Starting phenix.real_space_refine on Wed Sep 17 06:37:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6l_38990/09_2025/8y6l_38990_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6l_38990/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8y6l_38990/09_2025/8y6l_38990_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6l_38990/09_2025/8y6l_38990_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y6l_38990/09_2025/8y6l_38990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6l_38990/09_2025/8y6l_38990.map" } resolution = 3.4 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= 0.032 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): 0.01s 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: 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: 1.75, per 1000 atoms: 0.28 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: 0.56 Conformation dependent library (CDL) restraints added in 386.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.20 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: 0.91 Time building geometry restraints manager: 0.75 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: 0.01 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: 1.150 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.740 Find NCS groups from input model: 0.050 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.310 ------------------------------------------------------------------------------- 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 6396 Z= 0.387 Angle : 1.015 12.735 8684 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 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: -1.61 (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 ARG 0.002 0.000 ARG B 369 TYR 0.010 0.001 TYR B 224 PHE 0.015 0.002 PHE B 543 TRP 0.027 0.002 TRP B 551 HIS 0.007 0.001 HIS B 546 Details of bonding type rmsd covalent geometry : bond 0.00585 ( 6394) covalent geometry : angle 1.01547 ( 8680) SS BOND : bond 0.00036 ( 2) SS BOND : angle 0.59858 ( 4) hydrogen bonds : bond 0.15649 ( 362) hydrogen bonds : angle 6.29347 ( 1044) *********************** 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 : 0.231 Fit side-chains REVERT: A 77 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7684 (mmp) REVERT: A 341 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6479 (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: 0.7654 (mmp) REVERT: B 341 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6404 (mmm160) REVERT: B 549 GLN cc_start: 0.7346 (mm110) cc_final: 0.7033 (mp10) outliers start: 24 outliers final: 14 residues processed: 184 average time/residue: 0.0806 time to fit residues: 19.5730 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 : 0.242 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.0370 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.4418 r_free = 0.4418 target = 0.212061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.190688 restraints weight = 7903.826| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 1.90 r_work: 0.4106 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3973 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6396 Z= 0.156 Angle : 0.718 9.118 8684 Z= 0.358 Chirality : 0.042 0.134 1046 Planarity : 0.006 0.075 1056 Dihedral : 8.702 59.874 904 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.73 % Favored : 90.02 % Rotamer: Outliers : 6.18 % Allowed : 21.03 % Favored : 72.79 % 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: 802 helix: 0.07 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -1.81 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 504 TYR 0.020 0.001 TYR A 224 PHE 0.014 0.002 PHE A 265 TRP 0.008 0.001 TRP A 551 HIS 0.003 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6394) covalent geometry : angle 0.71793 ( 8680) SS BOND : bond 0.00101 ( 2) SS BOND : angle 1.07350 ( 4) hydrogen bonds : bond 0.03736 ( 362) hydrogen bonds : angle 4.46543 ( 1044) *********************** 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 210 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.168 Fit side-chains REVERT: A 337 SER cc_start: 0.8047 (OUTLIER) cc_final: 0.7683 (m) REVERT: A 341 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6078 (mmm160) REVERT: A 366 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8278 (p0) REVERT: A 453 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8145 (mt) REVERT: A 535 MET cc_start: 0.5426 (ttt) cc_final: 0.5172 (mtp) REVERT: B 77 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7921 (mmt) REVERT: B 341 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6049 (mmm160) REVERT: B 453 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8144 (mt) outliers start: 42 outliers final: 21 residues processed: 193 average time/residue: 0.0752 time to fit residues: 19.3072 Evaluate side-chains 180 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 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 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 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 366 ASP 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 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 0.0000 chunk 74 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 0.0170 chunk 4 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 73 optimal weight: 0.3980 chunk 70 optimal weight: 0.1980 overall best weight: 0.2422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 333 HIS B 549 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.207628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.187047 restraints weight = 7817.786| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 1.87 r_work: 0.4038 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3913 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6396 Z= 0.128 Angle : 0.651 9.000 8684 Z= 0.321 Chirality : 0.040 0.219 1046 Planarity : 0.005 0.065 1056 Dihedral : 8.073 58.683 898 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.60 % Favored : 91.15 % Rotamer: Outliers : 6.91 % Allowed : 20.74 % Favored : 72.35 % 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: -0.58 (0.30), residues: 802 helix: 0.38 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -1.66 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 504 TYR 0.020 0.001 TYR A 224 PHE 0.013 0.001 PHE B 265 TRP 0.011 0.001 TRP B 516 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6394) covalent geometry : angle 0.65055 ( 8680) SS BOND : bond 0.00026 ( 2) SS BOND : angle 0.62648 ( 4) hydrogen bonds : bond 0.03216 ( 362) hydrogen bonds : angle 4.17791 ( 1044) *********************** 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 208 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.218 Fit side-chains REVERT: A 49 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7938 (mp) REVERT: A 341 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6219 (mmm160) REVERT: A 366 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8353 (p0) REVERT: A 453 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8248 (mt) REVERT: B 49 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7960 (mp) REVERT: B 77 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7612 (mmt) REVERT: B 341 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6201 (mmm160) REVERT: B 366 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8348 (p0) REVERT: B 453 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8348 (mt) REVERT: B 532 MET cc_start: 0.6542 (mtm) cc_final: 0.6203 (mtm) REVERT: B 549 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7481 (mp10) outliers start: 47 outliers final: 25 residues processed: 190 average time/residue: 0.0758 time to fit residues: 19.2915 Evaluate side-chains 187 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 240 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 265 PHE 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 453 LEU 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 49 LEU Chi-restraints excluded: chain B residue 77 MET 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 341 ARG Chi-restraints excluded: chain B residue 366 ASP 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 Chi-restraints excluded: chain B residue 549 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.209474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.187538 restraints weight = 7935.456| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 1.91 r_work: 0.4074 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6396 Z= 0.187 Angle : 0.702 9.191 8684 Z= 0.344 Chirality : 0.041 0.148 1046 Planarity : 0.005 0.057 1056 Dihedral : 7.733 58.261 896 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.60 % Favored : 91.15 % Rotamer: Outliers : 6.91 % Allowed : 21.03 % Favored : 72.06 % 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: -0.54 (0.30), residues: 802 helix: 0.33 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -1.50 (0.40), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 341 TYR 0.019 0.002 TYR A 224 PHE 0.015 0.002 PHE B 265 TRP 0.011 0.001 TRP B 516 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 6394) covalent geometry : angle 0.70161 ( 8680) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.72708 ( 4) hydrogen bonds : bond 0.03350 ( 362) hydrogen bonds : angle 4.26672 ( 1044) *********************** 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 208 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.217 Fit side-chains REVERT: A 91 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6594 (mp) REVERT: A 366 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8407 (p0) REVERT: A 453 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8200 (mt) REVERT: B 49 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8129 (mp) REVERT: B 77 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7743 (mmt) REVERT: B 91 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6591 (mp) REVERT: B 366 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8402 (p0) REVERT: B 453 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8182 (mt) outliers start: 47 outliers final: 28 residues processed: 191 average time/residue: 0.0691 time to fit residues: 18.0055 Evaluate side-chains 178 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 257 VAL Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 372 THR 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 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 49 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 366 ASP 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 546 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.203162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.180420 restraints weight = 8007.345| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.13 r_work: 0.3950 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6396 Z= 0.148 Angle : 0.691 9.659 8684 Z= 0.337 Chirality : 0.040 0.140 1046 Planarity : 0.005 0.052 1056 Dihedral : 7.088 59.933 886 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.60 % Favored : 91.15 % Rotamer: Outliers : 7.21 % Allowed : 21.47 % Favored : 71.32 % 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: -0.42 (0.30), residues: 802 helix: 0.42 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.44 (0.40), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 324 TYR 0.019 0.002 TYR A 224 PHE 0.015 0.001 PHE B 265 TRP 0.014 0.001 TRP B 516 HIS 0.002 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6394) covalent geometry : angle 0.69085 ( 8680) SS BOND : bond 0.00065 ( 2) SS BOND : angle 0.71636 ( 4) hydrogen bonds : bond 0.03090 ( 362) hydrogen bonds : angle 4.12229 ( 1044) *********************** 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 205 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 0.198 Fit side-chains REVERT: A 91 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6392 (mp) REVERT: A 270 GLU cc_start: 0.8186 (mp0) cc_final: 0.7976 (mm-30) REVERT: A 366 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8341 (p0) REVERT: A 453 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7979 (mt) REVERT: A 496 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8221 (m-10) REVERT: A 532 MET cc_start: 0.6508 (mtm) cc_final: 0.6120 (mtm) REVERT: B 77 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7579 (mmt) REVERT: B 91 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6404 (mp) REVERT: B 270 GLU cc_start: 0.8219 (mp0) cc_final: 0.7987 (mm-30) REVERT: B 453 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.7963 (mt) REVERT: B 549 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7358 (mp10) REVERT: B 553 ILE cc_start: 0.7960 (mm) cc_final: 0.7669 (mm) outliers start: 49 outliers final: 30 residues processed: 186 average time/residue: 0.0696 time to fit residues: 17.4431 Evaluate side-chains 182 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 265 PHE Chi-restraints excluded: chain A residue 366 ASP 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 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 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 450 MET Chi-restraints excluded: chain B residue 453 LEU 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 546 HIS Chi-restraints excluded: chain B residue 549 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 73 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.198455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.174738 restraints weight = 7873.371| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.10 r_work: 0.3878 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6396 Z= 0.226 Angle : 0.777 9.344 8684 Z= 0.382 Chirality : 0.043 0.148 1046 Planarity : 0.005 0.049 1056 Dihedral : 7.053 59.730 884 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.98 % Favored : 90.77 % Rotamer: Outliers : 6.32 % Allowed : 22.50 % Favored : 71.18 % 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: -0.65 (0.30), residues: 802 helix: 0.19 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -1.41 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 324 TYR 0.019 0.002 TYR A 224 PHE 0.016 0.002 PHE B 265 TRP 0.011 0.001 TRP B 516 HIS 0.007 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 6394) covalent geometry : angle 0.77680 ( 8680) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.88694 ( 4) hydrogen bonds : bond 0.03503 ( 362) hydrogen bonds : angle 4.30928 ( 1044) *********************** 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: 43 poor density : 151 time to evaluate : 0.241 Fit side-chains REVERT: A 91 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6397 (mp) REVERT: A 453 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8020 (mt) REVERT: B 77 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.6746 (mpt) REVERT: B 91 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6424 (mp) REVERT: B 453 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.7996 (mt) outliers start: 43 outliers final: 31 residues processed: 178 average time/residue: 0.0724 time to fit residues: 17.5010 Evaluate side-chains 179 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 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 253 ILE 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 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 546 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.202667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.181705 restraints weight = 7912.753| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 1.82 r_work: 0.3977 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3855 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6396 Z= 0.169 Angle : 0.723 9.887 8684 Z= 0.354 Chirality : 0.041 0.148 1046 Planarity : 0.005 0.049 1056 Dihedral : 6.917 58.949 884 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.48 % Favored : 91.27 % Rotamer: Outliers : 6.18 % Allowed : 23.38 % 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 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: -0.51 (0.30), residues: 802 helix: 0.32 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.40 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 504 TYR 0.018 0.002 TYR A 224 PHE 0.022 0.002 PHE B 37 TRP 0.015 0.001 TRP B 516 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 6394) covalent geometry : angle 0.72318 ( 8680) SS BOND : bond 0.00075 ( 2) SS BOND : angle 0.88821 ( 4) hydrogen bonds : bond 0.03189 ( 362) hydrogen bonds : angle 4.21345 ( 1044) *********************** 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 191 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.230 Fit side-chains REVERT: A 91 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6497 (mp) REVERT: A 270 GLU cc_start: 0.8267 (mp0) cc_final: 0.8019 (mm-30) REVERT: A 324 ARG cc_start: 0.7818 (pmt-80) cc_final: 0.7599 (pmt-80) REVERT: A 453 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8179 (mt) REVERT: B 49 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7579 (mp) REVERT: B 91 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6507 (mp) REVERT: B 270 GLU cc_start: 0.8237 (mp0) cc_final: 0.7975 (mm-30) REVERT: B 324 ARG cc_start: 0.7849 (pmt-80) cc_final: 0.7604 (pmt-80) REVERT: B 453 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8163 (mt) outliers start: 42 outliers final: 32 residues processed: 178 average time/residue: 0.0688 time to fit residues: 16.7298 Evaluate side-chains 177 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 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 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 49 LEU 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 372 THR 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 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 546 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 43 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.203984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.182482 restraints weight = 7874.259| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 1.88 r_work: 0.3971 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3844 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6396 Z= 0.144 Angle : 0.708 10.996 8684 Z= 0.345 Chirality : 0.040 0.157 1046 Planarity : 0.005 0.048 1056 Dihedral : 6.572 58.945 881 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.10 % Favored : 90.65 % Rotamer: Outliers : 5.15 % Allowed : 23.97 % Favored : 70.88 % 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: -0.37 (0.30), residues: 802 helix: 0.45 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.38 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 504 TYR 0.018 0.001 TYR A 224 PHE 0.022 0.001 PHE B 37 TRP 0.014 0.002 TRP B 516 HIS 0.003 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6394) covalent geometry : angle 0.70802 ( 8680) SS BOND : bond 0.00045 ( 2) SS BOND : angle 0.74150 ( 4) hydrogen bonds : bond 0.03018 ( 362) hydrogen bonds : angle 4.13809 ( 1044) *********************** 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 191 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.255 Fit side-chains REVERT: A 91 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6423 (mp) REVERT: A 270 GLU cc_start: 0.8281 (mp0) cc_final: 0.7998 (mm-30) REVERT: A 324 ARG cc_start: 0.7911 (pmt-80) cc_final: 0.7688 (pmt-80) REVERT: A 411 MET cc_start: 0.7152 (tpp) cc_final: 0.6870 (mpp) REVERT: A 453 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8072 (mt) REVERT: B 270 GLU cc_start: 0.8301 (mp0) cc_final: 0.8006 (mm-30) REVERT: B 324 ARG cc_start: 0.7957 (pmt-80) cc_final: 0.7733 (pmt-80) REVERT: B 362 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6518 (mm-30) REVERT: B 411 MET cc_start: 0.7237 (tpp) cc_final: 0.6923 (mpp) REVERT: B 453 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8052 (mt) outliers start: 35 outliers final: 29 residues processed: 179 average time/residue: 0.0705 time to fit residues: 17.3689 Evaluate side-chains 174 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 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 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 450 MET Chi-restraints excluded: chain B residue 453 LEU 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 546 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 0.0170 chunk 7 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.204092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.182548 restraints weight = 7876.607| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.90 r_work: 0.3974 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6396 Z= 0.143 Angle : 0.721 14.304 8684 Z= 0.350 Chirality : 0.040 0.152 1046 Planarity : 0.005 0.048 1056 Dihedral : 6.465 59.371 880 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.73 % Favored : 91.02 % Rotamer: Outliers : 5.00 % Allowed : 24.41 % 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 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: -0.36 (0.31), residues: 802 helix: 0.47 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.40 (0.40), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 504 TYR 0.017 0.001 TYR A 224 PHE 0.014 0.001 PHE B 265 TRP 0.013 0.002 TRP B 516 HIS 0.003 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6394) covalent geometry : angle 0.72070 ( 8680) SS BOND : bond 0.00038 ( 2) SS BOND : angle 0.65545 ( 4) hydrogen bonds : bond 0.02995 ( 362) hydrogen bonds : angle 4.14406 ( 1044) *********************** 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 187 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.242 Fit side-chains REVERT: A 91 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6530 (mp) REVERT: A 270 GLU cc_start: 0.8217 (mp0) cc_final: 0.7961 (mm-30) REVERT: A 324 ARG cc_start: 0.7957 (pmt-80) cc_final: 0.7738 (pmt-80) REVERT: A 411 MET cc_start: 0.7128 (tpp) cc_final: 0.6854 (mpp) REVERT: A 453 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8081 (mt) REVERT: B 270 GLU cc_start: 0.8261 (mp0) cc_final: 0.8010 (mm-30) REVERT: B 453 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8043 (mt) outliers start: 34 outliers final: 27 residues processed: 176 average time/residue: 0.0677 time to fit residues: 16.3680 Evaluate side-chains 176 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 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 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 453 LEU 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 546 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.204725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.181714 restraints weight = 7787.655| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.11 r_work: 0.3974 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6396 Z= 0.145 Angle : 0.755 16.172 8684 Z= 0.364 Chirality : 0.041 0.158 1046 Planarity : 0.005 0.050 1056 Dihedral : 6.429 59.279 880 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.98 % Favored : 90.77 % Rotamer: Outliers : 5.00 % Allowed : 25.00 % Favored : 70.00 % 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: -0.34 (0.31), residues: 802 helix: 0.46 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -1.36 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 324 TYR 0.017 0.001 TYR A 224 PHE 0.013 0.001 PHE B 342 TRP 0.013 0.002 TRP B 516 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6394) covalent geometry : angle 0.75504 ( 8680) SS BOND : bond 0.00059 ( 2) SS BOND : angle 0.60229 ( 4) hydrogen bonds : bond 0.03022 ( 362) hydrogen bonds : angle 4.15522 ( 1044) ********************** 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 187 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.246 Fit side-chains REVERT: A 91 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6450 (mp) REVERT: A 270 GLU cc_start: 0.8153 (mp0) cc_final: 0.7939 (mm-30) REVERT: A 320 LEU cc_start: 0.8559 (mm) cc_final: 0.8351 (pt) REVERT: A 411 MET cc_start: 0.6888 (tpp) cc_final: 0.6604 (mpp) REVERT: A 453 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.7996 (mt) REVERT: B 45 MET cc_start: 0.4655 (ttp) cc_final: 0.4388 (ttt) REVERT: B 91 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6468 (mp) REVERT: B 270 GLU cc_start: 0.8174 (mp0) cc_final: 0.7948 (mm-30) REVERT: B 320 LEU cc_start: 0.8471 (mm) cc_final: 0.8175 (pt) REVERT: B 453 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7963 (mt) outliers start: 34 outliers final: 29 residues processed: 176 average time/residue: 0.0762 time to fit residues: 18.3463 Evaluate side-chains 187 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 372 THR 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 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 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 453 LEU Chi-restraints excluded: chain B residue 467 GLU 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 546 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 44 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN B 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.204576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.181503 restraints weight = 7950.502| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.12 r_work: 0.3970 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6396 Z= 0.141 Angle : 0.759 16.331 8684 Z= 0.364 Chirality : 0.041 0.155 1046 Planarity : 0.005 0.051 1056 Dihedral : 6.326 58.619 880 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.10 % Favored : 90.65 % Rotamer: Outliers : 4.85 % Allowed : 25.74 % 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 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: -0.26 (0.31), residues: 802 helix: 0.54 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.36 (0.40), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 324 TYR 0.017 0.001 TYR A 224 PHE 0.013 0.001 PHE B 358 TRP 0.012 0.002 TRP B 516 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6394) covalent geometry : angle 0.75867 ( 8680) SS BOND : bond 0.00044 ( 2) SS BOND : angle 0.56048 ( 4) hydrogen bonds : bond 0.02989 ( 362) hydrogen bonds : angle 4.16921 ( 1044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1570.27 seconds wall clock time: 27 minutes 40.49 seconds (1660.49 seconds total)