Starting phenix.real_space_refine on Tue Feb 11 05:03:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ckr_30391/02_2025/7ckr_30391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ckr_30391/02_2025/7ckr_30391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ckr_30391/02_2025/7ckr_30391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ckr_30391/02_2025/7ckr_30391.map" model { file = "/net/cci-nas-00/data/ceres_data/7ckr_30391/02_2025/7ckr_30391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ckr_30391/02_2025/7ckr_30391.cif" } resolution = 3.0 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= 0.004 sd= 0.070 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 Cl 1 4.86 5 C 2669 2.51 5 N 687 2.21 5 O 711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4094 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2900 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1166 Classifications: {'peptide': 215} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 155} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 204} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 527 Unresolved non-hydrogen angles: 675 Unresolved non-hydrogen dihedrals: 438 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': 7} Unresolved non-hydrogen planarities: 282 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'G5O': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.35, per 1000 atoms: 0.82 Number of scatterers: 4094 At special positions: 0 Unit cell: (102.883, 58.1877, 112.159, 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) Cl 1 17.00 S 26 16.00 O 711 8.00 N 687 7.00 C 2669 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: 1.22 Conformation dependent library (CDL) restraints added in 587.9 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: 1066 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 4 sheets defined 65.7% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 18 through 41 removed outlier: 3.942A pdb=" N VAL A 22 " --> pdb=" O TRP A 18 " (cutoff:3.500A) Proline residue: A 37 - end of helix Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.663A pdb=" N ILE A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 72 removed outlier: 3.983A pdb=" N TRP A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 83 Processing helix chain 'A' and resid 84 through 104 removed outlier: 3.702A pdb=" N VAL A 88 " --> pdb=" O GLY A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 139 Proline residue: A 130 - end of helix removed outlier: 3.634A pdb=" N THR A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.871A pdb=" N ALA A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Proline residue: A 155 - end of helix removed outlier: 3.802A pdb=" N LEU A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 260 through 278 removed outlier: 4.048A pdb=" N GLY A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 291 removed outlier: 5.024A pdb=" N SER A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N SER A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 321 removed outlier: 3.576A pdb=" N ALA A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 328 through 347 removed outlier: 3.945A pdb=" N HIS A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 352 through 382 removed outlier: 3.918A pdb=" N TYR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 416 Proline residue: A 401 - end of helix removed outlier: 4.226A pdb=" N LEU A 404 " --> pdb=" O CYS A 400 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 419 through 449 removed outlier: 3.820A pdb=" N GLY A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 153 through 156 Processing helix chain 'B' and resid 208 through 237 removed outlier: 4.080A pdb=" N PHE B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Proline residue: B 235 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 33 Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.067A 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 117 removed outlier: 6.449A pdb=" N GLU B 114 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ARG B 203 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE B 116 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 192 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TRP B 139 " --> pdb=" O LEU B 150 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 930 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: 1.32 Time building geometry restraints manager: 1.35 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: 644 1.31 - 1.43: 1150 1.43 - 1.56: 2344 1.56 - 1.69: 8 1.69 - 1.81: 41 Bond restraints: 4187 Sorted by residual: bond pdb=" C12 G5O A 601 " pdb=" C13 G5O A 601 " ideal model delta sigma weight residual 1.387 1.525 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C10 G5O A 601 " pdb=" C11 G5O A 601 " ideal model delta sigma weight residual 1.388 1.524 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C14 G5O A 601 " pdb=" C15 G5O A 601 " ideal model delta sigma weight residual 1.387 1.522 -0.135 2.00e-02 2.50e+03 4.59e+01 bond pdb=" C17 G5O A 601 " pdb=" N18 G5O A 601 " ideal model delta sigma weight residual 1.339 1.453 -0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" N PRO B 91 " pdb=" CD PRO B 91 " ideal model delta sigma weight residual 1.474 1.538 -0.064 1.40e-02 5.10e+03 2.10e+01 ... (remaining 4182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 5599 3.64 - 7.29: 112 7.29 - 10.93: 5 10.93 - 14.57: 3 14.57 - 18.22: 1 Bond angle restraints: 5720 Sorted by residual: angle pdb=" CA PRO B 91 " pdb=" N PRO B 91 " pdb=" CD PRO B 91 " ideal model delta sigma weight residual 111.50 97.99 13.51 1.40e+00 5.10e-01 9.31e+01 angle pdb=" CA PRO B 132 " pdb=" N PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 111.50 98.07 13.43 1.40e+00 5.10e-01 9.21e+01 angle pdb=" CA PRO B 93 " pdb=" N PRO B 93 " pdb=" CD PRO B 93 " ideal model delta sigma weight residual 111.50 99.09 12.41 1.40e+00 5.10e-01 7.85e+01 angle pdb=" O8 G5O A 601 " pdb=" S7 G5O A 601 " pdb=" O9 G5O A 601 " ideal model delta sigma weight residual 119.81 101.59 18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" N ILE B 142 " pdb=" CA ILE B 142 " pdb=" C ILE B 142 " ideal model delta sigma weight residual 108.12 114.96 -6.84 1.34e+00 5.57e-01 2.61e+01 ... (remaining 5715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 2056 16.50 - 33.01: 200 33.01 - 49.51: 82 49.51 - 66.02: 27 66.02 - 82.52: 4 Dihedral angle restraints: 2369 sinusoidal: 690 harmonic: 1679 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 -139.04 17.04 0 2.50e+00 1.60e-01 4.65e+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 123.40 139.11 -15.71 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" CA TYR A 293 " pdb=" C TYR A 293 " pdb=" N SER A 294 " pdb=" CA SER A 294 " ideal model delta harmonic sigma weight residual 180.00 150.26 29.74 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 2366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 595 0.112 - 0.224: 60 0.224 - 0.336: 7 0.336 - 0.448: 5 0.448 - 0.560: 3 Chirality restraints: 670 Sorted by residual: 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 7.84e+00 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 7.74e+00 chirality pdb=" CA GLU B 155 " pdb=" N GLU B 155 " pdb=" C GLU B 155 " pdb=" CB GLU B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.78e+00 ... (remaining 667 not shown) Planarity restraints: 731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 131 " 0.117 5.00e-02 4.00e+02 1.63e-01 4.28e+01 pdb=" N PRO B 132 " -0.281 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " 0.098 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 90 " -0.081 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO B 91 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO B 91 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 91 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 27 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.74e+00 pdb=" C PHE A 27 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE A 27 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE A 28 " -0.015 2.00e-02 2.50e+03 ... (remaining 728 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 24 2.50 - 3.10: 3316 3.10 - 3.70: 6203 3.70 - 4.30: 8787 4.30 - 4.90: 14435 Nonbonded interactions: 32765 Sorted by model distance: nonbonded pdb=" O GLY A 173 " pdb=" OG SER A 177 " model vdw 1.896 3.040 nonbonded pdb=" O PRO A 324 " pdb=" NH1 ARG A 328 " model vdw 1.989 3.120 nonbonded pdb=" OE1 GLN A 330 " pdb=" OG1 THR A 377 " model vdw 2.059 3.040 nonbonded pdb=" O LYS A 38 " pdb=" OG1 THR A 41 " model vdw 2.141 3.040 nonbonded pdb=" OD1 ASP A 418 " pdb=" N TYR A 419 " model vdw 2.157 3.120 ... (remaining 32760 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: 0.990 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 14.900 Find NCS groups from input model: 0.040 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:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 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 : 0.009 0.138 4187 Z= 0.650 Angle : 1.223 18.216 5720 Z= 0.792 Chirality : 0.085 0.560 670 Planarity : 0.010 0.163 731 Dihedral : 17.221 82.520 1303 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.95 % Favored : 91.88 % Rotamer: Outliers : 11.04 % Allowed : 20.90 % Favored : 68.06 % Cbeta Deviations : 1.69 % Peptide Plane: Cis-proline : 11.11 % 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: -2.89 (0.31), residues: 591 helix: -1.92 (0.24), residues: 357 sheet: 0.30 (0.53), residues: 94 loop : -2.94 (0.43), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 174 HIS 0.003 0.001 HIS A 260 PHE 0.028 0.001 PHE A 27 TYR 0.011 0.001 TYR A 266 ARG 0.002 0.000 ARG A 386 *********************** 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 108 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 71 time to evaluate : 0.450 Fit side-chains REVERT: A 128 LEU cc_start: 0.8649 (tp) cc_final: 0.8444 (tp) REVERT: A 137 LYS cc_start: 0.8453 (tttt) cc_final: 0.8183 (ttmt) REVERT: A 380 ASP cc_start: 0.6159 (OUTLIER) cc_final: 0.5847 (m-30) REVERT: B 204 SER cc_start: 0.5404 (OUTLIER) cc_final: 0.5163 (m) outliers start: 37 outliers final: 14 residues processed: 99 average time/residue: 0.6710 time to fit residues: 70.5820 Evaluate side-chains 81 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 220 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 127 ASN A 270 ASN A 330 GLN B 115 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.228392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.198327 restraints weight = 5384.588| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 1.91 r_work: 0.4205 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.4118 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4187 Z= 0.264 Angle : 0.716 8.143 5720 Z= 0.377 Chirality : 0.045 0.135 670 Planarity : 0.007 0.062 731 Dihedral : 7.300 56.927 657 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 6.57 % Allowed : 23.88 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.35), residues: 591 helix: -0.07 (0.27), residues: 369 sheet: 0.87 (0.53), residues: 101 loop : -2.34 (0.51), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 174 HIS 0.007 0.002 HIS B 115 PHE 0.030 0.002 PHE A 27 TYR 0.017 0.002 TYR B 229 ARG 0.008 0.001 ARG A 446 *********************** 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 109 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 255 LEU cc_start: 0.4112 (OUTLIER) cc_final: 0.3482 (pt) REVERT: A 272 ILE cc_start: 0.8266 (mt) cc_final: 0.7994 (tt) REVERT: A 373 VAL cc_start: 0.8104 (t) cc_final: 0.7861 (m) REVERT: B 204 SER cc_start: 0.5133 (p) cc_final: 0.4896 (t) outliers start: 22 outliers final: 9 residues processed: 102 average time/residue: 0.4823 time to fit residues: 53.2753 Evaluate side-chains 92 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 220 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 42 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 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 127 ASN A 291 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.229126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.200037 restraints weight = 5398.513| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 1.94 r_work: 0.4215 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4129 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4187 Z= 0.206 Angle : 0.661 7.968 5720 Z= 0.343 Chirality : 0.045 0.154 670 Planarity : 0.006 0.049 731 Dihedral : 6.242 52.828 641 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.97 % Allowed : 27.76 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.35), residues: 591 helix: 0.55 (0.28), residues: 364 sheet: 1.13 (0.53), residues: 101 loop : -2.00 (0.50), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 174 HIS 0.004 0.001 HIS A 344 PHE 0.025 0.001 PHE A 27 TYR 0.013 0.001 TYR A 423 ARG 0.006 0.001 ARG A 196 *********************** 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 106 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8215 (m-10) cc_final: 0.7838 (m-10) REVERT: A 255 LEU cc_start: 0.4001 (OUTLIER) cc_final: 0.3294 (pt) REVERT: A 272 ILE cc_start: 0.8247 (mt) cc_final: 0.7979 (tt) REVERT: A 376 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.5881 (tm-30) REVERT: A 380 ASP cc_start: 0.6180 (m-30) cc_final: 0.5508 (m-30) REVERT: A 400 CYS cc_start: 0.7882 (t) cc_final: 0.7398 (m) REVERT: B 204 SER cc_start: 0.5187 (p) cc_final: 0.4898 (t) outliers start: 20 outliers final: 9 residues processed: 99 average time/residue: 0.4954 time to fit residues: 52.8750 Evaluate side-chains 89 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 220 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 127 ASN A 330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.229162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.200486 restraints weight = 5419.832| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 1.92 r_work: 0.4210 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4121 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4187 Z= 0.203 Angle : 0.664 8.578 5720 Z= 0.341 Chirality : 0.045 0.156 670 Planarity : 0.005 0.050 731 Dihedral : 6.088 49.511 641 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.37 % Allowed : 30.45 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.37 (0.36), residues: 591 helix: 0.68 (0.29), residues: 365 sheet: 1.27 (0.52), residues: 101 loop : -1.76 (0.52), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 174 HIS 0.002 0.001 HIS A 260 PHE 0.024 0.001 PHE A 27 TYR 0.033 0.002 TYR A 266 ARG 0.005 0.001 ARG A 196 *********************** 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 109 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8186 (m-10) cc_final: 0.7758 (m-10) REVERT: A 255 LEU cc_start: 0.4061 (OUTLIER) cc_final: 0.3332 (pt) REVERT: A 376 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.5823 (tm-30) REVERT: A 380 ASP cc_start: 0.6171 (m-30) cc_final: 0.5526 (m-30) REVERT: A 400 CYS cc_start: 0.7823 (t) cc_final: 0.7322 (m) REVERT: B 204 SER cc_start: 0.5313 (p) cc_final: 0.5033 (t) outliers start: 18 outliers final: 8 residues processed: 102 average time/residue: 0.5740 time to fit residues: 62.5999 Evaluate side-chains 96 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 220 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 165 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 = 0.4598 r_free = 0.4598 target = 0.228145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.198602 restraints weight = 5462.605| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 1.89 r_work: 0.4198 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4111 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4187 Z= 0.213 Angle : 0.676 8.799 5720 Z= 0.346 Chirality : 0.045 0.164 670 Planarity : 0.005 0.053 731 Dihedral : 5.973 47.155 639 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.67 % Allowed : 31.64 % Favored : 62.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.36), residues: 591 helix: 0.72 (0.29), residues: 366 sheet: 1.33 (0.51), residues: 101 loop : -1.58 (0.53), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 174 HIS 0.003 0.001 HIS A 260 PHE 0.025 0.001 PHE A 27 TYR 0.015 0.002 TYR A 423 ARG 0.004 0.000 ARG A 196 *********************** 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 110 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8097 (m-10) cc_final: 0.7619 (m-80) REVERT: A 129 ASN cc_start: 0.8328 (t0) cc_final: 0.8100 (t0) REVERT: A 255 LEU cc_start: 0.4232 (OUTLIER) cc_final: 0.3615 (pt) REVERT: A 376 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.5817 (tm-30) REVERT: A 380 ASP cc_start: 0.6124 (m-30) cc_final: 0.5571 (m-30) REVERT: A 400 CYS cc_start: 0.7706 (t) cc_final: 0.7223 (m) REVERT: A 435 ILE cc_start: 0.8526 (mp) cc_final: 0.8150 (mt) REVERT: B 204 SER cc_start: 0.5287 (p) cc_final: 0.5021 (t) outliers start: 19 outliers final: 8 residues processed: 104 average time/residue: 0.5200 time to fit residues: 58.1343 Evaluate side-chains 97 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain B residue 115 HIS 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 49 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.225484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.194713 restraints weight = 5322.804| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 2.00 r_work: 0.4165 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4076 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4187 Z= 0.244 Angle : 0.704 9.316 5720 Z= 0.364 Chirality : 0.047 0.198 670 Planarity : 0.005 0.051 731 Dihedral : 5.445 46.385 635 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 7.16 % Allowed : 31.34 % Favored : 61.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.41 (0.36), residues: 591 helix: 0.66 (0.29), residues: 362 sheet: 1.39 (0.51), residues: 99 loop : -1.52 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 174 HIS 0.002 0.001 HIS A 260 PHE 0.025 0.002 PHE A 27 TYR 0.024 0.002 TYR A 266 ARG 0.002 0.000 ARG A 196 *********************** 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 114 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8135 (m-10) cc_final: 0.7634 (m-80) REVERT: A 166 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7206 (pm20) REVERT: A 255 LEU cc_start: 0.4288 (OUTLIER) cc_final: 0.3739 (pt) REVERT: A 376 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.5813 (tm-30) REVERT: A 380 ASP cc_start: 0.6353 (m-30) cc_final: 0.5804 (m-30) REVERT: A 400 CYS cc_start: 0.7575 (t) cc_final: 0.7042 (m) REVERT: A 435 ILE cc_start: 0.8538 (mt) cc_final: 0.8090 (mt) REVERT: B 204 SER cc_start: 0.5534 (p) cc_final: 0.5187 (m) outliers start: 24 outliers final: 8 residues processed: 105 average time/residue: 0.4925 time to fit residues: 55.8599 Evaluate side-chains 97 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 399 CYS Chi-restraints excluded: chain B residue 115 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 40 optimal weight: 40.0000 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.226976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.196037 restraints weight = 5341.471| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 1.99 r_work: 0.4173 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4081 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4187 Z= 0.224 Angle : 0.695 9.534 5720 Z= 0.355 Chirality : 0.047 0.191 670 Planarity : 0.005 0.053 731 Dihedral : 5.352 47.255 635 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.37 % Allowed : 32.84 % Favored : 61.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.56 (0.36), residues: 591 helix: 0.73 (0.29), residues: 363 sheet: 1.53 (0.51), residues: 99 loop : -1.41 (0.55), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 174 HIS 0.003 0.001 HIS A 260 PHE 0.025 0.002 PHE A 332 TYR 0.012 0.002 TYR A 423 ARG 0.002 0.000 ARG A 196 *********************** 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 108 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8078 (m-10) cc_final: 0.7625 (m-10) REVERT: A 129 ASN cc_start: 0.8311 (t0) cc_final: 0.8090 (t0) REVERT: A 166 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: A 255 LEU cc_start: 0.4345 (OUTLIER) cc_final: 0.3812 (pt) REVERT: A 376 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.5880 (tm-30) REVERT: A 379 MET cc_start: 0.7792 (ttt) cc_final: 0.7502 (ttp) REVERT: A 380 ASP cc_start: 0.6395 (m-30) cc_final: 0.5905 (m-30) REVERT: A 400 CYS cc_start: 0.7446 (t) cc_final: 0.7000 (m) REVERT: A 435 ILE cc_start: 0.8547 (mt) cc_final: 0.8097 (mt) REVERT: B 204 SER cc_start: 0.5572 (p) cc_final: 0.5218 (m) outliers start: 18 outliers final: 6 residues processed: 102 average time/residue: 0.5279 time to fit residues: 57.9401 Evaluate side-chains 95 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 399 CYS 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 51 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 39 optimal weight: 20.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.218379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.188081 restraints weight = 5268.873| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.04 r_work: 0.4092 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4001 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 4187 Z= 0.398 Angle : 0.815 9.789 5720 Z= 0.430 Chirality : 0.052 0.203 670 Planarity : 0.006 0.052 731 Dihedral : 6.106 46.999 635 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.57 % Allowed : 32.84 % Favored : 60.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.07 (0.35), residues: 591 helix: 0.30 (0.27), residues: 360 sheet: 1.30 (0.49), residues: 109 loop : -1.61 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 18 HIS 0.004 0.001 HIS A 260 PHE 0.026 0.002 PHE A 27 TYR 0.017 0.003 TYR A 423 ARG 0.003 0.001 ARG A 313 *********************** 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 119 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8168 (m-10) cc_final: 0.7644 (m-80) REVERT: A 166 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: A 255 LEU cc_start: 0.4580 (OUTLIER) cc_final: 0.4212 (pt) REVERT: A 270 ASN cc_start: 0.8144 (m-40) cc_final: 0.7803 (m-40) REVERT: A 380 ASP cc_start: 0.6732 (m-30) cc_final: 0.6462 (m-30) REVERT: A 416 TYR cc_start: 0.6014 (OUTLIER) cc_final: 0.4846 (t80) REVERT: A 435 ILE cc_start: 0.8555 (mt) cc_final: 0.8123 (mt) REVERT: B 204 SER cc_start: 0.5966 (p) cc_final: 0.5620 (m) outliers start: 22 outliers final: 11 residues processed: 111 average time/residue: 0.5177 time to fit residues: 61.8312 Evaluate side-chains 104 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 399 CYS Chi-restraints excluded: chain A residue 416 TYR 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 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 A 147 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.225697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.195334 restraints weight = 5235.763| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.02 r_work: 0.4167 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4078 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4187 Z= 0.227 Angle : 0.740 9.872 5720 Z= 0.378 Chirality : 0.047 0.190 670 Planarity : 0.006 0.056 731 Dihedral : 5.517 48.416 635 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.18 % Allowed : 35.22 % Favored : 60.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.58 (0.28), residues: 363 sheet: 1.39 (0.49), residues: 109 loop : -1.43 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 174 HIS 0.003 0.001 HIS A 260 PHE 0.034 0.002 PHE A 332 TYR 0.013 0.001 TYR A 266 ARG 0.002 0.000 ARG A 196 *********************** 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 104 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8124 (m-10) cc_final: 0.7667 (m-10) REVERT: A 166 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7231 (pm20) REVERT: A 255 LEU cc_start: 0.4407 (OUTLIER) cc_final: 0.4033 (pt) REVERT: A 379 MET cc_start: 0.7756 (ttt) cc_final: 0.7524 (ttp) REVERT: A 380 ASP cc_start: 0.6551 (m-30) cc_final: 0.6296 (m-30) REVERT: A 400 CYS cc_start: 0.7272 (t) cc_final: 0.6845 (m) REVERT: A 435 ILE cc_start: 0.8526 (mt) cc_final: 0.8108 (mt) REVERT: B 204 SER cc_start: 0.5727 (p) cc_final: 0.5334 (m) outliers start: 14 outliers final: 7 residues processed: 100 average time/residue: 0.5449 time to fit residues: 58.8705 Evaluate side-chains 96 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 399 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 0.0170 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.228644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.198661 restraints weight = 5338.002| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 2.07 r_work: 0.4196 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4103 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4187 Z= 0.213 Angle : 0.729 9.657 5720 Z= 0.372 Chirality : 0.047 0.181 670 Planarity : 0.005 0.055 731 Dihedral : 5.282 49.659 635 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.18 % Allowed : 35.52 % Favored : 60.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.63 (0.36), residues: 591 helix: 0.69 (0.28), residues: 362 sheet: 1.53 (0.49), residues: 109 loop : -1.29 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 369 HIS 0.002 0.001 HIS A 260 PHE 0.035 0.002 PHE A 332 TYR 0.012 0.001 TYR A 138 ARG 0.002 0.000 ARG A 196 ********************** 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 105 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8033 (m-10) cc_final: 0.7584 (m-10) REVERT: A 166 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7299 (pm20) REVERT: A 255 LEU cc_start: 0.4304 (OUTLIER) cc_final: 0.3849 (pt) REVERT: A 271 VAL cc_start: 0.8158 (t) cc_final: 0.7914 (m) REVERT: A 379 MET cc_start: 0.7585 (ttt) cc_final: 0.7331 (ttp) REVERT: A 380 ASP cc_start: 0.6473 (m-30) cc_final: 0.6191 (m-30) REVERT: A 400 CYS cc_start: 0.7265 (t) cc_final: 0.6880 (m) REVERT: A 435 ILE cc_start: 0.8540 (mt) cc_final: 0.8091 (mt) REVERT: B 204 SER cc_start: 0.5779 (p) cc_final: 0.5564 (t) outliers start: 14 outliers final: 7 residues processed: 98 average time/residue: 0.5384 time to fit residues: 56.7129 Evaluate side-chains 97 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 399 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 42 optimal weight: 40.0000 chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.223060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.192746 restraints weight = 5271.057| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.09 r_work: 0.4128 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4038 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4187 Z= 0.299 Angle : 0.782 9.929 5720 Z= 0.406 Chirality : 0.050 0.189 670 Planarity : 0.006 0.055 731 Dihedral : 5.673 48.279 635 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.88 % Allowed : 36.12 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.42 (0.36), residues: 591 helix: 0.48 (0.28), residues: 362 sheet: 1.55 (0.50), residues: 109 loop : -1.32 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 174 HIS 0.004 0.001 HIS A 260 PHE 0.042 0.002 PHE A 332 TYR 0.017 0.002 TYR A 138 ARG 0.003 0.001 ARG A 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3343.24 seconds wall clock time: 59 minutes 38.77 seconds (3578.77 seconds total)