Starting phenix.real_space_refine on Thu Mar 6 00:31:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ckr_30391/03_2025/7ckr_30391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ckr_30391/03_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_30391/03_2025/7ckr_30391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ckr_30391/03_2025/7ckr_30391.map" model { file = "/net/cci-nas-00/data/ceres_data/7ckr_30391/03_2025/7ckr_30391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ckr_30391/03_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-5624/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: 3.34, 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: 1.23 Conformation dependent library (CDL) restraints added in 527.8 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: 0.47 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: 1.23 Time building geometry restraints manager: 1.30 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: 5.190 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: 0.040 Process input model: 14.530 Find NCS groups from input model: 0.050 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:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.710 ------------------------------------------------------------------------------- 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 : 0.391 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: 0.6045 time to fit residues: 63.6243 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 : 0.402 ------------------------------------------------------------------------------- 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: 0.9980 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.228365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.198201 restraints weight = 5374.750| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 1.91 r_work: 0.4202 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4117 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2567 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= 0.268 Angle : 0.714 8.080 5720 Z= 0.377 Chirality : 0.045 0.134 670 Planarity : 0.007 0.064 731 Dihedral : 7.320 56.985 657 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 6.87 % Allowed : 22.99 % Favored : 70.15 % 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: -0.69 (0.34), residues: 591 helix: -0.10 (0.27), residues: 369 sheet: 0.85 (0.53), residues: 101 loop : -2.37 (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 0.031 0.002 PHE A 27 TYR 0.017 0.002 TYR B 229 ARG 0.007 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 108 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 255 LEU cc_start: 0.4057 (OUTLIER) cc_final: 0.3462 (pt) REVERT: A 272 ILE cc_start: 0.8249 (mt) cc_final: 0.7961 (tt) REVERT: B 204 SER cc_start: 0.5273 (p) cc_final: 0.5005 (t) outliers start: 23 outliers final: 9 residues processed: 101 average time/residue: 0.4880 time to fit residues: 53.2989 Evaluate side-chains 89 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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: 10.0000 chunk 42 optimal weight: 0.0570 chunk 6 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.4599 r_free = 0.4599 target = 0.228754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.199489 restraints weight = 5392.031| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 1.93 r_work: 0.4211 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4121 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.3261 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= 0.209 Angle : 0.659 7.929 5720 Z= 0.342 Chirality : 0.044 0.160 670 Planarity : 0.006 0.049 731 Dihedral : 6.255 52.666 641 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 6.27 % Allowed : 27.46 % 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: 0.12 (0.35), residues: 591 helix: 0.55 (0.28), residues: 365 sheet: 1.12 (0.52), residues: 101 loop : -2.02 (0.50), residues: 125 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 0.014 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 107 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8220 (m-10) cc_final: 0.7859 (m-10) REVERT: A 255 LEU cc_start: 0.3986 (OUTLIER) cc_final: 0.3296 (pt) REVERT: A 272 ILE cc_start: 0.8261 (mt) cc_final: 0.7952 (tt) REVERT: A 376 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.5903 (tm-30) REVERT: A 377 THR cc_start: 0.8331 (t) cc_final: 0.8128 (p) REVERT: A 380 ASP cc_start: 0.6219 (m-30) cc_final: 0.5598 (m-30) REVERT: A 400 CYS cc_start: 0.7886 (t) cc_final: 0.7364 (m) REVERT: B 204 SER cc_start: 0.5224 (p) cc_final: 0.4931 (t) outliers start: 21 outliers final: 9 residues processed: 99 average time/residue: 0.5325 time to fit residues: 57.1478 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 : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 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 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: 2.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 0.0470 chunk 42 optimal weight: 40.0000 chunk 54 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.224793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.194676 restraints weight = 5403.450| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 1.95 r_work: 0.4141 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4045 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4187 Z= 0.253 Angle : 0.696 8.553 5720 Z= 0.362 Chirality : 0.046 0.167 670 Planarity : 0.006 0.051 731 Dihedral : 6.306 49.587 641 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 6.57 % Allowed : 28.66 % Favored : 64.78 % 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: 0.20 (0.35), residues: 591 helix: 0.55 (0.28), residues: 367 sheet: 1.20 (0.51), residues: 101 loop : -1.83 (0.52), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 174 HIS 0.003 0.001 HIS A 260 PHE 0.024 0.002 PHE A 27 TYR 0.015 0.002 TYR A 423 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 112 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8206 (m-10) cc_final: 0.7804 (m-10) REVERT: A 255 LEU cc_start: 0.4357 (OUTLIER) cc_final: 0.3721 (pt) REVERT: A 272 ILE cc_start: 0.8302 (mt) cc_final: 0.8002 (tt) REVERT: A 380 ASP cc_start: 0.6241 (m-30) cc_final: 0.5765 (m-30) REVERT: A 400 CYS cc_start: 0.7858 (t) cc_final: 0.7323 (m) REVERT: A 420 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.6855 (ptpt) REVERT: B 204 SER cc_start: 0.5318 (p) cc_final: 0.5074 (t) outliers start: 22 outliers final: 8 residues processed: 103 average time/residue: 0.4800 time to fit residues: 53.5414 Evaluate side-chains 95 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 282 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain B residue 115 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4575 r_free = 0.4575 target = 0.225717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.195383 restraints weight = 5473.370| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.01 r_work: 0.4162 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4067 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.4240 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= 0.239 Angle : 0.695 8.975 5720 Z= 0.360 Chirality : 0.046 0.155 670 Planarity : 0.005 0.051 731 Dihedral : 5.776 47.043 637 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 6.87 % Allowed : 30.15 % Favored : 62.99 % 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: 0.35 (0.36), residues: 591 helix: 0.64 (0.29), residues: 365 sheet: 1.20 (0.51), residues: 101 loop : -1.60 (0.54), residues: 125 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 0.024 0.002 PHE A 27 TYR 0.016 0.002 TYR A 423 ARG 0.003 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 115 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8159 (m-10) cc_final: 0.7679 (m-80) REVERT: A 255 LEU cc_start: 0.4391 (OUTLIER) cc_final: 0.3844 (pt) REVERT: A 272 ILE cc_start: 0.8407 (mt) cc_final: 0.8067 (tt) REVERT: A 296 GLU cc_start: 0.7278 (pp20) cc_final: 0.7045 (pp20) REVERT: A 379 MET cc_start: 0.7885 (ttt) cc_final: 0.7641 (ttp) REVERT: A 380 ASP cc_start: 0.6375 (m-30) cc_final: 0.6033 (m-30) REVERT: A 400 CYS cc_start: 0.7539 (t) cc_final: 0.6989 (m) REVERT: A 416 TYR cc_start: 0.5775 (OUTLIER) cc_final: 0.4780 (t80) REVERT: A 435 ILE cc_start: 0.8511 (mp) cc_final: 0.8122 (mt) REVERT: B 204 SER cc_start: 0.5503 (p) cc_final: 0.5143 (m) outliers start: 23 outliers final: 13 residues processed: 107 average time/residue: 0.4704 time to fit residues: 54.4266 Evaluate side-chains 100 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 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 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 399 CYS Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 416 TYR 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: 7.9990 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** 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 = 0.4580 r_free = 0.4580 target = 0.226640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.196556 restraints weight = 5353.331| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 1.96 r_work: 0.4183 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.4092 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.4484 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= 0.213 Angle : 0.695 9.376 5720 Z= 0.356 Chirality : 0.046 0.167 670 Planarity : 0.005 0.058 731 Dihedral : 5.606 46.867 637 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 7.16 % Allowed : 30.75 % Favored : 62.09 % 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: 0.50 (0.36), residues: 591 helix: 0.71 (0.29), residues: 363 sheet: 1.39 (0.51), residues: 99 loop : -1.46 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 174 HIS 0.003 0.001 HIS A 260 PHE 0.024 0.002 PHE A 27 TYR 0.012 0.001 TYR A 423 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 115 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8109 (m-10) cc_final: 0.7534 (m-80) REVERT: A 129 ASN cc_start: 0.8316 (t0) cc_final: 0.8080 (t0) REVERT: A 255 LEU cc_start: 0.4249 (OUTLIER) cc_final: 0.3734 (pt) REVERT: A 271 VAL cc_start: 0.8137 (t) cc_final: 0.7884 (m) REVERT: A 272 ILE cc_start: 0.8373 (mt) cc_final: 0.8098 (tt) REVERT: A 296 GLU cc_start: 0.7175 (pp20) cc_final: 0.6951 (pp20) REVERT: A 379 MET cc_start: 0.7842 (ttt) cc_final: 0.7611 (ttp) REVERT: A 380 ASP cc_start: 0.6392 (m-30) cc_final: 0.6064 (m-30) REVERT: A 400 CYS cc_start: 0.7459 (t) cc_final: 0.6960 (m) REVERT: A 435 ILE cc_start: 0.8554 (mp) cc_final: 0.8123 (mt) REVERT: B 204 SER cc_start: 0.5564 (p) cc_final: 0.5210 (m) outliers start: 24 outliers final: 10 residues processed: 108 average time/residue: 0.4430 time to fit residues: 51.9797 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 : 0.500 ------------------------------------------------------------------------------- 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 198 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 258 PHE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 50.0000 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 0.0270 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 330 GLN ** 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 = 0.4585 r_free = 0.4585 target = 0.227063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.196884 restraints weight = 5344.580| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 1.98 r_work: 0.4187 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4099 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4678 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= 0.217 Angle : 0.708 9.564 5720 Z= 0.361 Chirality : 0.047 0.185 670 Planarity : 0.005 0.051 731 Dihedral : 5.249 47.349 635 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 6.57 % Allowed : 31.64 % 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: 0.61 (0.36), residues: 591 helix: 0.76 (0.29), residues: 363 sheet: 1.54 (0.51), residues: 99 loop : -1.37 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 369 HIS 0.002 0.001 HIS A 260 PHE 0.027 0.002 PHE A 263 TYR 0.012 0.001 TYR A 423 ARG 0.002 0.000 ARG A 175 *********************** 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 112 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8052 (m-10) cc_final: 0.7543 (m-80) REVERT: A 129 ASN cc_start: 0.8286 (t0) cc_final: 0.8052 (t0) REVERT: A 255 LEU cc_start: 0.4247 (OUTLIER) cc_final: 0.3761 (pt) REVERT: A 271 VAL cc_start: 0.8133 (t) cc_final: 0.7916 (m) REVERT: A 272 ILE cc_start: 0.8382 (mt) cc_final: 0.8133 (tt) REVERT: A 296 GLU cc_start: 0.7156 (pp20) cc_final: 0.6936 (pp20) REVERT: A 379 MET cc_start: 0.7761 (ttt) cc_final: 0.7546 (ttp) REVERT: A 380 ASP cc_start: 0.6318 (m-30) cc_final: 0.6113 (m-30) REVERT: A 400 CYS cc_start: 0.7438 (t) cc_final: 0.6991 (m) REVERT: A 435 ILE cc_start: 0.8565 (mt) cc_final: 0.8081 (mt) REVERT: B 204 SER cc_start: 0.5578 (p) cc_final: 0.5199 (m) outliers start: 22 outliers final: 10 residues processed: 107 average time/residue: 0.4780 time to fit residues: 55.2721 Evaluate side-chains 98 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 258 PHE 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 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: 8.9990 chunk 50 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 30.0000 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.0980 chunk 39 optimal weight: 10.0000 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 127 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** 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 = 0.4570 r_free = 0.4570 target = 0.225769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.195435 restraints weight = 5249.894| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 1.96 r_work: 0.4179 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4081 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4187 Z= 0.236 Angle : 0.721 9.481 5720 Z= 0.373 Chirality : 0.048 0.210 670 Planarity : 0.005 0.051 731 Dihedral : 5.343 47.928 635 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 6.57 % Allowed : 32.24 % Favored : 61.19 % 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 (0.36), residues: 591 helix: 0.75 (0.29), residues: 362 sheet: 1.47 (0.48), residues: 109 loop : -1.42 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.003 0.001 HIS A 260 PHE 0.024 0.002 PHE A 332 TYR 0.017 0.002 TYR A 266 ARG 0.001 0.000 ARG A 196 *********************** 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 112 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8069 (m-10) cc_final: 0.7560 (m-80) REVERT: A 255 LEU cc_start: 0.4451 (OUTLIER) cc_final: 0.3991 (pt) REVERT: A 271 VAL cc_start: 0.8098 (t) cc_final: 0.7890 (m) REVERT: A 272 ILE cc_start: 0.8452 (mt) cc_final: 0.8170 (tt) REVERT: A 379 MET cc_start: 0.7748 (ttt) cc_final: 0.7521 (ttp) REVERT: A 380 ASP cc_start: 0.6370 (m-30) cc_final: 0.6153 (m-30) REVERT: A 400 CYS cc_start: 0.7414 (t) cc_final: 0.6960 (m) REVERT: A 435 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8099 (mt) REVERT: B 204 SER cc_start: 0.5731 (p) cc_final: 0.5362 (m) outliers start: 22 outliers final: 13 residues processed: 106 average time/residue: 0.4936 time to fit residues: 56.4471 Evaluate side-chains 104 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 135 ILE 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 258 PHE 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 435 ILE 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: 4.9990 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 129 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.225799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.194735 restraints weight = 5240.503| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 1.97 r_work: 0.4170 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4079 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4187 Z= 0.234 Angle : 0.731 9.688 5720 Z= 0.375 Chirality : 0.047 0.193 670 Planarity : 0.005 0.054 731 Dihedral : 5.322 48.787 635 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.97 % Allowed : 33.73 % 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: 0.68 (0.36), residues: 591 helix: 0.76 (0.29), residues: 362 sheet: 1.54 (0.49), residues: 109 loop : -1.38 (0.59), residues: 120 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 0.032 0.002 PHE A 332 TYR 0.013 0.002 TYR A 423 ARG 0.001 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 108 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8020 (m-10) cc_final: 0.7560 (m-10) REVERT: A 129 ASN cc_start: 0.8237 (t0) cc_final: 0.8024 (t0) REVERT: A 255 LEU cc_start: 0.4502 (OUTLIER) cc_final: 0.4092 (pt) REVERT: A 272 ILE cc_start: 0.8456 (mt) cc_final: 0.8188 (tt) REVERT: A 379 MET cc_start: 0.7743 (ttt) cc_final: 0.7503 (ttp) REVERT: A 400 CYS cc_start: 0.7340 (t) cc_final: 0.6915 (m) REVERT: A 435 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8123 (mt) REVERT: B 204 SER cc_start: 0.5797 (p) cc_final: 0.5364 (m) outliers start: 20 outliers final: 13 residues processed: 104 average time/residue: 0.8440 time to fit residues: 94.5331 Evaluate side-chains 102 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 258 PHE 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 435 ILE 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 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 45 optimal weight: 0.0770 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** 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 = 0.4601 r_free = 0.4601 target = 0.229254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.198825 restraints weight = 5347.473| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.01 r_work: 0.4206 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4118 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.5121 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= 0.207 Angle : 0.730 9.728 5720 Z= 0.371 Chirality : 0.047 0.191 670 Planarity : 0.005 0.054 731 Dihedral : 5.151 49.247 635 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.07 % Allowed : 34.33 % 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: 0.80 (0.36), residues: 591 helix: 0.82 (0.28), residues: 363 sheet: 1.63 (0.49), residues: 109 loop : -1.25 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 174 HIS 0.002 0.001 HIS A 260 PHE 0.035 0.002 PHE A 332 TYR 0.011 0.001 TYR A 423 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 106 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.7980 (m-10) cc_final: 0.7701 (m-10) REVERT: A 129 ASN cc_start: 0.8217 (t0) cc_final: 0.8003 (t0) REVERT: A 255 LEU cc_start: 0.4205 (OUTLIER) cc_final: 0.3793 (pt) REVERT: A 272 ILE cc_start: 0.8369 (mt) cc_final: 0.8166 (tt) REVERT: A 400 CYS cc_start: 0.7190 (t) cc_final: 0.6826 (m) REVERT: A 435 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8076 (mt) REVERT: B 204 SER cc_start: 0.5720 (p) cc_final: 0.5509 (t) outliers start: 17 outliers final: 11 residues processed: 102 average time/residue: 0.7486 time to fit residues: 82.2182 Evaluate side-chains 99 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 135 ILE 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 258 PHE 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 435 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.224862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.194896 restraints weight = 5250.185| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.02 r_work: 0.4133 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.4044 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4187 Z= 0.294 Angle : 0.786 9.969 5720 Z= 0.407 Chirality : 0.050 0.196 670 Planarity : 0.006 0.050 731 Dihedral : 5.602 48.247 635 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.67 % Allowed : 34.03 % 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: 0.52 (0.36), residues: 591 helix: 0.59 (0.28), residues: 361 sheet: 1.64 (0.50), residues: 109 loop : -1.40 (0.59), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 174 HIS 0.004 0.001 HIS A 260 PHE 0.036 0.002 PHE A 332 TYR 0.018 0.002 TYR A 423 ARG 0.002 0.000 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3615.37 seconds wall clock time: 64 minutes 15.83 seconds (3855.83 seconds total)