Starting phenix.real_space_refine on Sat May 10 12:27:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6l_38990/05_2025/8y6l_38990_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6l_38990/05_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_38990/05_2025/8y6l_38990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6l_38990/05_2025/8y6l_38990.map" model { file = "/net/cci-nas-00/data/ceres_data/8y6l_38990/05_2025/8y6l_38990_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6l_38990/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 4.35, per 1000 atoms: 0.70 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: 1.79 Conformation dependent library (CDL) restraints added in 999.8 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: 0.48 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: 1.55 Time building geometry restraints manager: 2.08 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 18.620 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.970 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.15649 ( 362) hydrogen bonds : angle 6.29347 ( 1044) SS BOND : bond 0.00036 ( 2) SS BOND : angle 0.59858 ( 4) covalent geometry : bond 0.00585 ( 6394) covalent geometry : angle 1.01547 ( 8680) *********************** 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 : 0.636 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: 0.1757 time to fit residues: 41.9486 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 : 0.676 ------------------------------------------------------------------------------- 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 6396 Z= 0.161 Angle : 0.723 9.351 8684 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 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 362) hydrogen bonds : angle 4.49239 ( 1044) SS BOND : bond 0.00106 ( 2) SS BOND : angle 1.09885 ( 4) covalent geometry : bond 0.00379 ( 6394) covalent geometry : angle 0.72291 ( 8680) *********************** 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 : 0.570 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: 0.1660 time to fit residues: 42.3697 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 : 0.631 ------------------------------------------------------------------------------- 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 6396 Z= 0.199 Angle : 0.726 9.519 8684 Z= 0.358 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 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 362) hydrogen bonds : angle 4.41482 ( 1044) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.96962 ( 4) covalent geometry : bond 0.00477 ( 6394) covalent geometry : angle 0.72590 ( 8680) *********************** 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 : 0.692 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: 0.1656 time to fit residues: 42.1218 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 : 0.702 ------------------------------------------------------------------------------- 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: 0.9980 chunk 64 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 32 optimal weight: 0.0770 chunk 76 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.211702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.190173 restraints weight = 7963.585| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 1.89 r_work: 0.4110 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6396 Z= 0.141 Angle : 0.663 9.315 8684 Z= 0.325 Chirality : 0.040 0.132 1046 Planarity : 0.005 0.056 1056 Dihedral : 7.728 59.240 893 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.60 % Favored : 91.15 % Rotamer: Outliers : 5.74 % Allowed : 22.65 % 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: -0.58 (0.30), residues: 802 helix: 0.28 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -1.47 (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 Details of bonding type rmsd hydrogen bonds : bond 0.03088 ( 362) hydrogen bonds : angle 4.19044 ( 1044) SS BOND : bond 0.00067 ( 2) SS BOND : angle 0.83171 ( 4) covalent geometry : bond 0.00332 ( 6394) covalent geometry : angle 0.66315 ( 8680) *********************** 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 202 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.711 Fit side-chains REVERT: A 49 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7966 (mp) REVERT: A 342 PHE cc_start: 0.7066 (m-80) cc_final: 0.6814 (m-80) REVERT: A 453 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8107 (mt) REVERT: A 532 MET cc_start: 0.6298 (mtm) cc_final: 0.5925 (mtm) REVERT: B 77 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7625 (mmt) REVERT: B 453 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8081 (mt) outliers start: 39 outliers final: 28 residues processed: 184 average time/residue: 0.1690 time to fit residues: 41.2409 Evaluate side-chains 175 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 40 optimal weight: 4.9990 chunk 55 optimal weight: 0.0010 chunk 71 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.4448 r_free = 0.4448 target = 0.216082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.195684 restraints weight = 7903.445| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 1.84 r_work: 0.4144 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4017 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6396 Z= 0.137 Angle : 0.684 9.787 8684 Z= 0.336 Chirality : 0.040 0.143 1046 Planarity : 0.005 0.053 1056 Dihedral : 7.179 58.986 888 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.98 % Favored : 91.77 % Rotamer: Outliers : 6.76 % Allowed : 22.50 % Favored : 70.74 % 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: -0.41 (0.31), residues: 802 helix: 0.42 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -1.41 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 516 HIS 0.002 0.001 HIS A 389 PHE 0.015 0.001 PHE A 265 TYR 0.018 0.001 TYR A 224 ARG 0.008 0.001 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 362) hydrogen bonds : angle 4.06021 ( 1044) SS BOND : bond 0.00050 ( 2) SS BOND : angle 0.69938 ( 4) covalent geometry : bond 0.00320 ( 6394) covalent geometry : angle 0.68387 ( 8680) *********************** 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 199 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 91 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6619 (mp) REVERT: A 453 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8150 (mt) REVERT: A 496 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8287 (m-10) REVERT: B 77 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7638 (mmt) REVERT: B 91 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6473 (mp) REVERT: B 453 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8150 (mt) REVERT: B 496 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8278 (m-10) outliers start: 46 outliers final: 29 residues processed: 182 average time/residue: 0.1647 time to fit residues: 40.0036 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 : 0.719 ------------------------------------------------------------------------------- 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 421 VAL 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 421 VAL 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: 0.9990 chunk 53 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 79 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 0.0010 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.201686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.177816 restraints weight = 7910.531| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.23 r_work: 0.3921 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2882 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= 0.138 Angle : 0.681 9.649 8684 Z= 0.335 Chirality : 0.040 0.145 1046 Planarity : 0.005 0.052 1056 Dihedral : 6.900 58.001 886 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.10 % Favored : 91.65 % Rotamer: Outliers : 5.88 % Allowed : 22.94 % 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 (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: -0.22 (0.31), residues: 802 helix: 0.56 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.31 (0.41), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 516 HIS 0.002 0.001 HIS A 389 PHE 0.020 0.001 PHE B 37 TYR 0.018 0.002 TYR A 224 ARG 0.002 0.000 ARG B 324 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 362) hydrogen bonds : angle 3.98010 ( 1044) SS BOND : bond 0.00027 ( 2) SS BOND : angle 0.64602 ( 4) covalent geometry : bond 0.00327 ( 6394) covalent geometry : angle 0.68135 ( 8680) *********************** 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 197 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.812 Fit side-chains REVERT: A 49 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7289 (mp) REVERT: A 91 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6301 (mp) REVERT: A 411 MET cc_start: 0.6873 (tpp) cc_final: 0.6591 (mpp) REVERT: A 453 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7992 (mt) REVERT: A 496 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8060 (m-10) REVERT: B 77 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7487 (mmt) REVERT: B 91 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6382 (mp) REVERT: B 411 MET cc_start: 0.6965 (tpp) cc_final: 0.6657 (mpp) REVERT: B 453 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7986 (mt) REVERT: B 496 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8029 (m-10) REVERT: B 532 MET cc_start: 0.6660 (mtm) cc_final: 0.6256 (mtm) outliers start: 40 outliers final: 28 residues processed: 185 average time/residue: 0.1565 time to fit residues: 38.9352 Evaluate side-chains 181 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 421 VAL 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 4 optimal weight: 0.0870 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.205176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.182301 restraints weight = 7879.086| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.11 r_work: 0.3988 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3030 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= 0.139 Angle : 0.695 9.905 8684 Z= 0.341 Chirality : 0.040 0.157 1046 Planarity : 0.005 0.049 1056 Dihedral : 6.818 58.066 885 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.10 % Favored : 91.65 % Rotamer: Outliers : 6.62 % Allowed : 23.68 % Favored : 69.71 % 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: 0.60 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.34 (0.40), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 516 HIS 0.002 0.001 HIS A 220 PHE 0.021 0.001 PHE B 37 TYR 0.017 0.001 TYR B 224 ARG 0.001 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.02984 ( 362) hydrogen bonds : angle 3.98204 ( 1044) SS BOND : bond 0.00051 ( 2) SS BOND : angle 0.62447 ( 4) covalent geometry : bond 0.00329 ( 6394) covalent geometry : angle 0.69550 ( 8680) *********************** 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 196 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 0.635 Fit side-chains REVERT: A 49 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7036 (mp) REVERT: A 91 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6379 (mp) REVERT: A 411 MET cc_start: 0.6817 (tpp) cc_final: 0.6543 (mpp) REVERT: A 453 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7978 (mt) REVERT: A 496 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8118 (m-10) REVERT: B 77 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.6689 (mpt) REVERT: B 91 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6425 (mp) REVERT: B 453 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7966 (mt) REVERT: B 496 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8122 (m-10) REVERT: B 535 MET cc_start: 0.5642 (mtp) cc_final: 0.5372 (mtp) outliers start: 45 outliers final: 32 residues processed: 183 average time/residue: 0.1589 time to fit residues: 39.3368 Evaluate side-chains 185 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 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 209 MET 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: 0.2980 chunk 59 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4267 r_free = 0.4267 target = 0.201924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.180262 restraints weight = 7825.614| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 1.88 r_work: 0.3943 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6396 Z= 0.176 Angle : 0.734 11.942 8684 Z= 0.358 Chirality : 0.041 0.149 1046 Planarity : 0.005 0.047 1056 Dihedral : 6.842 58.269 885 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.10 % Favored : 91.65 % Rotamer: Outliers : 6.62 % Allowed : 23.68 % Favored : 69.71 % 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: -0.41 (0.30), residues: 802 helix: 0.43 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.44 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 516 HIS 0.004 0.001 HIS B 216 PHE 0.022 0.002 PHE B 37 TYR 0.017 0.002 TYR A 224 ARG 0.001 0.000 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 362) hydrogen bonds : angle 4.17843 ( 1044) SS BOND : bond 0.00089 ( 2) SS BOND : angle 0.68408 ( 4) covalent geometry : bond 0.00427 ( 6394) covalent geometry : angle 0.73393 ( 8680) *********************** 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 196 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 0.635 Fit side-chains REVERT: A 49 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7131 (mp) REVERT: A 91 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6528 (mp) REVERT: A 209 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7461 (ttp) REVERT: A 324 ARG cc_start: 0.7897 (pmt-80) cc_final: 0.7675 (pmt-80) REVERT: A 453 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8113 (mt) REVERT: A 496 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8291 (m-10) REVERT: B 77 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.6824 (mpt) REVERT: B 91 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6551 (mp) REVERT: B 270 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7856 (mm-30) REVERT: B 324 ARG cc_start: 0.8034 (pmt-80) cc_final: 0.7772 (pmt-80) REVERT: B 453 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8091 (mt) REVERT: B 496 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8291 (m-10) REVERT: B 535 MET cc_start: 0.5590 (mtp) cc_final: 0.5286 (mtp) outliers start: 45 outliers final: 30 residues processed: 179 average time/residue: 0.1658 time to fit residues: 40.2074 Evaluate side-chains 182 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 209 MET 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 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: 0.7980 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.4296 r_free = 0.4296 target = 0.205062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.183723 restraints weight = 7945.967| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 1.90 r_work: 0.3980 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3854 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3113 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= 0.144 Angle : 0.733 15.137 8684 Z= 0.353 Chirality : 0.040 0.148 1046 Planarity : 0.005 0.049 1056 Dihedral : 6.798 59.974 885 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.60 % Favored : 91.15 % Rotamer: Outliers : 6.32 % Allowed : 24.41 % Favored : 69.26 % 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: -0.36 (0.30), residues: 802 helix: 0.49 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -1.45 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 516 HIS 0.003 0.001 HIS A 389 PHE 0.014 0.001 PHE B 265 TYR 0.017 0.001 TYR B 224 ARG 0.001 0.000 ARG B 504 Details of bonding type rmsd hydrogen bonds : bond 0.02937 ( 362) hydrogen bonds : angle 4.15103 ( 1044) SS BOND : bond 0.00040 ( 2) SS BOND : angle 0.66023 ( 4) covalent geometry : bond 0.00346 ( 6394) covalent geometry : angle 0.73265 ( 8680) *********************** 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 197 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.671 Fit side-chains REVERT: A 49 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7188 (mp) REVERT: A 91 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.6461 (mp) REVERT: A 270 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7776 (mm-30) REVERT: A 324 ARG cc_start: 0.8058 (pmt-80) cc_final: 0.7723 (pmt-80) REVERT: A 411 MET cc_start: 0.7132 (tpp) cc_final: 0.6879 (mpp) REVERT: A 453 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8076 (mt) REVERT: A 496 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8172 (m-10) REVERT: B 91 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6560 (mp) REVERT: B 270 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7153 (mm-30) REVERT: B 324 ARG cc_start: 0.8040 (pmt-80) cc_final: 0.7780 (pmt-80) REVERT: B 411 MET cc_start: 0.7201 (tpp) cc_final: 0.6905 (mpp) REVERT: B 453 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8067 (mt) REVERT: B 496 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8100 (m-10) REVERT: B 535 MET cc_start: 0.5552 (mtp) cc_final: 0.5317 (mtp) outliers start: 43 outliers final: 29 residues processed: 184 average time/residue: 0.1562 time to fit residues: 38.8606 Evaluate side-chains 183 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 270 GLU 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 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 372 THR 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 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: 1.9990 chunk 48 optimal weight: 0.8980 chunk 15 optimal weight: 0.0670 chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.4292 r_free = 0.4292 target = 0.204477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.182993 restraints weight = 7943.611| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 1.90 r_work: 0.3974 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3850 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6396 Z= 0.152 Angle : 0.767 16.433 8684 Z= 0.368 Chirality : 0.041 0.157 1046 Planarity : 0.005 0.049 1056 Dihedral : 6.528 59.647 880 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.35 % Favored : 91.40 % Rotamer: Outliers : 6.76 % Allowed : 23.82 % 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: -0.40 (0.30), residues: 802 helix: 0.45 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -1.47 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 516 HIS 0.003 0.001 HIS B 220 PHE 0.026 0.001 PHE A 37 TYR 0.017 0.002 TYR A 224 ARG 0.002 0.000 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 362) hydrogen bonds : angle 4.19536 ( 1044) SS BOND : bond 0.00070 ( 2) SS BOND : angle 0.60145 ( 4) covalent geometry : bond 0.00363 ( 6394) covalent geometry : angle 0.76736 ( 8680) ********************** 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 194 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.630 Fit side-chains REVERT: A 49 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7217 (mp) REVERT: A 91 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6554 (mp) REVERT: A 270 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7772 (mm-30) REVERT: A 324 ARG cc_start: 0.8085 (pmt-80) cc_final: 0.7738 (pmt-80) REVERT: A 453 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8088 (mt) REVERT: A 496 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8188 (m-10) REVERT: A 535 MET cc_start: 0.5574 (mtp) cc_final: 0.5298 (mtp) REVERT: B 45 MET cc_start: 0.4625 (OUTLIER) cc_final: 0.4376 (ttt) REVERT: B 77 MET cc_start: 0.7749 (mmm) cc_final: 0.7544 (mmt) REVERT: B 91 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6738 (mp) REVERT: B 270 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: B 320 LEU cc_start: 0.8603 (mm) cc_final: 0.8347 (pt) REVERT: B 324 ARG cc_start: 0.8098 (pmt-80) cc_final: 0.7850 (pmt-80) REVERT: B 453 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8073 (mt) REVERT: B 496 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8172 (m-10) REVERT: B 535 MET cc_start: 0.5561 (mtp) cc_final: 0.5345 (mtp) outliers start: 46 outliers final: 30 residues processed: 179 average time/residue: 0.1531 time to fit residues: 37.1245 Evaluate side-chains 188 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 270 GLU 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 45 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 372 THR 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 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: 0.0170 chunk 35 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 67 optimal weight: 0.0070 chunk 47 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS B 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.208045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.186930 restraints weight = 7979.130| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 1.92 r_work: 0.4018 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3895 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3364 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= 0.129 Angle : 0.742 15.520 8684 Z= 0.358 Chirality : 0.041 0.156 1046 Planarity : 0.005 0.051 1056 Dihedral : 6.444 58.233 880 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.48 % Favored : 91.27 % Rotamer: Outliers : 6.32 % Allowed : 25.29 % Favored : 68.38 % 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: -0.24 (0.31), residues: 802 helix: 0.57 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.40 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 516 HIS 0.004 0.001 HIS A 389 PHE 0.012 0.001 PHE B 265 TYR 0.016 0.001 TYR A 224 ARG 0.002 0.000 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 362) hydrogen bonds : angle 4.12732 ( 1044) SS BOND : bond 0.00004 ( 2) SS BOND : angle 0.48303 ( 4) covalent geometry : bond 0.00299 ( 6394) covalent geometry : angle 0.74243 ( 8680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3252.76 seconds wall clock time: 57 minutes 15.95 seconds (3435.95 seconds total)