Starting phenix.real_space_refine on Tue Jan 14 08:28:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6l_38990/01_2025/8y6l_38990_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6l_38990/01_2025/8y6l_38990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y6l_38990/01_2025/8y6l_38990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6l_38990/01_2025/8y6l_38990.map" model { file = "/net/cci-nas-00/data/ceres_data/8y6l_38990/01_2025/8y6l_38990_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6l_38990/01_2025/8y6l_38990_neut.cif" } resolution = 3.4 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= 0.032 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 50 5.16 5 C 4112 2.51 5 N 1028 2.21 5 O 1066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6256 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3128 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 393} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3128 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 393} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 4.06, per 1000 atoms: 0.65 Number of scatterers: 6256 At special positions: 0 Unit cell: (71.76, 105.04, 78, 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 50 16.00 O 1066 8.00 N 1028 7.00 C 4112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 502 " - pdb=" SG CYS A 512 " distance=2.03 Simple disulfide: pdb=" SG CYS B 502 " - pdb=" SG CYS B 512 " 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: 1.57 Conformation dependent library (CDL) restraints added in 914.4 milliseconds 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 2 sheets defined 66.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 26 through 49 Processing helix chain 'A' and resid 60 through 73 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.711A pdb=" N PHE A 85 " --> pdb=" O MET A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 98 removed outlier: 3.943A pdb=" N LEU A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 removed outlier: 3.524A pdb=" N PHE A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 234 removed outlier: 4.448A pdb=" N VAL A 228 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 285 through 293 removed outlier: 3.513A pdb=" N VAL A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 removed outlier: 3.770A pdb=" N PHE A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.845A pdb=" N GLY A 330 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 362 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.783A pdb=" N ARG A 369 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 387 removed outlier: 4.181A pdb=" N GLY A 379 " --> pdb=" O GLN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 414 removed outlier: 3.630A pdb=" N LEU A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 467 Processing helix chain 'A' and resid 479 through 493 Processing helix chain 'A' and resid 501 through 505 Processing helix chain 'A' and resid 524 through 540 removed outlier: 3.572A pdb=" N LEU A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 544 Processing helix chain 'B' and resid 26 through 49 Processing helix chain 'B' and resid 60 through 73 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.712A pdb=" N PHE B 85 " --> pdb=" O MET B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 98 removed outlier: 3.945A pdb=" N LEU B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.524A pdb=" N PHE B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 234 removed outlier: 4.449A pdb=" N VAL B 228 " --> pdb=" O TYR B 224 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.512A pdb=" N VAL B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 308 removed outlier: 3.771A pdb=" N PHE B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.845A pdb=" N GLY B 330 " --> pdb=" O GLY B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 362 Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.783A pdb=" N ARG B 369 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 387 removed outlier: 4.181A pdb=" N GLY B 379 " --> pdb=" O GLN B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 414 removed outlier: 3.630A pdb=" N LEU B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 414 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 467 Processing helix chain 'B' and resid 479 through 493 Processing helix chain 'B' and resid 501 through 505 Processing helix chain 'B' and resid 524 through 540 removed outlier: 3.571A pdb=" N LEU B 540 " --> pdb=" O PHE B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 544 Processing sheet with id=AA1, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AA2, first strand: chain 'A' and resid 551 through 552 362 hydrogen bonds defined for protein. 1044 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: 1.45 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 930 1.30 - 1.42: 1696 1.42 - 1.55: 3680 1.55 - 1.68: 0 1.68 - 1.81: 88 Bond restraints: 6394 Sorted by residual: bond pdb=" C CYS A 263 " pdb=" O CYS A 263 " ideal model delta sigma weight residual 1.235 1.168 0.067 1.10e-02 8.26e+03 3.69e+01 bond pdb=" C CYS B 263 " pdb=" O CYS B 263 " ideal model delta sigma weight residual 1.235 1.168 0.067 1.10e-02 8.26e+03 3.69e+01 bond pdb=" C SER A 75 " pdb=" O SER A 75 " ideal model delta sigma weight residual 1.235 1.168 0.067 1.26e-02 6.30e+03 2.87e+01 bond pdb=" C SER B 75 " pdb=" O SER B 75 " ideal model delta sigma weight residual 1.235 1.168 0.067 1.26e-02 6.30e+03 2.87e+01 bond pdb=" C SER B 76 " pdb=" O SER B 76 " ideal model delta sigma weight residual 1.235 1.189 0.047 1.26e-02 6.30e+03 1.38e+01 ... (remaining 6389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 8356 2.55 - 5.09: 278 5.09 - 7.64: 32 7.64 - 10.19: 12 10.19 - 12.74: 2 Bond angle restraints: 8680 Sorted by residual: angle pdb=" CA PRO A 422 " pdb=" N PRO A 422 " pdb=" CD PRO A 422 " ideal model delta sigma weight residual 112.00 99.26 12.74 1.40e+00 5.10e-01 8.27e+01 angle pdb=" CA PRO B 422 " pdb=" N PRO B 422 " pdb=" CD PRO B 422 " ideal model delta sigma weight residual 112.00 99.26 12.74 1.40e+00 5.10e-01 8.27e+01 angle pdb=" C CYS B 263 " pdb=" N GLY B 264 " pdb=" CA GLY B 264 " ideal model delta sigma weight residual 123.08 114.20 8.88 1.35e+00 5.49e-01 4.33e+01 angle pdb=" C CYS A 263 " pdb=" N GLY A 264 " pdb=" CA GLY A 264 " ideal model delta sigma weight residual 123.08 114.22 8.86 1.35e+00 5.49e-01 4.30e+01 angle pdb=" C THR B 259 " pdb=" CA THR B 259 " pdb=" CB THR B 259 " ideal model delta sigma weight residual 110.74 101.57 9.17 1.66e+00 3.63e-01 3.05e+01 ... (remaining 8675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 3146 15.99 - 31.97: 388 31.97 - 47.96: 154 47.96 - 63.94: 38 63.94 - 79.93: 8 Dihedral angle restraints: 3734 sinusoidal: 1402 harmonic: 2332 Sorted by residual: dihedral pdb=" C PHE B 420 " pdb=" N PHE B 420 " pdb=" CA PHE B 420 " pdb=" CB PHE B 420 " ideal model delta harmonic sigma weight residual -122.60 -110.00 -12.60 0 2.50e+00 1.60e-01 2.54e+01 dihedral pdb=" C PHE A 420 " pdb=" N PHE A 420 " pdb=" CA PHE A 420 " pdb=" CB PHE A 420 " ideal model delta harmonic sigma weight residual -122.60 -110.02 -12.58 0 2.50e+00 1.60e-01 2.53e+01 dihedral pdb=" C THR A 105 " pdb=" N THR A 105 " pdb=" CA THR A 105 " pdb=" CB THR A 105 " ideal model delta harmonic sigma weight residual -122.00 -132.81 10.81 0 2.50e+00 1.60e-01 1.87e+01 ... (remaining 3731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 954 0.084 - 0.168: 64 0.168 - 0.252: 18 0.252 - 0.336: 6 0.336 - 0.420: 4 Chirality restraints: 1046 Sorted by residual: chirality pdb=" CA PHE B 420 " pdb=" N PHE B 420 " pdb=" C PHE B 420 " pdb=" CB PHE B 420 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CA PHE A 420 " pdb=" N PHE A 420 " pdb=" C PHE A 420 " pdb=" CB PHE A 420 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CA ASN B 262 " pdb=" N ASN B 262 " pdb=" C ASN B 262 " pdb=" CB ASN B 262 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 1043 not shown) Planarity restraints: 1056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 416 " 0.025 2.00e-02 2.50e+03 4.84e-02 2.34e+01 pdb=" C PRO B 416 " -0.084 2.00e-02 2.50e+03 pdb=" O PRO B 416 " 0.030 2.00e-02 2.50e+03 pdb=" N TYR B 417 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 416 " -0.025 2.00e-02 2.50e+03 4.82e-02 2.33e+01 pdb=" C PRO A 416 " 0.083 2.00e-02 2.50e+03 pdb=" O PRO A 416 " -0.030 2.00e-02 2.50e+03 pdb=" N TYR A 417 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 56 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO B 57 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO B 57 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 57 " -0.058 5.00e-02 4.00e+02 ... (remaining 1053 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 2 2.10 - 2.80: 1831 2.80 - 3.50: 9202 3.50 - 4.20: 14318 4.20 - 4.90: 26322 Nonbonded interactions: 51675 Sorted by model distance: nonbonded pdb=" CE2 PHE A 342 " pdb=" CD PRO A 422 " model vdw 1.397 3.740 nonbonded pdb=" CE2 PHE B 342 " pdb=" CD PRO B 422 " model vdw 1.398 3.740 nonbonded pdb=" N GLN B 375 " pdb=" OE1 GLN B 375 " model vdw 2.119 3.120 nonbonded pdb=" N GLN A 375 " pdb=" OE1 GLN A 375 " model vdw 2.119 3.120 nonbonded pdb=" OG SER B 247 " pdb=" OG1 THR B 250 " model vdw 2.157 3.040 ... (remaining 51670 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.890 Find NCS groups from input model: 0.100 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 0.067 6394 Z= 0.387 Angle : 1.015 12.735 8680 Z= 0.653 Chirality : 0.059 0.420 1046 Planarity : 0.007 0.108 1056 Dihedral : 17.310 79.927 2232 Min Nonbonded Distance : 1.397 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 1.50 % Allowed : 9.98 % Favored : 88.53 % Rotamer: Outliers : 3.53 % Allowed : 20.88 % Favored : 75.59 % Cbeta Deviations : 1.07 % 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: -1.61 (0.29), residues: 802 helix: -0.42 (0.23), residues: 492 sheet: None (None), residues: 0 loop : -2.06 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 551 HIS 0.007 0.001 HIS B 546 PHE 0.015 0.002 PHE B 543 TYR 0.010 0.001 TYR B 224 ARG 0.002 0.000 ARG B 369 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.640 Fit side-chains REVERT: A 77 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7682 (mmp) REVERT: A 341 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6482 (mmm160) REVERT: A 549 GLN cc_start: 0.7379 (mm110) cc_final: 0.6925 (mp10) REVERT: B 77 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7652 (mmp) REVERT: B 341 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6408 (mmm160) REVERT: B 549 GLN cc_start: 0.7346 (mm110) cc_final: 0.7032 (mp10) outliers start: 24 outliers final: 14 residues processed: 184 average time/residue: 0.1900 time to fit residues: 45.6528 Evaluate side-chains 163 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS B 26 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.211845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.190522 restraints weight = 7876.368| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 1.89 r_work: 0.4105 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3969 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6394 Z= 0.238 Angle : 0.723 9.351 8680 Z= 0.362 Chirality : 0.041 0.139 1046 Planarity : 0.006 0.075 1056 Dihedral : 8.687 59.848 904 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.60 % Favored : 90.15 % Rotamer: Outliers : 6.03 % Allowed : 21.47 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.29), residues: 802 helix: 0.06 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -1.81 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 551 HIS 0.003 0.001 HIS B 389 PHE 0.014 0.002 PHE A 265 TYR 0.020 0.002 TYR A 224 ARG 0.005 0.001 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.681 Fit side-chains REVERT: A 49 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7950 (mp) REVERT: A 337 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7693 (m) REVERT: A 341 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6107 (mmm160) REVERT: A 453 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8152 (mt) REVERT: A 496 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8450 (m-10) REVERT: A 535 MET cc_start: 0.5427 (ttt) cc_final: 0.5179 (mtp) REVERT: B 49 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7880 (mp) REVERT: B 77 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7929 (mmt) REVERT: B 341 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6078 (mmm160) REVERT: B 453 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8146 (mt) REVERT: B 535 MET cc_start: 0.5458 (ttt) cc_final: 0.5203 (mtp) outliers start: 41 outliers final: 21 residues processed: 193 average time/residue: 0.1758 time to fit residues: 45.2683 Evaluate side-chains 177 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.207527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.185591 restraints weight = 7935.067| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 1.89 r_work: 0.4074 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3945 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6394 Z= 0.302 Angle : 0.726 9.519 8680 Z= 0.357 Chirality : 0.042 0.182 1046 Planarity : 0.005 0.063 1056 Dihedral : 8.232 58.831 898 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.73 % Favored : 92.02 % Rotamer: Outliers : 7.65 % Allowed : 21.32 % Favored : 71.03 % 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: -0.94 (0.29), residues: 802 helix: 0.05 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -1.73 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 516 HIS 0.005 0.001 HIS B 216 PHE 0.018 0.002 PHE A 275 TYR 0.019 0.002 TYR B 224 ARG 0.002 0.000 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 0.638 Fit side-chains REVERT: A 91 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6580 (mp) REVERT: A 453 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8188 (mt) REVERT: B 77 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.6500 (mpt) REVERT: B 91 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6580 (mp) REVERT: B 341 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6301 (mmm160) REVERT: B 453 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8177 (mt) REVERT: B 535 MET cc_start: 0.5642 (ttt) cc_final: 0.5414 (mtp) outliers start: 52 outliers final: 34 residues processed: 191 average time/residue: 0.1680 time to fit residues: 42.9980 Evaluate side-chains 187 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.211107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.189383 restraints weight = 7973.608| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 1.91 r_work: 0.4103 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6394 Z= 0.219 Angle : 0.667 9.405 8680 Z= 0.327 Chirality : 0.040 0.130 1046 Planarity : 0.005 0.056 1056 Dihedral : 7.739 59.208 893 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.73 % Favored : 91.02 % Rotamer: Outliers : 6.18 % Allowed : 22.21 % Favored : 71.62 % 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: -0.61 (0.30), residues: 802 helix: 0.26 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -1.48 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 516 HIS 0.003 0.001 HIS A 389 PHE 0.015 0.001 PHE A 265 TYR 0.019 0.002 TYR A 224 ARG 0.002 0.000 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 0.754 Fit side-chains REVERT: A 49 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7976 (mp) REVERT: A 91 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6518 (mp) REVERT: A 453 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8118 (mt) REVERT: B 77 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.6434 (mpt) REVERT: B 91 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6501 (mp) REVERT: B 453 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8097 (mt) outliers start: 42 outliers final: 29 residues processed: 186 average time/residue: 0.1824 time to fit residues: 45.6172 Evaluate side-chains 177 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 78 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 55 optimal weight: 0.0030 chunk 71 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.215847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.194993 restraints weight = 7897.819| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 1.89 r_work: 0.4133 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4006 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6394 Z= 0.208 Angle : 0.687 9.487 8680 Z= 0.339 Chirality : 0.040 0.147 1046 Planarity : 0.005 0.053 1056 Dihedral : 7.181 58.971 888 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.98 % Favored : 91.77 % Rotamer: Outliers : 5.88 % Allowed : 23.68 % Favored : 70.44 % 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: -0.39 (0.31), residues: 802 helix: 0.45 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -1.43 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 516 HIS 0.002 0.001 HIS A 216 PHE 0.015 0.001 PHE A 265 TYR 0.019 0.002 TYR B 224 ARG 0.006 0.001 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.631 Fit side-chains REVERT: A 91 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6655 (mp) REVERT: A 411 MET cc_start: 0.6990 (tpp) cc_final: 0.6657 (mpp) REVERT: A 453 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8180 (mt) REVERT: A 496 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8214 (m-10) REVERT: B 77 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7654 (mmt) REVERT: B 91 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6503 (mp) REVERT: B 453 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8168 (mt) REVERT: B 496 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8318 (m-10) outliers start: 40 outliers final: 27 residues processed: 176 average time/residue: 0.1610 time to fit residues: 38.1596 Evaluate side-chains 174 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 24 optimal weight: 0.0370 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.202178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.178413 restraints weight = 7895.471| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.23 r_work: 0.3924 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6394 Z= 0.205 Angle : 0.675 9.613 8680 Z= 0.333 Chirality : 0.039 0.149 1046 Planarity : 0.005 0.052 1056 Dihedral : 6.900 58.590 885 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.23 % Favored : 91.52 % Rotamer: Outliers : 5.88 % Allowed : 23.53 % Favored : 70.59 % 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: -0.27 (0.31), residues: 802 helix: 0.56 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -1.41 (0.41), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 516 HIS 0.002 0.001 HIS B 389 PHE 0.020 0.001 PHE B 37 TYR 0.018 0.001 TYR A 224 ARG 0.003 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.740 Fit side-chains REVERT: A 49 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7245 (mp) REVERT: A 91 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6293 (mp) REVERT: A 411 MET cc_start: 0.6848 (tpp) cc_final: 0.6577 (mpp) REVERT: A 453 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8063 (mt) REVERT: A 496 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8004 (m-10) REVERT: B 45 MET cc_start: 0.4615 (ttt) cc_final: 0.4351 (ttp) REVERT: B 77 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7469 (mmt) REVERT: B 91 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6417 (mp) REVERT: B 453 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8156 (mt) REVERT: B 496 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.8057 (m-10) REVERT: B 532 MET cc_start: 0.6658 (mtm) cc_final: 0.6235 (mtm) outliers start: 40 outliers final: 27 residues processed: 181 average time/residue: 0.1643 time to fit residues: 40.1774 Evaluate side-chains 180 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 0.0670 chunk 6 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN B 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.204945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.183685 restraints weight = 7888.578| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 1.89 r_work: 0.3982 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6394 Z= 0.210 Angle : 0.681 9.917 8680 Z= 0.334 Chirality : 0.040 0.154 1046 Planarity : 0.005 0.050 1056 Dihedral : 6.823 58.246 885 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.23 % Favored : 91.52 % Rotamer: Outliers : 6.47 % Allowed : 24.12 % Favored : 69.41 % 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: -0.23 (0.31), residues: 802 helix: 0.58 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.37 (0.40), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 516 HIS 0.002 0.001 HIS A 220 PHE 0.021 0.001 PHE A 37 TYR 0.017 0.001 TYR B 224 ARG 0.001 0.000 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 0.667 Fit side-chains REVERT: A 49 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7120 (mp) REVERT: A 323 ARG cc_start: 0.7307 (tpt-90) cc_final: 0.6975 (tpt-90) REVERT: A 411 MET cc_start: 0.7077 (tpp) cc_final: 0.6814 (mpp) REVERT: A 453 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8073 (mt) REVERT: A 496 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8194 (m-10) REVERT: A 553 ILE cc_start: 0.8014 (mm) cc_final: 0.7752 (mm) REVERT: B 45 MET cc_start: 0.4602 (ttt) cc_final: 0.4384 (ttp) REVERT: B 77 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.6707 (mpt) REVERT: B 91 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6565 (mp) REVERT: B 411 MET cc_start: 0.7090 (tpp) cc_final: 0.6824 (mpp) REVERT: B 453 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8057 (mt) REVERT: B 496 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8205 (m-10) outliers start: 44 outliers final: 31 residues processed: 184 average time/residue: 0.1710 time to fit residues: 42.9773 Evaluate side-chains 184 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 20 optimal weight: 0.0370 chunk 66 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.203487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.180435 restraints weight = 7829.449| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.10 r_work: 0.3962 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6394 Z= 0.230 Angle : 0.709 11.515 8680 Z= 0.345 Chirality : 0.040 0.155 1046 Planarity : 0.005 0.047 1056 Dihedral : 6.720 58.273 885 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.60 % Favored : 91.15 % Rotamer: Outliers : 6.62 % Allowed : 23.53 % Favored : 69.85 % 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: -0.28 (0.31), residues: 802 helix: 0.55 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.40 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 516 HIS 0.003 0.001 HIS A 216 PHE 0.023 0.002 PHE A 37 TYR 0.017 0.002 TYR B 224 ARG 0.001 0.000 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.686 Fit side-chains REVERT: A 49 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6990 (mp) REVERT: A 91 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6431 (mp) REVERT: A 324 ARG cc_start: 0.7803 (pmt-80) cc_final: 0.7593 (pmt-80) REVERT: A 411 MET cc_start: 0.6855 (tpp) cc_final: 0.6593 (mpp) REVERT: A 453 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8004 (mt) REVERT: A 496 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8177 (m-10) REVERT: A 553 ILE cc_start: 0.7978 (mm) cc_final: 0.7678 (mm) REVERT: B 77 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.6661 (mpt) REVERT: B 91 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6487 (mp) REVERT: B 270 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7799 (mm-30) REVERT: B 453 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.7980 (mt) REVERT: B 496 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8045 (m-10) outliers start: 45 outliers final: 31 residues processed: 177 average time/residue: 0.1594 time to fit residues: 38.4542 Evaluate side-chains 181 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.0670 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.204849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.182024 restraints weight = 7943.254| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.09 r_work: 0.3982 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6394 Z= 0.226 Angle : 0.744 15.863 8680 Z= 0.357 Chirality : 0.040 0.163 1046 Planarity : 0.005 0.049 1056 Dihedral : 6.668 58.574 885 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.85 % Favored : 90.90 % Rotamer: Outliers : 6.32 % Allowed : 24.26 % Favored : 69.41 % 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: -0.26 (0.31), residues: 802 helix: 0.55 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -1.39 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 516 HIS 0.003 0.001 HIS A 220 PHE 0.014 0.001 PHE B 342 TYR 0.017 0.001 TYR A 224 ARG 0.013 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.613 Fit side-chains REVERT: A 49 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7165 (mp) REVERT: A 91 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6390 (mp) REVERT: A 411 MET cc_start: 0.6854 (tpp) cc_final: 0.6594 (mpp) REVERT: A 453 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8003 (mt) REVERT: A 496 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8081 (m-10) REVERT: A 553 ILE cc_start: 0.7990 (mm) cc_final: 0.7679 (mm) REVERT: B 77 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6594 (mpt) REVERT: B 91 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6466 (mp) REVERT: B 270 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: B 411 MET cc_start: 0.6900 (tpp) cc_final: 0.6601 (mpp) REVERT: B 453 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7986 (mt) REVERT: B 496 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8062 (m-10) outliers start: 43 outliers final: 30 residues processed: 180 average time/residue: 0.1585 time to fit residues: 38.8635 Evaluate side-chains 187 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 15 optimal weight: 0.0470 chunk 18 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 55 optimal weight: 0.0970 chunk 53 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.206067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.182917 restraints weight = 8053.540| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.17 r_work: 0.3953 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6394 Z= 0.203 Angle : 0.754 15.994 8680 Z= 0.360 Chirality : 0.041 0.163 1046 Planarity : 0.005 0.050 1056 Dihedral : 6.600 58.913 883 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.60 % Favored : 91.15 % Rotamer: Outliers : 6.32 % Allowed : 24.56 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.31), residues: 802 helix: 0.64 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.41 (0.40), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 516 HIS 0.003 0.001 HIS A 220 PHE 0.012 0.001 PHE B 265 TYR 0.017 0.001 TYR A 224 ARG 0.016 0.000 ARG A 324 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.643 Fit side-chains REVERT: A 81 GLU cc_start: 0.7974 (mp0) cc_final: 0.7738 (mp0) REVERT: A 91 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6334 (mp) REVERT: A 270 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7103 (mm-30) REVERT: A 411 MET cc_start: 0.6931 (tpp) cc_final: 0.6688 (mpp) REVERT: A 453 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7914 (mt) REVERT: A 496 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7975 (m-10) REVERT: B 39 SER cc_start: 0.7686 (OUTLIER) cc_final: 0.6749 (m) REVERT: B 77 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7596 (mmt) REVERT: B 91 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6339 (mp) REVERT: B 270 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7594 (mm-30) REVERT: B 453 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7911 (mt) REVERT: B 496 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8304 (m-10) outliers start: 43 outliers final: 30 residues processed: 186 average time/residue: 0.1648 time to fit residues: 41.5428 Evaluate side-chains 191 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.206233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.184968 restraints weight = 7986.748| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 1.92 r_work: 0.3997 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6394 Z= 0.207 Angle : 0.763 15.886 8680 Z= 0.364 Chirality : 0.041 0.156 1046 Planarity : 0.005 0.050 1056 Dihedral : 6.537 58.710 883 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.35 % Favored : 91.40 % Rotamer: Outliers : 6.62 % Allowed : 24.26 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.31), residues: 802 helix: 0.58 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.43 (0.40), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 516 HIS 0.004 0.001 HIS A 220 PHE 0.012 0.001 PHE B 265 TYR 0.016 0.001 TYR A 224 ARG 0.003 0.000 ARG A 504 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2958.25 seconds wall clock time: 54 minutes 35.51 seconds (3275.51 seconds total)