Starting phenix.real_space_refine on Wed Sep 17 07:03:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6m_38991/09_2025/8y6m_38991_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6m_38991/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8y6m_38991/09_2025/8y6m_38991_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6m_38991/09_2025/8y6m_38991_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y6m_38991/09_2025/8y6m_38991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6m_38991/09_2025/8y6m_38991.map" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.76, per 1000 atoms: 0.27 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: 0.55 Conformation dependent library (CDL) restraints added in 321.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.19 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: 0.89 Time building geometry restraints manager: 0.74 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: 0.01 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: 1.180 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.240 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.040 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG A 213 TYR 0.021 0.003 TYR B 47 PHE 0.012 0.002 PHE B 204 TRP 0.012 0.002 TRP B 499 HIS 0.010 0.003 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 6662) covalent geometry : angle 0.69916 ( 9052) SS BOND : bond 0.00076 ( 2) SS BOND : angle 1.27078 ( 4) hydrogen bonds : bond 0.11959 ( 428) hydrogen bonds : angle 5.39631 ( 1230) *********************** 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 : 0.286 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: 0.3547 time to fit residues: 47.2065 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 : 0.253 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.197417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.183452 restraints weight = 7756.703| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.39 r_work: 0.3888 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3804 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.0848 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= 0.137 Angle : 0.557 7.428 9056 Z= 0.285 Chirality : 0.041 0.134 1082 Planarity : 0.004 0.050 1084 Dihedral : 7.905 51.597 934 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.52 % Allowed : 28.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.29), residues: 810 helix: 1.59 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.38 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 528 TYR 0.017 0.002 TYR B 47 PHE 0.008 0.001 PHE A 78 TRP 0.007 0.001 TRP A 499 HIS 0.006 0.002 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6662) covalent geometry : angle 0.55693 ( 9052) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.77406 ( 4) hydrogen bonds : bond 0.03410 ( 428) hydrogen bonds : angle 4.38847 ( 1230) *********************** 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 118 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 78 time to evaluate : 0.260 Fit side-chains REVERT: A 314 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7587 (tmmm) REVERT: B 509 PHE cc_start: 0.6202 (m-10) cc_final: 0.5393 (t80) outliers start: 40 outliers final: 18 residues processed: 106 average time/residue: 0.3869 time to fit residues: 44.0771 Evaluate side-chains 96 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 27 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.192206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.178459 restraints weight = 7680.917| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.34 r_work: 0.3839 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6664 Z= 0.210 Angle : 0.631 8.304 9056 Z= 0.321 Chirality : 0.043 0.145 1082 Planarity : 0.005 0.042 1084 Dihedral : 6.804 51.602 885 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 6.91 % Allowed : 28.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.29), residues: 810 helix: 1.37 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.45 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 213 TYR 0.022 0.002 TYR B 47 PHE 0.014 0.002 PHE B 41 TRP 0.009 0.001 TRP A 499 HIS 0.007 0.003 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 6662) covalent geometry : angle 0.63058 ( 9052) SS BOND : bond 0.00044 ( 2) SS BOND : angle 0.97136 ( 4) hydrogen bonds : bond 0.03758 ( 428) hydrogen bonds : angle 4.50152 ( 1230) *********************** 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 130 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 80 time to evaluate : 0.242 Fit side-chains REVERT: A 240 PHE cc_start: 0.5183 (OUTLIER) cc_final: 0.4645 (m-80) REVERT: A 360 MET cc_start: 0.8255 (mmm) cc_final: 0.7922 (mmp) REVERT: A 424 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7887 (OUTLIER) REVERT: B 38 ILE cc_start: 0.6028 (OUTLIER) cc_final: 0.5553 (mp) REVERT: B 360 MET cc_start: 0.8242 (mmm) cc_final: 0.7945 (mmp) REVERT: B 509 PHE cc_start: 0.6305 (m-10) cc_final: 0.5464 (t80) outliers start: 50 outliers final: 21 residues processed: 120 average time/residue: 0.3850 time to fit residues: 49.7311 Evaluate side-chains 104 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 240 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 ILE 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 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 317 THR Chi-restraints excluded: chain B residue 417 LEU 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 55 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 68 optimal weight: 0.0670 chunk 81 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- 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 ** 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 = 0.4116 r_free = 0.4116 target = 0.199329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.185301 restraints weight = 7811.651| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 1.40 r_work: 0.3924 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6664 Z= 0.113 Angle : 0.534 6.568 9056 Z= 0.272 Chirality : 0.040 0.147 1082 Planarity : 0.004 0.035 1084 Dihedral : 6.246 49.765 883 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 7.18 % Allowed : 27.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.29), residues: 810 helix: 1.78 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.41 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 528 TYR 0.019 0.002 TYR B 47 PHE 0.007 0.001 PHE A 78 TRP 0.005 0.001 TRP A 499 HIS 0.005 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6662) covalent geometry : angle 0.53376 ( 9052) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.55777 ( 4) hydrogen bonds : bond 0.03008 ( 428) hydrogen bonds : angle 4.13486 ( 1230) *********************** 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 137 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 85 time to evaluate : 0.244 Fit side-chains REVERT: A 76 MET cc_start: 0.5588 (tpt) cc_final: 0.5277 (mmm) REVERT: A 424 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: B 360 MET cc_start: 0.8065 (mmm) cc_final: 0.7800 (mmp) REVERT: B 424 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7664 (m-10) REVERT: B 509 PHE cc_start: 0.6263 (m-10) cc_final: 0.5472 (t80) REVERT: B 516 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7127 (mp) outliers start: 52 outliers final: 22 residues processed: 129 average time/residue: 0.3886 time to fit residues: 53.9644 Evaluate side-chains 106 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 293 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 LYS 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 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 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 Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 516 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 366 HIS 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.196822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.182855 restraints weight = 7882.247| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 1.39 r_work: 0.3877 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3793 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6664 Z= 0.148 Angle : 0.574 7.222 9056 Z= 0.291 Chirality : 0.042 0.143 1082 Planarity : 0.004 0.035 1084 Dihedral : 6.369 52.130 883 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 6.77 % Allowed : 27.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.29), residues: 810 helix: 1.69 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.46 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 528 TYR 0.018 0.002 TYR B 47 PHE 0.009 0.001 PHE B 41 TRP 0.008 0.001 TRP A 499 HIS 0.006 0.002 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6662) covalent geometry : angle 0.57407 ( 9052) SS BOND : bond 0.00028 ( 2) SS BOND : angle 0.69348 ( 4) hydrogen bonds : bond 0.03228 ( 428) hydrogen bonds : angle 4.17969 ( 1230) *********************** 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 129 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 80 time to evaluate : 0.253 Fit side-chains REVERT: A 360 MET cc_start: 0.8236 (mmm) cc_final: 0.7952 (mmp) REVERT: A 424 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7828 (m-10) REVERT: B 48 PHE cc_start: 0.7012 (m-80) cc_final: 0.6801 (m-10) REVERT: B 76 MET cc_start: 0.5961 (tpt) cc_final: 0.5397 (tpt) REVERT: B 360 MET cc_start: 0.8112 (mmm) cc_final: 0.7844 (mmp) REVERT: B 424 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7860 (m-10) REVERT: B 491 LYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6447 (mmtm) REVERT: B 509 PHE cc_start: 0.6318 (m-10) cc_final: 0.5531 (t80) outliers start: 49 outliers final: 23 residues processed: 121 average time/residue: 0.3901 time to fit residues: 50.8631 Evaluate side-chains 108 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 350 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 18 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 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 = 0.4092 r_free = 0.4092 target = 0.197080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.183096 restraints weight = 7800.626| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 1.38 r_work: 0.3884 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6664 Z= 0.146 Angle : 0.573 7.114 9056 Z= 0.290 Chirality : 0.042 0.144 1082 Planarity : 0.004 0.034 1084 Dihedral : 6.227 53.828 881 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.94 % Allowed : 28.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.29), residues: 810 helix: 1.68 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 528 TYR 0.018 0.002 TYR B 47 PHE 0.008 0.001 PHE B 41 TRP 0.008 0.001 TRP A 499 HIS 0.005 0.002 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6662) covalent geometry : angle 0.57298 ( 9052) SS BOND : bond 0.00032 ( 2) SS BOND : angle 0.68614 ( 4) hydrogen bonds : bond 0.03197 ( 428) hydrogen bonds : angle 4.18420 ( 1230) *********************** 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 125 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 82 time to evaluate : 0.251 Fit side-chains REVERT: A 360 MET cc_start: 0.8200 (mmm) cc_final: 0.7908 (mmp) REVERT: A 424 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7759 (m-10) REVERT: B 60 MET cc_start: 0.5707 (mpp) cc_final: 0.5374 (mmm) REVERT: B 76 MET cc_start: 0.5535 (tpt) cc_final: 0.5243 (mmm) REVERT: B 360 MET cc_start: 0.8095 (mmm) cc_final: 0.7820 (mmp) REVERT: B 424 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7798 (m-10) REVERT: B 491 LYS cc_start: 0.6629 (OUTLIER) cc_final: 0.6317 (mmtm) REVERT: B 509 PHE cc_start: 0.6265 (m-10) cc_final: 0.5402 (t80) outliers start: 43 outliers final: 26 residues processed: 116 average time/residue: 0.4009 time to fit residues: 50.0146 Evaluate side-chains 110 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 350 SER 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 75 ASP 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 296 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 58 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 2 optimal weight: 0.0870 chunk 77 optimal weight: 2.9990 chunk 20 optimal weight: 0.0050 chunk 76 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.5172 ------------------------------------------------------------------------------- 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 ** 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 = 0.4112 r_free = 0.4112 target = 0.199012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.185116 restraints weight = 7749.792| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.38 r_work: 0.3892 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6664 Z= 0.125 Angle : 0.563 7.299 9056 Z= 0.284 Chirality : 0.041 0.166 1082 Planarity : 0.004 0.033 1084 Dihedral : 6.123 54.704 881 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 6.49 % Allowed : 28.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.29), residues: 810 helix: 1.80 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.53 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 528 TYR 0.017 0.002 TYR B 47 PHE 0.008 0.001 PHE B 48 TRP 0.007 0.001 TRP A 499 HIS 0.005 0.002 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6662) covalent geometry : angle 0.56254 ( 9052) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.54991 ( 4) hydrogen bonds : bond 0.03027 ( 428) hydrogen bonds : angle 4.10529 ( 1230) *********************** 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 133 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 86 time to evaluate : 0.218 Fit side-chains REVERT: A 60 MET cc_start: 0.5631 (mpp) cc_final: 0.5378 (mmm) REVERT: A 76 MET cc_start: 0.5572 (tpt) cc_final: 0.5354 (mmm) REVERT: A 240 PHE cc_start: 0.5200 (OUTLIER) cc_final: 0.4811 (m-80) REVERT: A 360 MET cc_start: 0.8187 (mmm) cc_final: 0.7900 (mmp) REVERT: A 424 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7737 (m-10) REVERT: B 60 MET cc_start: 0.5661 (mpp) cc_final: 0.5456 (mmm) REVERT: B 76 MET cc_start: 0.5544 (tpt) cc_final: 0.5244 (mmm) REVERT: B 424 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7753 (m-10) REVERT: B 491 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6290 (mmtm) REVERT: B 509 PHE cc_start: 0.6263 (m-10) cc_final: 0.5437 (t80) outliers start: 47 outliers final: 25 residues processed: 122 average time/residue: 0.3907 time to fit residues: 51.3688 Evaluate side-chains 112 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 240 PHE 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 75 ASP 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 308 TYR 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 28 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN 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 = 0.4102 r_free = 0.4102 target = 0.198006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.183962 restraints weight = 7805.056| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.38 r_work: 0.3910 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6664 Z= 0.141 Angle : 0.586 7.237 9056 Z= 0.295 Chirality : 0.043 0.219 1082 Planarity : 0.004 0.034 1084 Dihedral : 6.157 57.486 881 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 6.22 % Allowed : 28.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.29), residues: 810 helix: 1.74 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.57 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 528 TYR 0.018 0.002 TYR B 47 PHE 0.009 0.001 PHE B 119 TRP 0.011 0.001 TRP B 499 HIS 0.005 0.002 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6662) covalent geometry : angle 0.58551 ( 9052) SS BOND : bond 0.00036 ( 2) SS BOND : angle 0.62114 ( 4) hydrogen bonds : bond 0.03184 ( 428) hydrogen bonds : angle 4.15954 ( 1230) *********************** 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 127 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 82 time to evaluate : 0.246 Fit side-chains REVERT: A 60 MET cc_start: 0.5670 (mpp) cc_final: 0.5422 (mmm) REVERT: A 76 MET cc_start: 0.5737 (tpt) cc_final: 0.5323 (mmm) REVERT: A 240 PHE cc_start: 0.5090 (OUTLIER) cc_final: 0.4677 (m-80) REVERT: A 424 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7784 (m-10) REVERT: B 60 MET cc_start: 0.5739 (mpp) cc_final: 0.5506 (mmm) REVERT: B 76 MET cc_start: 0.5534 (tpt) cc_final: 0.5274 (mmm) REVERT: B 245 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6892 (mp) REVERT: B 424 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7829 (m-10) REVERT: B 491 LYS cc_start: 0.6690 (OUTLIER) cc_final: 0.6370 (mmtm) REVERT: B 509 PHE cc_start: 0.6308 (m-10) cc_final: 0.5483 (t80) outliers start: 45 outliers final: 24 residues processed: 116 average time/residue: 0.3919 time to fit residues: 48.8048 Evaluate side-chains 112 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 211 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 308 TYR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 350 SER 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 75 ASP 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 245 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 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 5 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** 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 = 0.4071 r_free = 0.4071 target = 0.194786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.180714 restraints weight = 7886.883| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.39 r_work: 0.3880 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6664 Z= 0.187 Angle : 0.637 8.168 9056 Z= 0.322 Chirality : 0.045 0.195 1082 Planarity : 0.004 0.033 1084 Dihedral : 6.192 59.263 879 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.80 % Allowed : 29.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.28), residues: 810 helix: 1.46 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.61 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 528 TYR 0.019 0.002 TYR B 47 PHE 0.012 0.001 PHE B 41 TRP 0.013 0.001 TRP A 499 HIS 0.007 0.002 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 6662) covalent geometry : angle 0.63689 ( 9052) SS BOND : bond 0.00027 ( 2) SS BOND : angle 0.91344 ( 4) hydrogen bonds : bond 0.03513 ( 428) hydrogen bonds : angle 4.33972 ( 1230) *********************** 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 122 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 80 time to evaluate : 0.224 Fit side-chains REVERT: A 60 MET cc_start: 0.5850 (mpp) cc_final: 0.5556 (mmm) REVERT: A 76 MET cc_start: 0.5768 (tpt) cc_final: 0.5446 (mmm) REVERT: A 240 PHE cc_start: 0.5136 (OUTLIER) cc_final: 0.4661 (m-80) REVERT: A 314 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7489 (tmmm) REVERT: A 360 MET cc_start: 0.8259 (mmm) cc_final: 0.7913 (mmp) REVERT: A 424 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7925 (m-10) REVERT: B 60 MET cc_start: 0.5858 (mpp) cc_final: 0.5513 (mmm) REVERT: B 76 MET cc_start: 0.5610 (tpt) cc_final: 0.5327 (mmm) REVERT: B 424 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7877 (m-10) REVERT: B 491 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6414 (mmtm) REVERT: B 509 PHE cc_start: 0.6408 (m-10) cc_final: 0.5531 (t80) outliers start: 42 outliers final: 25 residues processed: 112 average time/residue: 0.3894 time to fit residues: 46.8644 Evaluate side-chains 112 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 211 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 308 TYR 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 350 SER 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 75 ASP 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 300 ILE Chi-restraints excluded: chain B residue 308 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 71 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.0010 chunk 62 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 ** 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 = 0.4103 r_free = 0.4103 target = 0.198397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.184547 restraints weight = 7671.127| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.35 r_work: 0.3901 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 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 0.050 6664 Z= 0.133 Angle : 0.591 7.202 9056 Z= 0.298 Chirality : 0.043 0.223 1082 Planarity : 0.004 0.033 1084 Dihedral : 5.999 57.826 879 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.97 % Allowed : 29.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.29), residues: 810 helix: 1.52 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.49 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 528 TYR 0.018 0.002 TYR A 47 PHE 0.007 0.001 PHE B 116 TRP 0.011 0.001 TRP A 499 HIS 0.005 0.002 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6662) covalent geometry : angle 0.59083 ( 9052) SS BOND : bond 0.00061 ( 2) SS BOND : angle 0.63262 ( 4) hydrogen bonds : bond 0.03138 ( 428) hydrogen bonds : angle 4.19221 ( 1230) ********************** 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 122 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 0.254 Fit side-chains REVERT: A 76 MET cc_start: 0.5714 (tpt) cc_final: 0.5382 (mmm) REVERT: A 240 PHE cc_start: 0.5150 (OUTLIER) cc_final: 0.4794 (m-80) REVERT: A 314 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7486 (tmmm) REVERT: A 424 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7857 (m-10) REVERT: B 60 MET cc_start: 0.5759 (mpp) cc_final: 0.5541 (mmm) REVERT: B 76 MET cc_start: 0.5517 (tpt) cc_final: 0.5306 (mmm) REVERT: B 360 MET cc_start: 0.8080 (mmm) cc_final: 0.7780 (mmp) REVERT: B 491 LYS cc_start: 0.6750 (OUTLIER) cc_final: 0.6422 (mmtm) REVERT: B 509 PHE cc_start: 0.6337 (m-10) cc_final: 0.5512 (t80) outliers start: 36 outliers final: 20 residues processed: 115 average time/residue: 0.3919 time to fit residues: 48.4347 Evaluate side-chains 108 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 240 PHE 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 350 SER 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 75 ASP 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 320 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 418 VAL 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 63 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 71 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ** 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 = 0.4084 r_free = 0.4084 target = 0.196247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.182200 restraints weight = 7750.035| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.38 r_work: 0.3881 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6664 Z= 0.169 Angle : 0.647 10.698 9056 Z= 0.323 Chirality : 0.044 0.216 1082 Planarity : 0.004 0.032 1084 Dihedral : 5.845 55.744 877 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.83 % Allowed : 30.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.29), residues: 810 helix: 1.41 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -1.39 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 528 TYR 0.019 0.002 TYR B 47 PHE 0.013 0.001 PHE B 69 TRP 0.015 0.001 TRP B 499 HIS 0.006 0.002 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6662) covalent geometry : angle 0.64646 ( 9052) SS BOND : bond 0.00013 ( 2) SS BOND : angle 0.78683 ( 4) hydrogen bonds : bond 0.03391 ( 428) hydrogen bonds : angle 4.28767 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2193.08 seconds wall clock time: 38 minutes 17.56 seconds (2297.56 seconds total)