Starting phenix.real_space_refine on Sat May 10 15:13:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6m_38991/05_2025/8y6m_38991_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6m_38991/05_2025/8y6m_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_38991/05_2025/8y6m_38991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6m_38991/05_2025/8y6m_38991.map" model { file = "/net/cci-nas-00/data/ceres_data/8y6m_38991/05_2025/8y6m_38991_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6m_38991/05_2025/8y6m_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 4.35, per 1000 atoms: 0.67 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: 1.58 Conformation dependent library (CDL) restraints added in 891.7 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: 0.64 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: 1.72 Time building geometry restraints manager: 1.85 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: 0.03 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.120 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.650 ------------------------------------------------------------------------------- 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 6664 Z= 0.238 Angle : 0.700 8.140 9056 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 Details of bonding type rmsd hydrogen bonds : bond 0.11959 ( 428) hydrogen bonds : angle 5.39631 ( 1230) SS BOND : bond 0.00076 ( 2) SS BOND : angle 1.27078 ( 4) covalent geometry : bond 0.00565 ( 6662) covalent geometry : angle 0.69916 ( 9052) *********************** 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 : 0.667 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: 0.6848 time to fit residues: 91.4925 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 : 0.639 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.197486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.183572 restraints weight = 7674.151| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.38 r_work: 0.3888 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 6664 Z= 0.140 Angle : 0.559 7.517 9056 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 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 428) hydrogen bonds : angle 4.39489 ( 1230) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.74869 ( 4) covalent geometry : bond 0.00325 ( 6662) covalent geometry : angle 0.55882 ( 9052) *********************** 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 : 0.701 Fit side-chains REVERT: A 60 MET cc_start: 0.5522 (mpp) cc_final: 0.5260 (mmm) REVERT: A 76 MET cc_start: 0.5648 (tpt) cc_final: 0.5280 (mmm) REVERT: A 314 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7568 (tmmm) REVERT: B 509 PHE cc_start: 0.6201 (m-10) cc_final: 0.5385 (t80) outliers start: 39 outliers final: 18 residues processed: 105 average time/residue: 0.7714 time to fit residues: 87.4274 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 : 0.650 ------------------------------------------------------------------------------- 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 28 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.194267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.180168 restraints weight = 7789.718| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.40 r_work: 0.3873 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6664 Z= 0.156 Angle : 0.572 7.887 9056 Z= 0.292 Chirality : 0.042 0.142 1082 Planarity : 0.004 0.040 1084 Dihedral : 6.585 51.366 885 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.94 % Allowed : 28.31 % Favored : 65.75 % 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: 1.60 (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 0.007 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 0.004 0.001 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 428) hydrogen bonds : angle 4.32706 ( 1230) SS BOND : bond 0.00023 ( 2) SS BOND : angle 0.78589 ( 4) covalent geometry : bond 0.00370 ( 6662) covalent geometry : angle 0.57175 ( 9052) *********************** 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 121 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 78 time to evaluate : 0.684 Fit side-chains REVERT: A 60 MET cc_start: 0.5572 (mpp) cc_final: 0.5283 (mmm) REVERT: A 240 PHE cc_start: 0.5062 (OUTLIER) cc_final: 0.4588 (m-80) REVERT: A 360 MET cc_start: 0.8218 (mmm) cc_final: 0.7894 (mmp) REVERT: A 424 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7762 (OUTLIER) REVERT: B 38 ILE cc_start: 0.5971 (OUTLIER) cc_final: 0.5537 (mp) REVERT: B 424 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7796 (OUTLIER) REVERT: B 509 PHE cc_start: 0.6258 (m-10) cc_final: 0.5451 (t80) outliers start: 43 outliers final: 19 residues processed: 113 average time/residue: 0.7964 time to fit residues: 97.3373 Evaluate side-chains 100 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 37 optimal weight: 0.0030 chunk 75 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.197368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.183405 restraints weight = 7832.657| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.40 r_work: 0.3895 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6664 Z= 0.136 Angle : 0.553 6.630 9056 Z= 0.282 Chirality : 0.041 0.147 1082 Planarity : 0.004 0.036 1084 Dihedral : 6.314 50.244 883 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 6.91 % Allowed : 27.62 % 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: 1.27 (0.29), residues: 810 helix: 1.73 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.40 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 499 HIS 0.006 0.002 HIS B 366 PHE 0.007 0.001 PHE B 41 TYR 0.019 0.002 TYR B 47 ARG 0.005 0.000 ARG A 528 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 428) hydrogen bonds : angle 4.20981 ( 1230) SS BOND : bond 0.00045 ( 2) SS BOND : angle 0.65652 ( 4) covalent geometry : bond 0.00323 ( 6662) covalent geometry : angle 0.55331 ( 9052) *********************** 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: 50 poor density : 77 time to evaluate : 0.717 Fit side-chains REVERT: A 60 MET cc_start: 0.5447 (mpp) cc_final: 0.5200 (mmm) REVERT: A 76 MET cc_start: 0.5605 (tpt) cc_final: 0.5382 (mmm) REVERT: A 240 PHE cc_start: 0.5175 (OUTLIER) cc_final: 0.4707 (m-80) REVERT: A 360 MET cc_start: 0.8240 (mmm) cc_final: 0.7941 (mmp) REVERT: A 424 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7751 (m-10) REVERT: B 38 ILE cc_start: 0.5976 (OUTLIER) cc_final: 0.5576 (mp) REVERT: B 424 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7715 (m-10) REVERT: B 509 PHE cc_start: 0.6315 (m-10) cc_final: 0.5511 (t80) outliers start: 50 outliers final: 25 residues processed: 119 average time/residue: 0.7418 time to fit residues: 95.1986 Evaluate side-chains 106 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 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 245 LEU Chi-restraints excluded: chain B residue 293 LEU 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 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 69 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.196949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.183027 restraints weight = 7742.506| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.39 r_work: 0.3904 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6664 Z= 0.143 Angle : 0.564 6.627 9056 Z= 0.289 Chirality : 0.041 0.146 1082 Planarity : 0.004 0.035 1084 Dihedral : 6.329 51.751 883 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 6.91 % Allowed : 27.76 % Favored : 65.33 % 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: 1.71 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.47 (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 0.009 0.001 PHE B 119 TYR 0.019 0.002 TYR B 47 ARG 0.005 0.001 ARG B 528 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 428) hydrogen bonds : angle 4.19279 ( 1230) SS BOND : bond 0.00033 ( 2) SS BOND : angle 0.67947 ( 4) covalent geometry : bond 0.00340 ( 6662) covalent geometry : angle 0.56442 ( 9052) *********************** 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 128 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 78 time to evaluate : 0.635 Fit side-chains REVERT: A 76 MET cc_start: 0.5608 (tpt) cc_final: 0.5385 (mmm) REVERT: A 360 MET cc_start: 0.8229 (mmm) cc_final: 0.7934 (mmp) REVERT: A 424 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7801 (m-10) REVERT: B 38 ILE cc_start: 0.5880 (OUTLIER) cc_final: 0.5455 (mp) REVERT: B 240 PHE cc_start: 0.5205 (OUTLIER) cc_final: 0.4714 (m-80) REVERT: B 424 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7836 (m-10) REVERT: B 491 LYS cc_start: 0.6721 (OUTLIER) cc_final: 0.6384 (mmtm) REVERT: B 509 PHE cc_start: 0.6315 (m-10) cc_final: 0.5493 (t80) outliers start: 50 outliers final: 22 residues processed: 120 average time/residue: 0.7314 time to fit residues: 94.8685 Evaluate side-chains 104 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP 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 482 LEU Chi-restraints excluded: chain A residue 502 GLU 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 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 491 LYS 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 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.196518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.182613 restraints weight = 7671.365| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.37 r_work: 0.3901 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6664 Z= 0.153 Angle : 0.584 7.327 9056 Z= 0.295 Chirality : 0.042 0.150 1082 Planarity : 0.004 0.034 1084 Dihedral : 6.011 53.475 879 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 6.08 % Allowed : 29.01 % 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: 1.10 (0.29), residues: 810 helix: 1.64 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.57 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 499 HIS 0.006 0.002 HIS B 366 PHE 0.009 0.001 PHE B 41 TYR 0.018 0.002 TYR B 47 ARG 0.004 0.000 ARG B 528 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 428) hydrogen bonds : angle 4.19858 ( 1230) SS BOND : bond 0.00023 ( 2) SS BOND : angle 0.71656 ( 4) covalent geometry : bond 0.00362 ( 6662) covalent geometry : angle 0.58440 ( 9052) *********************** 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 121 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 77 time to evaluate : 0.758 Fit side-chains REVERT: A 360 MET cc_start: 0.8234 (mmm) cc_final: 0.7937 (mmp) REVERT: A 424 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7823 (m-10) REVERT: B 76 MET cc_start: 0.5961 (tpt) cc_final: 0.5365 (tpt) REVERT: B 424 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7865 (m-10) REVERT: B 491 LYS cc_start: 0.6744 (OUTLIER) cc_final: 0.6441 (mmtm) REVERT: B 509 PHE cc_start: 0.6322 (m-10) cc_final: 0.5486 (t80) outliers start: 44 outliers final: 26 residues processed: 114 average time/residue: 0.7962 time to fit residues: 97.8190 Evaluate side-chains 107 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 75 ASP 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 301 LYS 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 491 LYS 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 81 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 53 optimal weight: 0.0670 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.198558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.184609 restraints weight = 7713.568| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.38 r_work: 0.3916 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6664 Z= 0.128 Angle : 0.568 6.509 9056 Z= 0.288 Chirality : 0.042 0.183 1082 Planarity : 0.004 0.033 1084 Dihedral : 5.926 54.025 879 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 6.08 % Allowed : 28.73 % Favored : 65.19 % 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: 1.26 (0.29), residues: 810 helix: 1.77 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 499 HIS 0.005 0.002 HIS B 366 PHE 0.007 0.001 PHE B 204 TYR 0.018 0.002 TYR B 47 ARG 0.004 0.000 ARG B 528 Details of bonding type rmsd hydrogen bonds : bond 0.03088 ( 428) hydrogen bonds : angle 4.15317 ( 1230) SS BOND : bond 0.00066 ( 2) SS BOND : angle 0.59577 ( 4) covalent geometry : bond 0.00306 ( 6662) covalent geometry : angle 0.56822 ( 9052) *********************** 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 127 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 83 time to evaluate : 0.693 Fit side-chains REVERT: A 76 MET cc_start: 0.5666 (tpt) cc_final: 0.5291 (mmm) REVERT: A 273 ASN cc_start: 0.7618 (t0) cc_final: 0.7399 (t0) REVERT: A 424 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7769 (m-10) REVERT: B 38 ILE cc_start: 0.5844 (OUTLIER) cc_final: 0.5450 (mp) REVERT: B 424 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7820 (m-10) REVERT: B 491 LYS cc_start: 0.6719 (OUTLIER) cc_final: 0.6388 (mmtm) REVERT: B 509 PHE cc_start: 0.6296 (m-10) cc_final: 0.5471 (t80) outliers start: 44 outliers final: 24 residues processed: 118 average time/residue: 0.7533 time to fit residues: 95.8173 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 : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 75 ASP 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 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 491 LYS 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 73 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 43 optimal weight: 0.3980 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 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 = 0.4107 r_free = 0.4107 target = 0.198544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.184646 restraints weight = 7739.857| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 1.38 r_work: 0.3914 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6664 Z= 0.133 Angle : 0.589 9.529 9056 Z= 0.294 Chirality : 0.042 0.203 1082 Planarity : 0.004 0.033 1084 Dihedral : 5.914 56.000 879 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.52 % Allowed : 29.28 % Favored : 65.19 % 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: 1.27 (0.29), residues: 810 helix: 1.79 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.56 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 499 HIS 0.005 0.002 HIS B 366 PHE 0.006 0.001 PHE B 204 TYR 0.017 0.002 TYR B 47 ARG 0.006 0.001 ARG A 528 Details of bonding type rmsd hydrogen bonds : bond 0.03101 ( 428) hydrogen bonds : angle 4.13447 ( 1230) SS BOND : bond 0.00057 ( 2) SS BOND : angle 0.58451 ( 4) covalent geometry : bond 0.00313 ( 6662) covalent geometry : angle 0.58916 ( 9052) *********************** 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 126 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 86 time to evaluate : 0.711 Fit side-chains REVERT: A 60 MET cc_start: 0.5638 (mmm) cc_final: 0.5415 (mpp) REVERT: A 273 ASN cc_start: 0.7658 (t0) cc_final: 0.7439 (t0) REVERT: A 424 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7769 (m-10) REVERT: B 76 MET cc_start: 0.5885 (tpt) cc_final: 0.5311 (tpt) REVERT: B 360 MET cc_start: 0.8092 (mmm) cc_final: 0.7789 (mmp) REVERT: B 424 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7831 (m-10) REVERT: B 491 LYS cc_start: 0.6779 (OUTLIER) cc_final: 0.6435 (mmtm) REVERT: B 509 PHE cc_start: 0.6315 (m-10) cc_final: 0.5476 (t80) outliers start: 40 outliers final: 24 residues processed: 117 average time/residue: 0.8101 time to fit residues: 102.0685 Evaluate side-chains 110 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 75 ASP 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 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 211 ILE Chi-restraints excluded: chain B residue 301 LYS 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 491 LYS 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 35 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 chunk 31 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 78 optimal weight: 0.0570 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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 B 44 GLN B 273 ASN B 366 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.202037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.187928 restraints weight = 7839.203| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.41 r_work: 0.3948 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3865 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6664 Z= 0.110 Angle : 0.566 9.086 9056 Z= 0.281 Chirality : 0.041 0.181 1082 Planarity : 0.004 0.032 1084 Dihedral : 5.478 58.012 877 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.56 % Allowed : 30.39 % 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: 1.51 (0.29), residues: 810 helix: 1.98 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.51 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 499 HIS 0.004 0.001 HIS B 366 PHE 0.010 0.001 PHE A 119 TYR 0.016 0.001 TYR A 47 ARG 0.007 0.001 ARG A 528 Details of bonding type rmsd hydrogen bonds : bond 0.02897 ( 428) hydrogen bonds : angle 4.01245 ( 1230) SS BOND : bond 0.00089 ( 2) SS BOND : angle 0.38068 ( 4) covalent geometry : bond 0.00258 ( 6662) covalent geometry : angle 0.56620 ( 9052) *********************** 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 116 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.680 Fit side-chains REVERT: A 38 ILE cc_start: 0.6074 (OUTLIER) cc_final: 0.5543 (mt) REVERT: A 60 MET cc_start: 0.5605 (mmm) cc_final: 0.5336 (mpp) REVERT: A 424 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7652 (m-10) REVERT: B 60 MET cc_start: 0.5695 (mpp) cc_final: 0.5471 (mmm) REVERT: B 76 MET cc_start: 0.5630 (tpt) cc_final: 0.5115 (tpt) REVERT: B 245 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6956 (mp) REVERT: B 424 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7688 (m-10) REVERT: B 509 PHE cc_start: 0.6302 (m-10) cc_final: 0.5491 (t80) outliers start: 33 outliers final: 14 residues processed: 107 average time/residue: 0.8223 time to fit residues: 94.6034 Evaluate side-chains 99 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 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 211 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 B residue 96 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 301 LYS 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 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN B 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.197344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.183369 restraints weight = 7862.727| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.40 r_work: 0.3901 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 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 : 0.004 0.045 6664 Z= 0.162 Angle : 0.638 7.873 9056 Z= 0.318 Chirality : 0.045 0.256 1082 Planarity : 0.004 0.033 1084 Dihedral : 5.659 58.293 876 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.59 % Allowed : 31.49 % 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: 1.21 (0.29), residues: 810 helix: 1.73 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 499 HIS 0.006 0.002 HIS A 366 PHE 0.009 0.001 PHE B 41 TYR 0.017 0.002 TYR B 47 ARG 0.006 0.001 ARG A 528 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 428) hydrogen bonds : angle 4.20783 ( 1230) SS BOND : bond 0.00021 ( 2) SS BOND : angle 0.68697 ( 4) covalent geometry : bond 0.00384 ( 6662) covalent geometry : angle 0.63804 ( 9052) ********************** 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 109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.672 Fit side-chains REVERT: A 60 MET cc_start: 0.5799 (mmm) cc_final: 0.5476 (mpp) REVERT: A 76 MET cc_start: 0.5764 (tpt) cc_final: 0.5299 (mmm) REVERT: A 424 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7852 (m-10) REVERT: B 76 MET cc_start: 0.5699 (tpt) cc_final: 0.5407 (mmm) REVERT: B 424 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7876 (m-10) REVERT: B 491 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6393 (mmtm) REVERT: B 509 PHE cc_start: 0.6402 (m-10) cc_final: 0.5539 (t80) outliers start: 26 outliers final: 14 residues processed: 103 average time/residue: 0.8305 time to fit residues: 91.9843 Evaluate side-chains 99 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 211 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 B residue 96 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 301 LYS 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 491 LYS 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 81 optimal weight: 0.0670 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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** B 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.200252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.186144 restraints weight = 7857.759| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.40 r_work: 0.3903 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6664 Z= 0.128 Angle : 0.610 7.617 9056 Z= 0.303 Chirality : 0.043 0.249 1082 Planarity : 0.004 0.033 1084 Dihedral : 5.544 56.595 876 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.90 % Allowed : 32.18 % 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: 1.33 (0.29), residues: 810 helix: 1.83 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.54 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 499 HIS 0.005 0.001 HIS A 200 PHE 0.010 0.001 PHE B 116 TYR 0.018 0.002 TYR B 47 ARG 0.006 0.001 ARG A 528 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 428) hydrogen bonds : angle 4.09752 ( 1230) SS BOND : bond 0.00062 ( 2) SS BOND : angle 0.53319 ( 4) covalent geometry : bond 0.00302 ( 6662) covalent geometry : angle 0.61046 ( 9052) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4028.29 seconds wall clock time: 70 minutes 26.87 seconds (4226.87 seconds total)