Starting phenix.real_space_refine on Thu Jul 31 00:23:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tdw_10469/07_2025/6tdw_10469.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tdw_10469/07_2025/6tdw_10469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tdw_10469/07_2025/6tdw_10469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tdw_10469/07_2025/6tdw_10469.map" model { file = "/net/cci-nas-00/data/ceres_data/6tdw_10469/07_2025/6tdw_10469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tdw_10469/07_2025/6tdw_10469.cif" } resolution = 3.8 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= 0.000 sd= 0.002 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 10 5.16 5 C 4087 2.51 5 N 1105 2.21 5 O 1234 1.98 5 H 6561 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12997 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 398 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 3, 'TRANS': 21} Chain: "H" Number of atoms: 4014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 4014 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 22, 'TRANS': 226} Chain breaks: 2 Chain: "B" Number of atoms: 4830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 4830 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "C" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2463 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "M" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 639 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 6, 'TRANS': 36} Chain: "N" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 509 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "T" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 144 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Time building chain proxies: 7.92, per 1000 atoms: 0.61 Number of scatterers: 12997 At special positions: 0 Unit cell: (113.4, 72.45, 107.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 1234 8.00 N 1105 7.00 C 4087 6.00 H 6561 1.00 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: 3.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1614 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 2 sheets defined 67.9% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 474 through 487 removed outlier: 5.596A pdb=" N LYS A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLU A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 58 removed outlier: 4.020A pdb=" N LYS H 56 " --> pdb=" O LYS H 52 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR H 57 " --> pdb=" O ALA H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 79 Processing helix chain 'H' and resid 81 through 103 Proline residue: H 100 - end of helix Processing helix chain 'H' and resid 111 through 125 removed outlier: 4.378A pdb=" N GLU H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 279 removed outlier: 3.950A pdb=" N MET H 271 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS H 274 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU H 277 " --> pdb=" O GLU H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 291 removed outlier: 3.782A pdb=" N LYS H 284 " --> pdb=" O ASN H 280 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU H 291 " --> pdb=" O PHE H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 297 removed outlier: 3.679A pdb=" N LYS H 296 " --> pdb=" O GLN H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 307 Processing helix chain 'H' and resid 309 through 330 removed outlier: 4.382A pdb=" N VAL H 313 " --> pdb=" O ASP H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 358 removed outlier: 3.694A pdb=" N GLU H 345 " --> pdb=" O GLN H 341 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE H 354 " --> pdb=" O LYS H 350 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP H 355 " --> pdb=" O GLY H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 444 through 455 removed outlier: 4.838A pdb=" N GLN H 450 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA H 453 " --> pdb=" O ALA H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 476 removed outlier: 3.860A pdb=" N SER H 460 " --> pdb=" O PRO H 456 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG H 464 " --> pdb=" O SER H 460 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA H 471 " --> pdb=" O THR H 467 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR H 472 " --> pdb=" O GLU H 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 30 Processing helix chain 'B' and resid 56 through 68 Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 104 through 107 removed outlier: 4.364A pdb=" N SER B 107 " --> pdb=" O PRO B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 104 through 107' Processing helix chain 'B' and resid 121 through 164 Processing helix chain 'B' and resid 180 through 197 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'B' and resid 235 through 249 Processing helix chain 'B' and resid 277 through 292 Processing helix chain 'B' and resid 293 through 310 Processing helix chain 'B' and resid 324 through 337 Processing helix chain 'C' and resid 13 through 25 Processing helix chain 'C' and resid 36 through 42 Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'C' and resid 65 through 87 Processing helix chain 'C' and resid 89 through 95 Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 105 through 130 Processing helix chain 'C' and resid 131 through 150 Processing helix chain 'C' and resid 153 through 168 Processing helix chain 'M' and resid 239 through 246 Processing helix chain 'M' and resid 249 through 263 Processing helix chain 'N' and resid 84 through 112 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 9 removed outlier: 5.916A pdb=" N LYS B 4 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL B 36 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 6 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THR B 38 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE B 8 " --> pdb=" O THR B 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 6.822A pdb=" N LEU B 50 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N SER B 268 " --> pdb=" O LEU B 50 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1260 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: 4.54 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6556 1.03 - 1.23: 9 1.23 - 1.42: 2561 1.42 - 1.62: 3969 1.62 - 1.81: 15 Bond restraints: 13110 Sorted by residual: bond pdb=" C LYS C 36 " pdb=" N ASP C 37 " ideal model delta sigma weight residual 1.334 1.175 0.159 1.27e-02 6.20e+03 1.58e+02 bond pdb=" C ASP C 57 " pdb=" N SER C 58 " ideal model delta sigma weight residual 1.333 1.231 0.102 1.26e-02 6.30e+03 6.56e+01 bond pdb=" N VAL H 313 " pdb=" CA VAL H 313 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.24e+00 bond pdb=" N VAL H 302 " pdb=" CA VAL H 302 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.22e+00 bond pdb=" N VAL H 312 " pdb=" CA VAL H 312 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.85e+00 ... (remaining 13105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.24: 23859 5.24 - 10.48: 22 10.48 - 15.72: 2 15.72 - 20.96: 0 20.96 - 26.20: 6 Bond angle restraints: 23889 Sorted by residual: angle pdb=" CG2 VAL B 119 " pdb=" CB VAL B 119 " pdb=" HB VAL B 119 " ideal model delta sigma weight residual 108.00 81.80 26.20 3.00e+00 1.11e-01 7.63e+01 angle pdb=" CG1 VAL B 119 " pdb=" CB VAL B 119 " pdb=" HB VAL B 119 " ideal model delta sigma weight residual 108.00 82.86 25.14 3.00e+00 1.11e-01 7.02e+01 angle pdb=" CD2 LEU M 246 " pdb=" CG LEU M 246 " pdb=" HG LEU M 246 " ideal model delta sigma weight residual 108.00 83.69 24.31 3.00e+00 1.11e-01 6.56e+01 angle pdb=" CD1 LEU M 246 " pdb=" CG LEU M 246 " pdb=" HG LEU M 246 " ideal model delta sigma weight residual 108.00 84.44 23.56 3.00e+00 1.11e-01 6.17e+01 angle pdb=" CA VAL B 119 " pdb=" CB VAL B 119 " pdb=" HB VAL B 119 " ideal model delta sigma weight residual 109.00 85.48 23.52 3.00e+00 1.11e-01 6.15e+01 ... (remaining 23884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.27: 5182 14.27 - 28.55: 702 28.55 - 42.82: 189 42.82 - 57.10: 72 57.10 - 71.37: 12 Dihedral angle restraints: 6157 sinusoidal: 3416 harmonic: 2741 Sorted by residual: dihedral pdb=" CA LEU C 29 " pdb=" C LEU C 29 " pdb=" N LYS C 30 " pdb=" CA LYS C 30 " ideal model delta harmonic sigma weight residual 180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA SER C 58 " pdb=" C SER C 58 " pdb=" N GLU C 59 " pdb=" CA GLU C 59 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA GLY B 179 " pdb=" C GLY B 179 " pdb=" N ASP B 180 " pdb=" CA ASP B 180 " ideal model delta harmonic sigma weight residual -180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 6154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.343: 1048 0.343 - 0.685: 0 0.685 - 1.028: 0 1.028 - 1.370: 0 1.370 - 1.713: 2 Chirality restraints: 1050 Sorted by residual: chirality pdb=" CG LEU M 246 " pdb=" CB LEU M 246 " pdb=" CD1 LEU M 246 " pdb=" CD2 LEU M 246 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.33e+01 chirality pdb=" CB VAL B 119 " pdb=" CA VAL B 119 " pdb=" CG1 VAL B 119 " pdb=" CG2 VAL B 119 " both_signs ideal model delta sigma weight residual False -2.63 -1.10 -1.53 2.00e-01 2.50e+01 5.82e+01 chirality pdb=" CA VAL B 73 " pdb=" N VAL B 73 " pdb=" C VAL B 73 " pdb=" CB VAL B 73 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.18e-01 ... (remaining 1047 not shown) Planarity restraints: 1929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 217 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.47e+00 pdb=" N PRO B 218 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 218 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 218 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 57 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C ASP C 57 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP C 57 " -0.013 2.00e-02 2.50e+03 pdb=" N SER C 58 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 314 " -0.012 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" N ALA H 315 " 0.037 2.00e-02 2.50e+03 pdb=" CA ALA H 315 " -0.010 2.00e-02 2.50e+03 pdb=" H ALA H 315 " -0.016 2.00e-02 2.50e+03 ... (remaining 1926 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 1812 2.26 - 2.85: 29645 2.85 - 3.43: 32052 3.43 - 4.02: 41178 4.02 - 4.60: 65451 Nonbonded interactions: 170138 Sorted by model distance: nonbonded pdb=" HG2 GLU H 311 " pdb="HG23 THR C 89 " model vdw 1.678 2.440 nonbonded pdb=" O PRO B 44 " pdb=" HH TYR B 67 " model vdw 1.725 2.450 nonbonded pdb="HH21 ARG H 319 " pdb=" OD1 ASP M 257 " model vdw 1.726 2.450 nonbonded pdb=" O ALA B 305 " pdb=" HG1 THR B 309 " model vdw 1.736 2.450 nonbonded pdb=" OE1 GLN B 240 " pdb="HH11 ARG C 90 " model vdw 1.748 2.450 ... (remaining 170133 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.800 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: 0.230 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.270 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.159 6549 Z= 0.362 Angle : 0.839 11.010 8899 Z= 0.465 Chirality : 0.083 1.713 1050 Planarity : 0.005 0.058 1150 Dihedral : 13.713 71.372 2442 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.15 % Allowed : 4.22 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.27), residues: 821 helix: -0.17 (0.20), residues: 523 sheet: -3.60 (0.56), residues: 59 loop : -2.97 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 152 HIS 0.006 0.001 HIS A 467 PHE 0.016 0.002 PHE B 223 TYR 0.011 0.002 TYR H 25 ARG 0.006 0.000 ARG H 41 Details of bonding type rmsd hydrogen bonds : bond 0.12677 ( 422) hydrogen bonds : angle 5.73342 ( 1260) covalent geometry : bond 0.00743 ( 6549) covalent geometry : angle 0.83853 ( 8899) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 276 ASN cc_start: 0.7669 (t0) cc_final: 0.7302 (t0) REVERT: C 148 LYS cc_start: 0.8632 (tttt) cc_final: 0.8253 (ttpt) REVERT: N 106 LEU cc_start: 0.8104 (mt) cc_final: 0.7819 (mt) outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.4806 time to fit residues: 111.9123 Evaluate side-chains 94 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 152 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS C 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.136310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.116936 restraints weight = 32444.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.121996 restraints weight = 14776.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.125230 restraints weight = 8644.990| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6549 Z= 0.149 Angle : 0.629 10.993 8899 Z= 0.317 Chirality : 0.078 1.690 1050 Planarity : 0.005 0.045 1150 Dihedral : 4.629 35.576 887 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.45 % Allowed : 12.79 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.29), residues: 821 helix: 1.07 (0.22), residues: 535 sheet: -3.42 (0.58), residues: 57 loop : -2.84 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 217 HIS 0.005 0.002 HIS B 335 PHE 0.017 0.001 PHE B 19 TYR 0.012 0.001 TYR H 25 ARG 0.003 0.000 ARG H 464 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 422) hydrogen bonds : angle 4.74072 ( 1260) covalent geometry : bond 0.00338 ( 6549) covalent geometry : angle 0.62941 ( 8899) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 HIS cc_start: 0.7888 (m170) cc_final: 0.7600 (m170) REVERT: B 23 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7537 (tp-100) REVERT: B 276 ASN cc_start: 0.7659 (t0) cc_final: 0.7266 (t0) REVERT: C 148 LYS cc_start: 0.8527 (tttt) cc_final: 0.8309 (ttpt) outliers start: 10 outliers final: 7 residues processed: 111 average time/residue: 0.4467 time to fit residues: 64.0719 Evaluate side-chains 94 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 157 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 0.0010 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.131409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.111983 restraints weight = 32858.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.116909 restraints weight = 15050.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.120072 restraints weight = 8885.528| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6549 Z= 0.157 Angle : 0.602 10.962 8899 Z= 0.301 Chirality : 0.078 1.701 1050 Planarity : 0.004 0.046 1150 Dihedral : 4.455 39.902 887 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.60 % Allowed : 13.66 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.31), residues: 821 helix: 1.78 (0.22), residues: 535 sheet: -3.22 (0.60), residues: 57 loop : -2.47 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 217 HIS 0.002 0.001 HIS H 116 PHE 0.017 0.001 PHE B 245 TYR 0.010 0.001 TYR T 51 ARG 0.002 0.000 ARG H 464 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 422) hydrogen bonds : angle 4.51747 ( 1260) covalent geometry : bond 0.00359 ( 6549) covalent geometry : angle 0.60174 ( 8899) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 HIS cc_start: 0.7966 (m170) cc_final: 0.7732 (m170) REVERT: B 23 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7686 (tp-100) REVERT: B 276 ASN cc_start: 0.7642 (t0) cc_final: 0.7408 (t0) REVERT: B 326 GLU cc_start: 0.7932 (mp0) cc_final: 0.7536 (tm-30) REVERT: C 148 LYS cc_start: 0.8689 (tttt) cc_final: 0.8487 (ttpt) outliers start: 11 outliers final: 8 residues processed: 106 average time/residue: 0.4731 time to fit residues: 64.1020 Evaluate side-chains 98 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 152 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 257 GLN C 28 HIS C 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.138761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.118495 restraints weight = 32040.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.123730 restraints weight = 14640.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127057 restraints weight = 8692.068| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6549 Z= 0.182 Angle : 0.608 11.045 8899 Z= 0.307 Chirality : 0.079 1.702 1050 Planarity : 0.004 0.045 1150 Dihedral : 4.514 43.433 887 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.89 % Allowed : 14.53 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.31), residues: 821 helix: 1.97 (0.22), residues: 535 sheet: -3.31 (0.56), residues: 62 loop : -2.19 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 217 HIS 0.003 0.001 HIS H 451 PHE 0.020 0.002 PHE B 245 TYR 0.009 0.001 TYR B 99 ARG 0.004 0.000 ARG M 233 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 422) hydrogen bonds : angle 4.57241 ( 1260) covalent geometry : bond 0.00413 ( 6549) covalent geometry : angle 0.60755 ( 8899) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 326 GLU cc_start: 0.8045 (mp0) cc_final: 0.7652 (tm-30) REVERT: C 112 LYS cc_start: 0.7579 (mttt) cc_final: 0.7142 (ttmt) outliers start: 13 outliers final: 9 residues processed: 114 average time/residue: 0.4343 time to fit residues: 63.9446 Evaluate side-chains 107 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 273 GLU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.135207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114774 restraints weight = 32667.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.120008 restraints weight = 15088.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.123320 restraints weight = 9006.392| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6549 Z= 0.213 Angle : 0.640 10.995 8899 Z= 0.324 Chirality : 0.079 1.719 1050 Planarity : 0.004 0.045 1150 Dihedral : 4.577 45.340 887 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.18 % Allowed : 15.12 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.31), residues: 821 helix: 1.95 (0.22), residues: 535 sheet: -3.37 (0.54), residues: 62 loop : -2.14 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 217 HIS 0.008 0.001 HIS A 467 PHE 0.029 0.002 PHE B 245 TYR 0.008 0.001 TYR B 67 ARG 0.004 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 422) hydrogen bonds : angle 4.69930 ( 1260) covalent geometry : bond 0.00482 ( 6549) covalent geometry : angle 0.64008 ( 8899) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8251 (mm-40) cc_final: 0.8012 (tp-100) REVERT: B 326 GLU cc_start: 0.8106 (mp0) cc_final: 0.7810 (tm-30) REVERT: C 112 LYS cc_start: 0.7621 (mttt) cc_final: 0.7156 (ttmt) outliers start: 15 outliers final: 11 residues processed: 115 average time/residue: 0.4431 time to fit residues: 67.4571 Evaluate side-chains 106 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 152 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 47 optimal weight: 0.4980 chunk 60 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN C 28 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.134640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.115702 restraints weight = 32336.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120878 restraints weight = 14624.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.124076 restraints weight = 8520.041| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6549 Z= 0.129 Angle : 0.579 11.030 8899 Z= 0.288 Chirality : 0.078 1.704 1050 Planarity : 0.004 0.046 1150 Dihedral : 4.473 46.624 887 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.47 % Allowed : 15.41 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.31), residues: 821 helix: 2.15 (0.23), residues: 535 sheet: -3.21 (0.54), residues: 62 loop : -1.95 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 48 HIS 0.004 0.001 HIS A 475 PHE 0.019 0.001 PHE B 245 TYR 0.008 0.001 TYR B 99 ARG 0.002 0.000 ARG H 41 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 422) hydrogen bonds : angle 4.48693 ( 1260) covalent geometry : bond 0.00297 ( 6549) covalent geometry : angle 0.57882 ( 8899) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7817 (tp-100) REVERT: C 112 LYS cc_start: 0.7656 (mttt) cc_final: 0.7244 (ttmt) outliers start: 17 outliers final: 14 residues processed: 118 average time/residue: 0.4185 time to fit residues: 64.5529 Evaluate side-chains 109 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.134565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.115702 restraints weight = 31847.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.120794 restraints weight = 14726.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123960 restraints weight = 8719.106| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6549 Z= 0.133 Angle : 0.583 10.999 8899 Z= 0.290 Chirality : 0.078 1.713 1050 Planarity : 0.004 0.045 1150 Dihedral : 4.403 47.633 887 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.91 % Allowed : 15.26 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.31), residues: 821 helix: 2.20 (0.22), residues: 536 sheet: -3.14 (0.54), residues: 62 loop : -1.82 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 48 HIS 0.003 0.001 HIS H 116 PHE 0.019 0.001 PHE B 19 TYR 0.013 0.001 TYR T 51 ARG 0.002 0.000 ARG H 464 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 422) hydrogen bonds : angle 4.43046 ( 1260) covalent geometry : bond 0.00307 ( 6549) covalent geometry : angle 0.58301 ( 8899) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 25 TYR cc_start: 0.9034 (t80) cc_final: 0.8724 (t80) REVERT: B 23 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7876 (tp-100) REVERT: C 112 LYS cc_start: 0.7652 (mttt) cc_final: 0.7227 (ttmt) outliers start: 20 outliers final: 18 residues processed: 113 average time/residue: 0.4235 time to fit residues: 63.4262 Evaluate side-chains 112 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.133980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115042 restraints weight = 32280.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.120169 restraints weight = 14938.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.123343 restraints weight = 8819.944| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6549 Z= 0.145 Angle : 0.587 11.000 8899 Z= 0.293 Chirality : 0.078 1.715 1050 Planarity : 0.004 0.043 1150 Dihedral : 4.361 48.807 887 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.62 % Allowed : 15.99 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.31), residues: 821 helix: 2.28 (0.23), residues: 536 sheet: -3.19 (0.53), residues: 62 loop : -1.70 (0.45), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 217 HIS 0.003 0.001 HIS H 116 PHE 0.020 0.001 PHE B 19 TYR 0.008 0.001 TYR B 99 ARG 0.002 0.000 ARG H 464 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 422) hydrogen bonds : angle 4.42727 ( 1260) covalent geometry : bond 0.00335 ( 6549) covalent geometry : angle 0.58689 ( 8899) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 25 TYR cc_start: 0.9060 (t80) cc_final: 0.8708 (t80) REVERT: B 23 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7925 (tp-100) REVERT: C 112 LYS cc_start: 0.7630 (mttt) cc_final: 0.7198 (ttmt) outliers start: 18 outliers final: 16 residues processed: 110 average time/residue: 0.4153 time to fit residues: 60.0157 Evaluate side-chains 110 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 152 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 74 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.136804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.116940 restraints weight = 32423.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122209 restraints weight = 14754.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.125505 restraints weight = 8637.461| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6549 Z= 0.130 Angle : 0.578 11.022 8899 Z= 0.288 Chirality : 0.078 1.713 1050 Planarity : 0.004 0.044 1150 Dihedral : 4.330 49.365 887 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.33 % Allowed : 16.72 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.32), residues: 821 helix: 2.38 (0.23), residues: 536 sheet: -3.16 (0.53), residues: 62 loop : -1.63 (0.45), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 48 HIS 0.003 0.001 HIS H 116 PHE 0.020 0.001 PHE B 19 TYR 0.013 0.001 TYR T 51 ARG 0.002 0.000 ARG H 41 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 422) hydrogen bonds : angle 4.35416 ( 1260) covalent geometry : bond 0.00300 ( 6549) covalent geometry : angle 0.57777 ( 8899) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 LYS cc_start: 0.7546 (mttt) cc_final: 0.7116 (ttmt) outliers start: 16 outliers final: 15 residues processed: 108 average time/residue: 0.4100 time to fit residues: 57.8874 Evaluate side-chains 105 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 152 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.136167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.115820 restraints weight = 32340.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.121118 restraints weight = 14718.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.124459 restraints weight = 8676.386| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6549 Z= 0.142 Angle : 0.586 11.014 8899 Z= 0.293 Chirality : 0.078 1.716 1050 Planarity : 0.004 0.043 1150 Dihedral : 4.321 49.835 887 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.18 % Allowed : 17.15 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.32), residues: 821 helix: 2.36 (0.23), residues: 537 sheet: -3.15 (0.54), residues: 62 loop : -1.55 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 48 HIS 0.003 0.001 HIS H 116 PHE 0.022 0.001 PHE B 19 TYR 0.008 0.001 TYR B 99 ARG 0.007 0.000 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 422) hydrogen bonds : angle 4.36792 ( 1260) covalent geometry : bond 0.00327 ( 6549) covalent geometry : angle 0.58550 ( 8899) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 LYS cc_start: 0.7558 (mttt) cc_final: 0.7116 (ttmt) outliers start: 15 outliers final: 14 residues processed: 104 average time/residue: 0.4456 time to fit residues: 60.8425 Evaluate side-chains 103 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 152 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 24 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.117871 restraints weight = 32292.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.123190 restraints weight = 14636.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.126421 restraints weight = 8559.031| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6549 Z= 0.110 Angle : 0.567 11.034 8899 Z= 0.281 Chirality : 0.078 1.705 1050 Planarity : 0.004 0.045 1150 Dihedral : 4.277 49.844 887 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.89 % Allowed : 17.44 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.32), residues: 821 helix: 2.45 (0.23), residues: 537 sheet: -2.95 (0.55), residues: 60 loop : -1.55 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 48 HIS 0.003 0.001 HIS H 116 PHE 0.018 0.001 PHE B 19 TYR 0.015 0.001 TYR T 51 ARG 0.001 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 422) hydrogen bonds : angle 4.25429 ( 1260) covalent geometry : bond 0.00256 ( 6549) covalent geometry : angle 0.56724 ( 8899) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4349.87 seconds wall clock time: 74 minutes 58.01 seconds (4498.01 seconds total)