z= 0.304 Chirality : 0.042 0.141 672 Planarity : 0.004 0.045 727 Dihedral : 4.289 24.983 641 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 6.89 % Allowed : 19.46 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.18 (0.37), residues: 591 helix: 0.70 (0.29), residues: 353 sheet: 1.13 (0.53), residues: 98 loop : -2.02 (0.56), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 174 HIS 0.003 0.001 HIS B 115 PHE 0.021 0.002 PHE A 27 TYR 0.008 0.001 TYR A 113 ARG 0.003 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.493 Fit side-chains REVERT: A 18 TRP cc_start: 0.7041 (OUTLIER) cc_final: 0.5643 (t60) REVERT: A 138 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: A 274 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7333 (t80) REVERT: A 412 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6495 (mp) REVERT: A 418 ASP cc_start: 0.7487 (t70) cc_final: 0.7110 (t0) outliers start: 23 outliers final: 12 residues processed: 91 average time/residue: 0.1064 time to fit residues: 13.8188 Evaluate side-chains 89 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 218 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 53 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** 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 = 0.4568 r_free = 0.4568 target = 0.225108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.193357 restraints weight = 6419.641| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.95 r_work: 0.4158 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4196 Z= 0.223 Angle : 0.636 8.360 5736 Z= 0.325 Chirality : 0.043 0.147 672 Planarity : 0.004 0.045 727 Dihedral : 4.457 24.868 641 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.99 % Allowed : 20.96 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.36), residues: 591 helix: 0.63 (0.29), residues: 354 sheet: 0.89 (0.51), residues: 103 loop : -1.98 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 174 HIS 0.004 0.001 HIS B 115 PHE 0.046 0.002 PHE A 332 TYR 0.009 0.001 TYR A 331 ARG 0.003 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.420 Fit side-chains REVERT: A 18 TRP cc_start: 0.7203 (OUTLIER) cc_final: 0.5645 (t60) REVERT: A 48 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.5485 (mp0) REVERT: A 138 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7082 (m-80) REVERT: A 274 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7346 (t80) REVERT: A 332 PHE cc_start: 0.8282 (t80) cc_final: 0.8056 (t80) REVERT: A 418 ASP cc_start: 0.7579 (t70) cc_final: 0.7186 (t0) outliers start: 20 outliers final: 11 residues processed: 86 average time/residue: 0.1028 time to fit residues: 12.3990 Evaluate side-chains 89 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 218 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 40 optimal weight: 50.0000 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 40.0000 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.223589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.193529 restraints weight = 6258.325| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 2.84 r_work: 0.4136 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4196 Z= 0.217 Angle : 0.646 9.095 5736 Z= 0.327 Chirality : 0.043 0.151 672 Planarity : 0.004 0.050 727 Dihedral : 4.545 24.919 641 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 6.29 % Allowed : 23.35 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.17 (0.36), residues: 591 helix: 0.71 (0.29), residues: 354 sheet: 0.71 (0.49), residues: 108 loop : -1.93 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 174 HIS 0.003 0.001 HIS B 115 PHE 0.045 0.002 PHE A 332 TYR 0.010 0.001 TYR A 138 ARG 0.003 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 1.227 Fit side-chains REVERT: A 18 TRP cc_start: 0.7149 (OUTLIER) cc_final: 0.5675 (t60) REVERT: A 46 GLU cc_start: 0.8589 (tp30) cc_final: 0.8242 (tp30) REVERT: A 48 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.5742 (mp0) REVERT: A 138 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7301 (m-80) REVERT: A 274 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7367 (t80) REVERT: A 418 ASP cc_start: 0.7729 (t70) cc_final: 0.7187 (t70) REVERT: B 201 ARG cc_start: 0.5966 (ttt180) cc_final: 0.5436 (ttp-170) outliers start: 21 outliers final: 15 residues processed: 94 average time/residue: 0.1682 time to fit residues: 22.9205 Evaluate side-chains 94 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 218 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 50.0000 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 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 127 ASN ** 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 = 0.4534 r_free = 0.4534 target = 0.223146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.192900 restraints weight = 6237.933| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.85 r_work: 0.4122 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4196 Z= 0.193 Angle : 0.632 9.510 5736 Z= 0.319 Chirality : 0.042 0.146 672 Planarity : 0.004 0.048 727 Dihedral : 4.486 24.580 641 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.69 % Allowed : 25.15 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.32 (0.36), residues: 591 helix: 0.83 (0.29), residues: 353 sheet: 0.96 (0.52), residues: 103 loop : -1.93 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 174 HIS 0.003 0.001 HIS B 115 PHE 0.042 0.002 PHE A 332 TYR 0.011 0.001 TYR A 419 ARG 0.003 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 1.390 Fit side-chains REVERT: A 18 TRP cc_start: 0.7181 (OUTLIER) cc_final: 0.5675 (t60) REVERT: A 46 GLU cc_start: 0.8482 (tp30) cc_final: 0.8135 (tp30) REVERT: A 48 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.5647 (mp0) REVERT: A 138 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7013 (m-80) REVERT: A 274 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7323 (t80) outliers start: 19 outliers final: 13 residues processed: 87 average time/residue: 0.1166 time to fit residues: 14.5449 Evaluate side-chains 88 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 218 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 38 optimal weight: 50.0000 chunk 51 optimal weight: 0.0270 chunk 23 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** 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 = 0.4549 r_free = 0.4549 target = 0.224856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.194614 restraints weight = 6296.675| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.90 r_work: 0.4141 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4196 Z= 0.188 Angle : 0.641 9.758 5736 Z= 0.321 Chirality : 0.042 0.138 672 Planarity : 0.004 0.041 727 Dihedral : 4.423 24.581 641 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.69 % Allowed : 25.15 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.37), residues: 591 helix: 0.91 (0.29), residues: 352 sheet: 0.90 (0.51), residues: 108 loop : -1.78 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 174 HIS 0.002 0.001 HIS A 292 PHE 0.022 0.001 PHE A 27 TYR 0.007 0.001 TYR A 113 ARG 0.002 0.000 ARG A 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.374 Fit side-chains REVERT: A 18 TRP cc_start: 0.7068 (OUTLIER) cc_final: 0.5666 (t60) REVERT: A 48 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.5601 (mp0) REVERT: A 138 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.6670 (m-80) REVERT: A 274 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7309 (t80) outliers start: 19 outliers final: 14 residues processed: 83 average time/residue: 0.1072 time to fit residues: 12.9555 Evaluate side-chains 87 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 218 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.0770 chunk 5 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** 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 = 0.4567 r_free = 0.4567 target = 0.227075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.197325 restraints weight = 6238.806| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.87 r_work: 0.4164 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.6614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4196 Z= 0.171 Angle : 0.620 9.413 5736 Z= 0.309 Chirality : 0.042 0.133 672 Planarity : 0.004 0.040 727 Dihedral : 4.285 24.518 641 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.49 % Allowed : 26.65 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.64 (0.37), residues: 591 helix: 1.00 (0.29), residues: 354 sheet: 1.61 (0.55), residues: 95 loop : -1.85 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 174 HIS 0.002 0.001 HIS A 292 PHE 0.020 0.001 PHE A 27 TYR 0.008 0.001 TYR A 113 ARG 0.002 0.000 ARG A 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2782.90 seconds wall clock time: 49 minutes 29.91 seconds (2969.91 seconds total)