Starting phenix.real_space_refine on Fri Dec 27 19:15:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6m_38991/12_2024/8y6m_38991_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6m_38991/12_2024/8y6m_38991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y6m_38991/12_2024/8y6m_38991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6m_38991/12_2024/8y6m_38991.map" model { file = "/net/cci-nas-00/data/ceres_data/8y6m_38991/12_2024/8y6m_38991_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6m_38991/12_2024/8y6m_38991_neut.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 4352 2.51 5 N 1010 2.21 5 O 1108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6502 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3251 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 16, 'TRANS': 396} Chain breaks: 3 Chain: "B" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3251 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 16, 'TRANS': 396} Chain breaks: 3 Time building chain proxies: 4.11, per 1000 atoms: 0.63 Number of scatterers: 6502 At special positions: 0 Unit cell: (69.68, 96.72, 83.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1108 8.00 N 1010 7.00 C 4352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 488 " distance=2.03 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: 1.61 Conformation dependent library (CDL) restraints added in 882.3 milliseconds 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 2 sheets defined 76.9% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 39 through 62 Processing helix chain 'A' and resid 72 through 85 removed outlier: 3.508A pdb=" N MET A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 112 removed outlier: 3.769A pdb=" N VAL A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 187 through 214 Processing helix chain 'A' and resid 214 through 223 Proline residue: A 220 - end of helix removed outlier: 3.582A pdb=" N LYS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 241 Processing helix chain 'A' and resid 250 through 256 removed outlier: 4.137A pdb=" N ILE A 254 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 273 Processing helix chain 'A' and resid 275 through 292 Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.547A pdb=" N LEU A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 339 Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.968A pdb=" N ASP A 346 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 365 removed outlier: 3.840A pdb=" N ARG A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 391 removed outlier: 3.522A pdb=" N LEU A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 423 Processing helix chain 'A' and resid 425 through 441 Processing helix chain 'A' and resid 441 through 448 Processing helix chain 'A' and resid 453 through 466 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 500 through 516 Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'B' and resid 39 through 62 Processing helix chain 'B' and resid 72 through 85 removed outlier: 3.554A pdb=" N MET B 76 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.612A pdb=" N LEU B 97 " --> pdb=" O MET B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 112 removed outlier: 4.239A pdb=" N VAL B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 123 Processing helix chain 'B' and resid 187 through 214 Processing helix chain 'B' and resid 214 through 225 Proline residue: B 220 - end of helix removed outlier: 4.123A pdb=" N LYS B 224 " --> pdb=" O PRO B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 241 Processing helix chain 'B' and resid 250 through 256 removed outlier: 4.086A pdb=" N ILE B 254 " --> pdb=" O ASN B 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER B 256 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 273 removed outlier: 3.573A pdb=" N LEU B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 313 through 339 Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.915A pdb=" N ASP B 346 " --> pdb=" O SER B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 365 removed outlier: 3.845A pdb=" N ARG B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 391 removed outlier: 3.529A pdb=" N LEU B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 423 Processing helix chain 'B' and resid 425 through 441 Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 453 through 466 Processing helix chain 'B' and resid 475 through 481 Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 500 through 516 removed outlier: 3.697A pdb=" N LEU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397 Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 528 428 hydrogen bonds defined for protein. 1230 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: 2.03 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1910 1.34 - 1.46: 1551 1.46 - 1.58: 3145 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 6662 Sorted by residual: bond pdb=" CG PRO A 316 " pdb=" CD PRO A 316 " ideal model delta sigma weight residual 1.503 1.457 0.046 3.40e-02 8.65e+02 1.81e+00 bond pdb=" CG1 ILE A 43 " pdb=" CD1 ILE A 43 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.42e+00 bond pdb=" CG LEU B 84 " pdb=" CD2 LEU B 84 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.17e+00 bond pdb=" CG1 ILE B 43 " pdb=" CD1 ILE B 43 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.15e+00 bond pdb=" CB ILE B 105 " pdb=" CG2 ILE B 105 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 ... (remaining 6657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 8746 1.63 - 3.26: 236 3.26 - 4.88: 50 4.88 - 6.51: 13 6.51 - 8.14: 7 Bond angle restraints: 9052 Sorted by residual: angle pdb=" CA PRO A 316 " pdb=" N PRO A 316 " pdb=" CD PRO A 316 " ideal model delta sigma weight residual 112.00 105.43 6.57 1.40e+00 5.10e-01 2.21e+01 angle pdb=" CA MET B 76 " pdb=" CB MET B 76 " pdb=" CG MET B 76 " ideal model delta sigma weight residual 114.10 122.24 -8.14 2.00e+00 2.50e-01 1.66e+01 angle pdb=" N PRO A 316 " pdb=" CD PRO A 316 " pdb=" CG PRO A 316 " ideal model delta sigma weight residual 103.20 98.50 4.70 1.50e+00 4.44e-01 9.81e+00 angle pdb=" N MET B 76 " pdb=" CA MET B 76 " pdb=" C MET B 76 " ideal model delta sigma weight residual 113.88 110.44 3.44 1.23e+00 6.61e-01 7.84e+00 angle pdb=" CG MET B 76 " pdb=" SD MET B 76 " pdb=" CE MET B 76 " ideal model delta sigma weight residual 100.90 106.87 -5.97 2.20e+00 2.07e-01 7.37e+00 ... (remaining 9047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 3196 17.38 - 34.75: 495 34.75 - 52.13: 167 52.13 - 69.50: 19 69.50 - 86.88: 5 Dihedral angle restraints: 3882 sinusoidal: 1492 harmonic: 2390 Sorted by residual: dihedral pdb=" CB CYS A 476 " pdb=" SG CYS A 476 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -53.16 -32.84 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CB CYS B 476 " pdb=" SG CYS B 476 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -53.17 -32.83 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CA ASN B 273 " pdb=" C ASN B 273 " pdb=" N THR B 274 " pdb=" CA THR B 274 " ideal model delta harmonic sigma weight residual -180.00 -161.14 -18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 3879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 787 0.047 - 0.094: 238 0.094 - 0.141: 50 0.141 - 0.187: 5 0.187 - 0.234: 2 Chirality restraints: 1082 Sorted by residual: chirality pdb=" CG LEU A 54 " pdb=" CB LEU A 54 " pdb=" CD1 LEU A 54 " pdb=" CD2 LEU A 54 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CG LEU B 54 " pdb=" CB LEU B 54 " pdb=" CD1 LEU B 54 " pdb=" CD2 LEU B 54 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CB ILE B 199 " pdb=" CA ILE B 199 " pdb=" CG1 ILE B 199 " pdb=" CG2 ILE B 199 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1079 not shown) Planarity restraints: 1084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 315 " -0.062 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO A 316 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 316 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 316 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 315 " 0.036 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO B 316 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 316 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 316 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 246 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO B 247 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " -0.023 5.00e-02 4.00e+02 ... (remaining 1081 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 78 2.63 - 3.20: 6053 3.20 - 3.77: 11072 3.77 - 4.33: 15185 4.33 - 4.90: 24941 Nonbonded interactions: 57329 Sorted by model distance: nonbonded pdb=" O VAL A 235 " pdb=" OG SER A 239 " model vdw 2.065 3.040 nonbonded pdb=" O VAL B 235 " pdb=" OG SER B 239 " model vdw 2.066 3.040 nonbonded pdb=" O SER A 234 " pdb=" OG SER A 238 " model vdw 2.104 3.040 nonbonded pdb=" O SER B 234 " pdb=" OG SER B 238 " model vdw 2.118 3.040 nonbonded pdb=" O SER A 88 " pdb=" OG SER A 88 " model vdw 2.183 3.040 ... (remaining 57324 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.040 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 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 : 0.006 0.047 6662 Z= 0.367 Angle : 0.699 8.140 9052 Z= 0.357 Chirality : 0.046 0.234 1082 Planarity : 0.006 0.090 1084 Dihedral : 18.430 86.877 2332 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 7.32 % Allowed : 28.59 % Favored : 64.09 % 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: 0.60 (0.29), residues: 810 helix: 1.12 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -1.18 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 499 HIS 0.010 0.003 HIS A 200 PHE 0.012 0.002 PHE B 204 TYR 0.021 0.003 TYR B 47 ARG 0.006 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 73 time to evaluate : 0.710 Fit side-chains REVERT: A 38 ILE cc_start: 0.5869 (OUTLIER) cc_final: 0.5108 (mt) REVERT: B 38 ILE cc_start: 0.5945 (OUTLIER) cc_final: 0.5338 (mp) outliers start: 53 outliers final: 43 residues processed: 123 average time/residue: 0.7393 time to fit residues: 98.4500 Evaluate side-chains 118 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 73 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6662 Z= 0.212 Angle : 0.559 7.517 9052 Z= 0.286 Chirality : 0.041 0.134 1082 Planarity : 0.004 0.053 1084 Dihedral : 7.900 51.625 934 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.39 % Allowed : 28.45 % Favored : 66.16 % 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: 1.12 (0.29), residues: 810 helix: 1.59 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.37 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 499 HIS 0.006 0.002 HIS B 200 PHE 0.008 0.001 PHE A 78 TYR 0.017 0.002 TYR B 47 ARG 0.004 0.001 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 78 time to evaluate : 0.710 Fit side-chains REVERT: A 60 MET cc_start: 0.5515 (mpp) cc_final: 0.5248 (mmm) REVERT: A 76 MET cc_start: 0.5578 (tpt) cc_final: 0.5285 (mmm) REVERT: A 314 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7698 (tmmm) REVERT: B 509 PHE cc_start: 0.6271 (m-10) cc_final: 0.5454 (t80) outliers start: 39 outliers final: 18 residues processed: 105 average time/residue: 0.8554 time to fit residues: 96.7408 Evaluate side-chains 97 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 424 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6662 Z= 0.251 Angle : 0.580 8.012 9052 Z= 0.296 Chirality : 0.042 0.142 1082 Planarity : 0.004 0.040 1084 Dihedral : 6.618 51.391 885 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 6.22 % Allowed : 28.31 % Favored : 65.47 % 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: 1.07 (0.29), residues: 810 helix: 1.56 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.41 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 499 HIS 0.007 0.002 HIS A 200 PHE 0.010 0.001 PHE B 41 TYR 0.020 0.002 TYR B 47 ARG 0.005 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 78 time to evaluate : 0.636 Fit side-chains REVERT: A 60 MET cc_start: 0.5567 (mpp) cc_final: 0.5265 (mmm) REVERT: A 240 PHE cc_start: 0.5128 (OUTLIER) cc_final: 0.4617 (m-80) REVERT: A 360 MET cc_start: 0.8254 (mmm) cc_final: 0.7925 (mmp) REVERT: A 424 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7825 (OUTLIER) REVERT: B 38 ILE cc_start: 0.5971 (OUTLIER) cc_final: 0.5555 (mp) REVERT: B 424 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7761 (OUTLIER) REVERT: B 509 PHE cc_start: 0.6314 (m-10) cc_final: 0.5471 (t80) outliers start: 45 outliers final: 19 residues processed: 115 average time/residue: 0.8357 time to fit residues: 103.2318 Evaluate side-chains 101 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 424 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6662 Z= 0.224 Angle : 0.563 6.846 9052 Z= 0.288 Chirality : 0.041 0.144 1082 Planarity : 0.004 0.036 1084 Dihedral : 6.380 50.422 883 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 6.63 % Allowed : 27.90 % Favored : 65.47 % 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: 1.16 (0.29), residues: 810 helix: 1.65 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.43 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 499 HIS 0.006 0.002 HIS B 366 PHE 0.008 0.001 PHE B 204 TYR 0.019 0.002 TYR B 47 ARG 0.005 0.001 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 79 time to evaluate : 0.695 Fit side-chains REVERT: A 76 MET cc_start: 0.5565 (tpt) cc_final: 0.5340 (mmm) REVERT: A 240 PHE cc_start: 0.5163 (OUTLIER) cc_final: 0.4654 (m-80) REVERT: A 360 MET cc_start: 0.8247 (mmm) cc_final: 0.7937 (mmp) REVERT: A 424 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7709 (m-10) REVERT: B 38 ILE cc_start: 0.5928 (OUTLIER) cc_final: 0.5510 (mp) REVERT: B 424 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7689 (m-10) REVERT: B 509 PHE cc_start: 0.6341 (m-10) cc_final: 0.5461 (t80) outliers start: 48 outliers final: 24 residues processed: 118 average time/residue: 0.8763 time to fit residues: 111.2680 Evaluate side-chains 105 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 502 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6662 Z= 0.236 Angle : 0.576 7.088 9052 Z= 0.294 Chirality : 0.042 0.143 1082 Planarity : 0.004 0.036 1084 Dihedral : 6.416 52.689 883 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 7.18 % Allowed : 27.90 % Favored : 64.92 % 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: 1.09 (0.29), residues: 810 helix: 1.61 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.51 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 499 HIS 0.006 0.002 HIS B 366 PHE 0.009 0.001 PHE B 119 TYR 0.019 0.002 TYR B 47 ARG 0.005 0.001 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 78 time to evaluate : 0.716 Fit side-chains REVERT: A 76 MET cc_start: 0.5486 (tpt) cc_final: 0.5261 (mmm) REVERT: A 360 MET cc_start: 0.8252 (mmm) cc_final: 0.7955 (mmp) REVERT: A 424 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7819 (m-10) REVERT: B 240 PHE cc_start: 0.5090 (OUTLIER) cc_final: 0.4554 (m-80) REVERT: B 424 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7809 (m-10) REVERT: B 509 PHE cc_start: 0.6348 (m-10) cc_final: 0.5465 (t80) outliers start: 52 outliers final: 24 residues processed: 123 average time/residue: 0.8096 time to fit residues: 107.5990 Evaluate side-chains 107 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 512 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6662 Z= 0.300 Angle : 0.632 8.228 9052 Z= 0.320 Chirality : 0.043 0.147 1082 Planarity : 0.004 0.036 1084 Dihedral : 6.237 55.650 879 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 6.35 % Allowed : 28.59 % Favored : 65.06 % 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: 0.77 (0.28), residues: 810 helix: 1.37 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.64 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 499 HIS 0.006 0.002 HIS A 200 PHE 0.012 0.001 PHE B 41 TYR 0.020 0.002 TYR B 47 ARG 0.004 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 81 time to evaluate : 0.741 Fit side-chains REVERT: A 360 MET cc_start: 0.8281 (mmm) cc_final: 0.7975 (mmp) REVERT: A 424 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7881 (m-10) REVERT: B 48 PHE cc_start: 0.7127 (m-80) cc_final: 0.6926 (m-10) REVERT: B 76 MET cc_start: 0.5756 (tpt) cc_final: 0.5368 (tpt) REVERT: B 360 MET cc_start: 0.8188 (mmm) cc_final: 0.7865 (mmp) REVERT: B 424 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7834 (m-10) REVERT: B 509 PHE cc_start: 0.6373 (m-10) cc_final: 0.5455 (t80) outliers start: 46 outliers final: 26 residues processed: 116 average time/residue: 0.7905 time to fit residues: 99.3785 Evaluate side-chains 109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 512 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 44 optimal weight: 0.0870 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6662 Z= 0.199 Angle : 0.568 6.589 9052 Z= 0.288 Chirality : 0.041 0.145 1082 Planarity : 0.004 0.034 1084 Dihedral : 5.754 55.744 877 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.80 % Allowed : 29.42 % Favored : 64.78 % 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: 1.15 (0.29), residues: 810 helix: 1.69 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.58 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 499 HIS 0.006 0.002 HIS B 366 PHE 0.007 0.001 PHE A 204 TYR 0.018 0.002 TYR B 47 ARG 0.004 0.000 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 83 time to evaluate : 0.873 Fit side-chains REVERT: A 43 ILE cc_start: 0.7241 (mp) cc_final: 0.7034 (mp) REVERT: A 76 MET cc_start: 0.5438 (tpt) cc_final: 0.5228 (mmm) REVERT: A 424 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7769 (m-10) REVERT: B 424 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7782 (m-10) REVERT: B 509 PHE cc_start: 0.6340 (m-10) cc_final: 0.5454 (t80) outliers start: 42 outliers final: 23 residues processed: 117 average time/residue: 0.8431 time to fit residues: 106.7744 Evaluate side-chains 105 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 512 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.0000 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6662 Z= 0.214 Angle : 0.586 6.779 9052 Z= 0.295 Chirality : 0.042 0.208 1082 Planarity : 0.004 0.034 1084 Dihedral : 5.785 58.396 877 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.97 % Allowed : 30.52 % Favored : 64.50 % 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: 1.13 (0.29), residues: 810 helix: 1.67 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.58 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 499 HIS 0.006 0.002 HIS B 366 PHE 0.012 0.001 PHE B 119 TYR 0.018 0.002 TYR B 47 ARG 0.006 0.000 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 0.640 Fit side-chains REVERT: A 43 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6972 (mp) REVERT: A 76 MET cc_start: 0.5474 (tpt) cc_final: 0.5215 (mmm) REVERT: A 314 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7583 (tmmm) REVERT: A 424 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7808 (m-10) REVERT: B 76 MET cc_start: 0.5947 (tpt) cc_final: 0.5358 (tpt) REVERT: B 424 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7818 (m-10) REVERT: B 509 PHE cc_start: 0.6362 (m-10) cc_final: 0.5460 (t80) outliers start: 36 outliers final: 24 residues processed: 114 average time/residue: 0.8765 time to fit residues: 107.5398 Evaluate side-chains 112 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 512 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6662 Z= 0.201 Angle : 0.590 10.536 9052 Z= 0.294 Chirality : 0.042 0.182 1082 Planarity : 0.004 0.035 1084 Dihedral : 5.746 58.526 877 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.83 % Allowed : 30.52 % Favored : 64.64 % 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: 1.17 (0.29), residues: 810 helix: 1.71 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.58 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 499 HIS 0.006 0.002 HIS B 366 PHE 0.008 0.001 PHE A 119 TYR 0.017 0.002 TYR B 47 ARG 0.006 0.000 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.718 Fit side-chains REVERT: A 43 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6953 (mp) REVERT: A 60 MET cc_start: 0.5669 (mmm) cc_final: 0.5371 (mpp) REVERT: B 76 MET cc_start: 0.5623 (tpt) cc_final: 0.5175 (tpt) REVERT: B 360 MET cc_start: 0.8059 (mmm) cc_final: 0.7750 (mmp) REVERT: B 424 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7753 (m-10) REVERT: B 509 PHE cc_start: 0.6350 (m-10) cc_final: 0.5449 (t80) outliers start: 35 outliers final: 23 residues processed: 111 average time/residue: 0.8633 time to fit residues: 103.0269 Evaluate side-chains 109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 512 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6662 Z= 0.210 Angle : 0.612 10.342 9052 Z= 0.303 Chirality : 0.043 0.251 1082 Planarity : 0.004 0.033 1084 Dihedral : 5.480 55.719 875 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.56 % Allowed : 30.80 % Favored : 64.64 % 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: 1.15 (0.29), residues: 810 helix: 1.69 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.60 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 499 HIS 0.006 0.002 HIS B 366 PHE 0.011 0.001 PHE B 69 TYR 0.017 0.002 TYR B 47 ARG 0.006 0.001 ARG A 528 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.691 Fit side-chains REVERT: A 43 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6944 (mp) REVERT: A 273 ASN cc_start: 0.7767 (t0) cc_final: 0.7542 (t0) REVERT: A 511 MET cc_start: 0.6057 (mtp) cc_final: 0.5840 (mtm) REVERT: B 76 MET cc_start: 0.5622 (tpt) cc_final: 0.5144 (tpt) REVERT: B 360 MET cc_start: 0.8079 (mmm) cc_final: 0.7758 (mmp) REVERT: B 424 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7765 (m-10) REVERT: B 509 PHE cc_start: 0.6355 (m-10) cc_final: 0.5453 (t80) outliers start: 33 outliers final: 21 residues processed: 109 average time/residue: 0.8869 time to fit residues: 103.9957 Evaluate side-chains 109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 512 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 0.0170 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** 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 = 0.4111 r_free = 0.4111 target = 0.198769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.184805 restraints weight = 7679.970| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.38 r_work: 0.3907 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3824 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6662 Z= 0.204 Angle : 0.614 8.488 9052 Z= 0.307 Chirality : 0.043 0.236 1082 Planarity : 0.004 0.033 1084 Dihedral : 5.442 52.816 875 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.14 % Allowed : 31.77 % Favored : 64.09 % 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: 1.22 (0.29), residues: 810 helix: 1.75 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.60 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 499 HIS 0.006 0.002 HIS B 366 PHE 0.027 0.001 PHE B 69 TYR 0.018 0.002 TYR B 47 ARG 0.006 0.001 ARG A 528 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2356.23 seconds wall clock time: 43 minutes 48.42 seconds (2628.42 seconds total)