Starting phenix.real_space_refine on Fri Sep 11 03:02:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vyi_21461/09_2026/6vyi_21461.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vyi_21461/09_2026/6vyi_21461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vyi_21461/09_2026/6vyi_21461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vyi_21461/09_2026/6vyi_21461.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vyi_21461/09_2026/6vyi_21461.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vyi_21461/09_2026/6vyi_21461.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vyi_21461/09_2026/6vyi_21461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vyi_21461/09_2026/6vyi_21461.map" } resolution = 3.0 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= 0.000 sd= 0.011 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 42 5.16 5 C 4620 2.51 5 N 1136 2.21 5 O 1114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6916 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3360 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 18, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3360 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 18, 'TRANS': 387} Chain breaks: 1 Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 147 Unusual residues: {'6OU': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.53, per 1000 atoms: 0.22 Number of scatterers: 6916 At special positions: 0 Unit cell: (109.725, 91.575, 81.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 4 15.00 O 1114 8.00 N 1136 7.00 C 4620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 308.2 milliseconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 78.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.627A pdb=" N GLY A 81 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 113 removed outlier: 3.505A pdb=" N CYS A 92 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ARG A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 removed outlier: 3.607A pdb=" N GLN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 155 removed outlier: 4.299A pdb=" N ASN A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 185 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 190 through 226 removed outlier: 3.693A pdb=" N ARG A 222 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 removed outlier: 3.785A pdb=" N PHE A 257 " --> pdb=" O TYR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 300 Processing helix chain 'A' and resid 300 through 307 removed outlier: 4.089A pdb=" N SER A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.838A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'A' and resid 399 through 420 Processing helix chain 'A' and resid 428 through 448 removed outlier: 3.700A pdb=" N THR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 438 " --> pdb=" O MET A 434 " (cutoff:3.500A) Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 449 through 463 Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.717A pdb=" N VAL A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.626A pdb=" N GLY B 81 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 113 removed outlier: 3.505A pdb=" N CYS B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ARG B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 127 removed outlier: 3.606A pdb=" N GLN B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 155 removed outlier: 4.298A pdb=" N ASN B 141 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 185 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 190 through 226 removed outlier: 3.693A pdb=" N ARG B 222 " --> pdb=" O CYS B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 removed outlier: 3.786A pdb=" N PHE B 257 " --> pdb=" O TYR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 300 Processing helix chain 'B' and resid 300 through 307 removed outlier: 4.089A pdb=" N SER B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 343 removed outlier: 3.838A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 369 through 375 Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 390 through 396 Processing helix chain 'B' and resid 399 through 420 Processing helix chain 'B' and resid 428 through 448 removed outlier: 3.699A pdb=" N THR B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE B 438 " --> pdb=" O MET B 434 " (cutoff:3.500A) Proline residue: B 439 - end of helix Processing helix chain 'B' and resid 449 through 463 Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.718A pdb=" N VAL B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1308 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: 1.00 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1018 1.32 - 1.44: 2138 1.44 - 1.56: 3894 1.56 - 1.68: 8 1.68 - 1.80: 68 Bond restraints: 7126 Sorted by residual: bond pdb=" O22 6OU A 502 " pdb=" P23 6OU A 502 " ideal model delta sigma weight residual 1.643 1.557 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" O22 6OU B 501 " pdb=" P23 6OU B 501 " ideal model delta sigma weight residual 1.643 1.566 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " ideal model delta sigma weight residual 1.643 1.568 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O22 6OU A 503 " pdb=" P23 6OU A 503 " ideal model delta sigma weight residual 1.643 1.573 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C27 6OU A 503 " pdb=" C28 6OU A 503 " ideal model delta sigma weight residual 1.512 1.563 -0.051 2.00e-02 2.50e+03 6.57e+00 ... (remaining 7121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 9555 3.49 - 6.98: 79 6.98 - 10.46: 3 10.46 - 13.95: 6 13.95 - 17.44: 5 Bond angle restraints: 9648 Sorted by residual: angle pdb=" C21 6OU A 502 " pdb=" O22 6OU A 502 " pdb=" P23 6OU A 502 " ideal model delta sigma weight residual 117.17 134.61 -17.44 3.00e+00 1.11e-01 3.38e+01 angle pdb=" C21 6OU A 501 " pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " ideal model delta sigma weight residual 117.17 134.50 -17.33 3.00e+00 1.11e-01 3.34e+01 angle pdb=" O22 6OU A 503 " pdb=" P23 6OU A 503 " pdb=" O26 6OU A 503 " ideal model delta sigma weight residual 93.95 110.09 -16.14 3.00e+00 1.11e-01 2.89e+01 angle pdb=" C21 6OU B 501 " pdb=" O22 6OU B 501 " pdb=" P23 6OU B 501 " ideal model delta sigma weight residual 117.17 131.43 -14.26 3.00e+00 1.11e-01 2.26e+01 angle pdb=" O22 6OU B 501 " pdb=" P23 6OU B 501 " pdb=" O26 6OU B 501 " ideal model delta sigma weight residual 93.95 108.05 -14.10 3.00e+00 1.11e-01 2.21e+01 ... (remaining 9643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.43: 4012 33.43 - 66.87: 103 66.87 - 100.30: 18 100.30 - 133.74: 11 133.74 - 167.17: 2 Dihedral angle restraints: 4146 sinusoidal: 1734 harmonic: 2412 Sorted by residual: dihedral pdb=" CA GLY A 87 " pdb=" C GLY A 87 " pdb=" N ILE A 88 " pdb=" CA ILE A 88 " ideal model delta harmonic sigma weight residual 180.00 156.65 23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA GLY B 87 " pdb=" C GLY B 87 " pdb=" N ILE B 88 " pdb=" CA ILE B 88 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" C34 6OU A 501 " pdb=" C31 6OU A 501 " pdb=" C33 6OU A 501 " pdb=" O30 6OU A 501 " ideal model delta sinusoidal sigma weight residual 180.29 13.12 167.17 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 4143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 751 0.051 - 0.102: 242 0.102 - 0.153: 35 0.153 - 0.204: 1 0.204 - 0.255: 3 Chirality restraints: 1032 Sorted by residual: chirality pdb=" C20 6OU A 503 " pdb=" C19 6OU A 503 " pdb=" C21 6OU A 503 " pdb=" O30 6OU A 503 " both_signs ideal model delta sigma weight residual False 2.35 2.60 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C20 6OU B 501 " pdb=" C19 6OU B 501 " pdb=" C21 6OU B 501 " pdb=" O30 6OU B 501 " both_signs ideal model delta sigma weight residual False 2.35 2.57 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C20 6OU A 502 " pdb=" C19 6OU A 502 " pdb=" C21 6OU A 502 " pdb=" O30 6OU A 502 " both_signs ideal model delta sigma weight residual False 2.35 2.56 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1029 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 296 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C ILE A 296 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE A 296 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN A 297 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 296 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C ILE B 296 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE B 296 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN B 297 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 243 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO B 244 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 244 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 244 " 0.022 5.00e-02 4.00e+02 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 284 2.71 - 3.25: 7272 3.25 - 3.80: 11658 3.80 - 4.35: 14141 4.35 - 4.90: 24318 Nonbonded interactions: 57673 Sorted by model distance: nonbonded pdb=" OE1 GLU A 351 " pdb=" NH2 ARG A 358 " model vdw 2.157 3.120 nonbonded pdb=" OE1 GLU B 351 " pdb=" NH2 ARG B 358 " model vdw 2.158 3.120 nonbonded pdb=" O GLU B 416 " pdb=" OG SER B 420 " model vdw 2.193 3.040 nonbonded pdb=" O GLU A 416 " pdb=" OG SER A 420 " model vdw 2.194 3.040 nonbonded pdb=" ND2 ASN A 366 " pdb=" O ASN B 84 " model vdw 2.218 3.120 ... (remaining 57668 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 66 through 501) 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: 1.540 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.660 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 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 : 0.010 0.086 7128 Z= 0.427 Angle : 0.941 17.441 9648 Z= 0.447 Chirality : 0.048 0.255 1032 Planarity : 0.005 0.039 1172 Dihedral : 18.128 167.174 2582 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % 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 are not related in a simple way. whole: -2.99 (0.26), residues: 804 helix: -1.16 (0.19), residues: 592 sheet: None (None), residues: 0 loop : -4.15 (0.33), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 272 TYR 0.015 0.002 TYR B 417 PHE 0.016 0.002 PHE B 338 TRP 0.010 0.002 TRP B 334 HIS 0.005 0.001 HIS B 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00980 / 0.43 ( 7126) covalent geometry : angle 0.94141 / 0.45 ( 9648) hydrogen bonds : bond 0.11351 / 7.42 ( 438) hydrogen bonds : angle 6.53297 / 4.67 ( 1308) Misc. bond : bond 0.00040 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 306 ASN cc_start: 0.8273 (m-40) cc_final: 0.7946 (m-40) REVERT: A 404 ARG cc_start: 0.7495 (mtt-85) cc_final: 0.6765 (mtm110) REVERT: B 404 ARG cc_start: 0.7480 (mtt-85) cc_final: 0.6777 (mtm110) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.6205 time to fit residues: 77.3356 Evaluate side-chains 92 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 119 GLN A 162 GLN A 239 HIS ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 GLN A 465 GLN B 119 GLN B 162 GLN B 239 HIS B 266 ASN B 292 GLN B 465 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.135474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.106414 restraints weight = 9577.177| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.96 r_work: 0.3089 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7128 Z= 0.134 Angle : 0.593 7.094 9648 Z= 0.299 Chirality : 0.039 0.124 1032 Planarity : 0.005 0.033 1172 Dihedral : 15.309 178.674 1038 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.22 % Allowed : 11.06 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.30), residues: 804 helix: 0.60 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -3.33 (0.34), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 358 TYR 0.013 0.001 TYR B 211 PHE 0.028 0.002 PHE B 443 TRP 0.010 0.001 TRP B 340 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7126) covalent geometry : angle 0.59307 / 0.30 ( 9648) hydrogen bonds : bond 0.03665 / 2.49 ( 438) hydrogen bonds : angle 5.06301 / 3.65 ( 1308) Misc. bond : bond 0.00036 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.293 Fit side-chains REVERT: A 315 ASP cc_start: 0.7970 (t70) cc_final: 0.7666 (t70) REVERT: A 404 ARG cc_start: 0.7429 (mtt-85) cc_final: 0.6405 (mtm110) REVERT: B 315 ASP cc_start: 0.7938 (t70) cc_final: 0.7636 (t70) REVERT: B 404 ARG cc_start: 0.7453 (mtt-85) cc_final: 0.6396 (mtm110) outliers start: 23 outliers final: 2 residues processed: 123 average time/residue: 0.4460 time to fit residues: 58.4569 Evaluate side-chains 102 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 248 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 66 optimal weight: 0.7980 chunk 25 optimal weight: 0.0270 chunk 68 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108389 restraints weight = 9465.788| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.92 r_work: 0.3133 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7128 Z= 0.117 Angle : 0.558 7.245 9648 Z= 0.277 Chirality : 0.037 0.125 1032 Planarity : 0.004 0.030 1172 Dihedral : 13.668 169.636 1038 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.20 % Allowed : 13.03 % Favored : 82.77 % 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 are not related in a simple way. whole: 0.29 (0.31), residues: 804 helix: 1.25 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -3.08 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 427 TYR 0.013 0.001 TYR A 316 PHE 0.010 0.001 PHE B 338 TRP 0.015 0.001 TRP B 340 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 7126) covalent geometry : angle 0.55822 / 0.28 ( 9648) hydrogen bonds : bond 0.03317 / 2.23 ( 438) hydrogen bonds : angle 4.82020 / 3.50 ( 1308) Misc. bond : bond 0.00038 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.258 Fit side-chains REVERT: A 73 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8009 (t0) REVERT: A 79 ASP cc_start: 0.8495 (p0) cc_final: 0.8193 (p0) REVERT: A 253 TYR cc_start: 0.8963 (m-80) cc_final: 0.8750 (m-80) REVERT: A 363 ASP cc_start: 0.8822 (p0) cc_final: 0.8317 (p0) REVERT: A 400 LYS cc_start: 0.7884 (ttmt) cc_final: 0.7547 (ttmt) REVERT: A 404 ARG cc_start: 0.7463 (mtt-85) cc_final: 0.6497 (mtm110) REVERT: B 253 TYR cc_start: 0.8955 (m-80) cc_final: 0.8747 (m-80) REVERT: B 363 ASP cc_start: 0.8834 (p0) cc_final: 0.8297 (p0) REVERT: B 400 LYS cc_start: 0.7577 (ttmt) cc_final: 0.7268 (ttmt) REVERT: B 402 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8297 (ttp) REVERT: B 404 ARG cc_start: 0.7504 (mtt-85) cc_final: 0.6457 (mtm110) outliers start: 30 outliers final: 6 residues processed: 151 average time/residue: 0.4748 time to fit residues: 76.0812 Evaluate side-chains 120 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 402 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 59 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.0040 chunk 33 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.5170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.143229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111483 restraints weight = 9197.990| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.13 r_work: 0.3203 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7128 Z= 0.112 Angle : 0.556 7.536 9648 Z= 0.276 Chirality : 0.037 0.120 1032 Planarity : 0.004 0.033 1172 Dihedral : 13.124 170.894 1038 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.34 % Allowed : 16.25 % Favored : 79.41 % 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 are not related in a simple way. whole: 0.71 (0.31), residues: 804 helix: 1.56 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -2.96 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 222 TYR 0.010 0.001 TYR B 211 PHE 0.029 0.001 PHE B 443 TRP 0.016 0.001 TRP B 340 HIS 0.004 0.001 HIS B 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 7126) covalent geometry : angle 0.55631 / 0.28 ( 9648) hydrogen bonds : bond 0.03187 / 2.13 ( 438) hydrogen bonds : angle 4.71592 / 3.42 ( 1308) Misc. bond : bond 0.00045 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.198 Fit side-chains REVERT: A 73 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7801 (t0) REVERT: A 79 ASP cc_start: 0.8486 (p0) cc_final: 0.8151 (p0) REVERT: A 224 LYS cc_start: 0.8731 (ttpp) cc_final: 0.7931 (tmmt) REVERT: A 253 TYR cc_start: 0.8849 (m-80) cc_final: 0.8595 (m-80) REVERT: A 363 ASP cc_start: 0.8694 (p0) cc_final: 0.8016 (p0) REVERT: A 400 LYS cc_start: 0.7566 (ttmt) cc_final: 0.7215 (ttmt) REVERT: A 404 ARG cc_start: 0.7242 (mtt-85) cc_final: 0.6258 (mtm110) REVERT: B 73 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7794 (t0) REVERT: B 224 LYS cc_start: 0.8732 (ttpp) cc_final: 0.7930 (tmmt) REVERT: B 253 TYR cc_start: 0.8854 (m-80) cc_final: 0.8608 (m-80) REVERT: B 363 ASP cc_start: 0.8736 (p0) cc_final: 0.8070 (p0) REVERT: B 404 ARG cc_start: 0.7238 (mtt-85) cc_final: 0.6199 (mtm110) REVERT: B 435 MET cc_start: 0.8232 (tpp) cc_final: 0.7147 (tmm) outliers start: 31 outliers final: 10 residues processed: 144 average time/residue: 0.4738 time to fit residues: 72.4993 Evaluate side-chains 133 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 45 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.139473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106879 restraints weight = 9281.721| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.14 r_work: 0.3136 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7128 Z= 0.178 Angle : 0.594 7.402 9648 Z= 0.294 Chirality : 0.039 0.121 1032 Planarity : 0.004 0.031 1172 Dihedral : 13.413 178.000 1038 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.62 % Allowed : 16.81 % Favored : 78.57 % 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 are not related in a simple way. whole: 0.77 (0.31), residues: 804 helix: 1.59 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -2.82 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 358 TYR 0.013 0.001 TYR B 417 PHE 0.015 0.002 PHE A 277 TRP 0.017 0.001 TRP A 340 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 7126) covalent geometry : angle 0.59356 / 0.29 ( 9648) hydrogen bonds : bond 0.03494 / 2.33 ( 438) hydrogen bonds : angle 4.76206 / 3.45 ( 1308) Misc. bond : bond 0.00033 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.235 Fit side-chains REVERT: A 73 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7994 (t0) REVERT: A 79 ASP cc_start: 0.8655 (p0) cc_final: 0.8348 (p0) REVERT: A 224 LYS cc_start: 0.8679 (ttpp) cc_final: 0.7919 (tmmt) REVERT: A 363 ASP cc_start: 0.8953 (p0) cc_final: 0.8339 (p0) REVERT: A 368 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8445 (pt0) REVERT: A 400 LYS cc_start: 0.7414 (ttmt) cc_final: 0.7075 (ttmt) REVERT: A 404 ARG cc_start: 0.7208 (mtt-85) cc_final: 0.6237 (mtm110) REVERT: B 73 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7948 (t0) REVERT: B 79 ASP cc_start: 0.8489 (p0) cc_final: 0.8229 (p0) REVERT: B 224 LYS cc_start: 0.8649 (ttpp) cc_final: 0.7858 (tmmt) REVERT: B 315 ASP cc_start: 0.7895 (t0) cc_final: 0.7609 (t70) REVERT: B 368 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8434 (pt0) REVERT: B 400 LYS cc_start: 0.7756 (ttmt) cc_final: 0.7384 (ttmt) REVERT: B 404 ARG cc_start: 0.7204 (mtt-85) cc_final: 0.6213 (mtm110) REVERT: B 435 MET cc_start: 0.8312 (tpp) cc_final: 0.7991 (tpp) outliers start: 33 outliers final: 8 residues processed: 132 average time/residue: 0.4830 time to fit residues: 67.5978 Evaluate side-chains 119 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.138747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106170 restraints weight = 9293.154| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.13 r_work: 0.3134 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7128 Z= 0.202 Angle : 0.611 7.770 9648 Z= 0.305 Chirality : 0.040 0.122 1032 Planarity : 0.004 0.042 1172 Dihedral : 13.437 172.372 1038 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 4.20 % Allowed : 18.63 % Favored : 77.17 % 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 are not related in a simple way. whole: 0.69 (0.31), residues: 804 helix: 1.49 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -2.80 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 358 TYR 0.014 0.001 TYR B 417 PHE 0.031 0.002 PHE A 443 TRP 0.018 0.001 TRP A 340 HIS 0.003 0.001 HIS A 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 ( 7126) covalent geometry : angle 0.61096 / 0.31 ( 9648) hydrogen bonds : bond 0.03574 / 2.39 ( 438) hydrogen bonds : angle 4.79943 / 3.47 ( 1308) Misc. bond : bond 0.00036 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.290 Fit side-chains REVERT: A 224 LYS cc_start: 0.8641 (ttpp) cc_final: 0.7885 (tmmt) REVERT: A 318 ARG cc_start: 0.7572 (mmp-170) cc_final: 0.7157 (ttm170) REVERT: A 363 ASP cc_start: 0.9019 (p0) cc_final: 0.8673 (p0) REVERT: A 368 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8415 (pt0) REVERT: A 400 LYS cc_start: 0.7420 (ttmt) cc_final: 0.7114 (ttmt) REVERT: A 404 ARG cc_start: 0.7235 (mtt-85) cc_final: 0.6271 (mtm110) REVERT: B 224 LYS cc_start: 0.8637 (ttpp) cc_final: 0.7888 (tmmt) REVERT: B 315 ASP cc_start: 0.7887 (t0) cc_final: 0.7618 (t70) REVERT: B 368 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8401 (pt0) REVERT: B 404 ARG cc_start: 0.7296 (mtt-85) cc_final: 0.6283 (mtm110) REVERT: B 435 MET cc_start: 0.8356 (tpp) cc_final: 0.8071 (tpp) outliers start: 30 outliers final: 12 residues processed: 125 average time/residue: 0.5073 time to fit residues: 67.1087 Evaluate side-chains 120 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 0.0270 chunk 16 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 19 optimal weight: 0.0070 chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.143324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.112022 restraints weight = 9116.322| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.12 r_work: 0.3205 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7128 Z= 0.108 Angle : 0.560 7.668 9648 Z= 0.279 Chirality : 0.037 0.121 1032 Planarity : 0.004 0.032 1172 Dihedral : 12.521 173.572 1038 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.92 % Allowed : 18.77 % Favored : 77.31 % 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 are not related in a simple way. whole: 1.10 (0.31), residues: 804 helix: 1.80 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -2.79 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 358 TYR 0.011 0.001 TYR A 211 PHE 0.015 0.001 PHE A 443 TRP 0.022 0.001 TRP A 340 HIS 0.004 0.001 HIS B 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 7126) covalent geometry : angle 0.55965 / 0.28 ( 9648) hydrogen bonds : bond 0.03114 / 2.07 ( 438) hydrogen bonds : angle 4.68283 / 3.40 ( 1308) Misc. bond : bond 0.00031 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.273 Fit side-chains REVERT: A 73 ASP cc_start: 0.8363 (m-30) cc_final: 0.8118 (t0) REVERT: A 250 ARG cc_start: 0.7536 (mtp85) cc_final: 0.7320 (mtp85) REVERT: A 318 ARG cc_start: 0.7611 (mmp-170) cc_final: 0.7132 (ttm170) REVERT: A 400 LYS cc_start: 0.7371 (ttmt) cc_final: 0.7066 (ttmt) REVERT: A 404 ARG cc_start: 0.7232 (mtt-85) cc_final: 0.6262 (mtm110) REVERT: B 73 ASP cc_start: 0.8329 (m-30) cc_final: 0.7983 (t0) REVERT: B 79 ASP cc_start: 0.8303 (p0) cc_final: 0.8094 (p0) REVERT: B 250 ARG cc_start: 0.7515 (mtp85) cc_final: 0.7306 (mtp85) REVERT: B 363 ASP cc_start: 0.8804 (p0) cc_final: 0.8156 (p0) REVERT: B 402 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8239 (ttp) REVERT: B 404 ARG cc_start: 0.7247 (mtt-85) cc_final: 0.6228 (mtm110) REVERT: B 435 MET cc_start: 0.8287 (tpp) cc_final: 0.7222 (tmm) outliers start: 28 outliers final: 10 residues processed: 151 average time/residue: 0.4906 time to fit residues: 78.7370 Evaluate side-chains 126 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 16 optimal weight: 0.0970 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 266 ASN A 292 GLN A 376 ASN B 162 GLN B 266 ASN B 292 GLN B 376 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.141933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.108617 restraints weight = 9414.244| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.21 r_work: 0.3167 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7128 Z= 0.147 Angle : 0.575 7.490 9648 Z= 0.287 Chirality : 0.039 0.121 1032 Planarity : 0.004 0.033 1172 Dihedral : 12.471 166.248 1038 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.64 % Allowed : 21.71 % Favored : 74.65 % 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 are not related in a simple way. whole: 1.10 (0.31), residues: 804 helix: 1.80 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.73 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 427 TYR 0.011 0.001 TYR B 417 PHE 0.031 0.001 PHE A 443 TRP 0.021 0.001 TRP B 340 HIS 0.004 0.001 HIS B 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 7126) covalent geometry : angle 0.57522 / 0.29 ( 9648) hydrogen bonds : bond 0.03255 / 2.19 ( 438) hydrogen bonds : angle 4.69286 / 3.40 ( 1308) Misc. bond : bond 0.00026 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.277 Fit side-chains REVERT: A 250 ARG cc_start: 0.7579 (mtp85) cc_final: 0.7364 (mtp85) REVERT: A 400 LYS cc_start: 0.7488 (ttmt) cc_final: 0.7175 (ttmt) REVERT: A 404 ARG cc_start: 0.7323 (mtt-85) cc_final: 0.6323 (mtm110) REVERT: B 73 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7979 (t0) REVERT: B 250 ARG cc_start: 0.7568 (mtp85) cc_final: 0.7358 (mtp85) REVERT: B 363 ASP cc_start: 0.8903 (p0) cc_final: 0.8593 (p0) REVERT: B 402 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8217 (ttp) REVERT: B 404 ARG cc_start: 0.7233 (mtt-85) cc_final: 0.6856 (mtt90) REVERT: B 435 MET cc_start: 0.8348 (tpp) cc_final: 0.7319 (tmm) outliers start: 26 outliers final: 11 residues processed: 131 average time/residue: 0.4742 time to fit residues: 66.0480 Evaluate side-chains 121 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.141166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108646 restraints weight = 9274.049| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.13 r_work: 0.3160 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7128 Z= 0.140 Angle : 0.571 7.543 9648 Z= 0.285 Chirality : 0.039 0.120 1032 Planarity : 0.005 0.034 1172 Dihedral : 12.348 163.267 1038 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.94 % Allowed : 22.55 % Favored : 74.51 % 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 are not related in a simple way. whole: 1.14 (0.31), residues: 804 helix: 1.82 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.69 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 427 TYR 0.011 0.001 TYR B 417 PHE 0.029 0.002 PHE A 443 TRP 0.023 0.001 TRP A 340 HIS 0.004 0.001 HIS B 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 7126) covalent geometry : angle 0.57083 / 0.29 ( 9648) hydrogen bonds : bond 0.03229 / 2.17 ( 438) hydrogen bonds : angle 4.69306 / 3.40 ( 1308) Misc. bond : bond 0.00024 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.280 Fit side-chains REVERT: A 73 ASP cc_start: 0.8314 (m-30) cc_final: 0.7990 (t0) REVERT: A 250 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7332 (mtp85) REVERT: A 400 LYS cc_start: 0.7378 (ttmt) cc_final: 0.7060 (ttmt) REVERT: A 404 ARG cc_start: 0.7197 (mtt-85) cc_final: 0.6200 (mtm110) REVERT: A 435 MET cc_start: 0.8255 (tpp) cc_final: 0.7171 (tmm) REVERT: B 250 ARG cc_start: 0.7552 (mtp85) cc_final: 0.7336 (mtp85) REVERT: B 389 PHE cc_start: 0.9032 (t80) cc_final: 0.8825 (t80) REVERT: B 404 ARG cc_start: 0.7181 (mtt-85) cc_final: 0.6836 (mtt180) REVERT: B 435 MET cc_start: 0.8347 (tpp) cc_final: 0.7345 (tmm) outliers start: 21 outliers final: 13 residues processed: 125 average time/residue: 0.4887 time to fit residues: 64.7777 Evaluate side-chains 121 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 12 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.108155 restraints weight = 9250.614| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.13 r_work: 0.3155 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7128 Z= 0.148 Angle : 0.583 7.493 9648 Z= 0.292 Chirality : 0.040 0.182 1032 Planarity : 0.005 0.035 1172 Dihedral : 12.245 159.310 1038 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.66 % Allowed : 23.11 % Favored : 74.23 % 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 are not related in a simple way. whole: 1.13 (0.31), residues: 804 helix: 1.81 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.70 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 427 TYR 0.011 0.001 TYR B 417 PHE 0.032 0.002 PHE B 443 TRP 0.024 0.001 TRP B 340 HIS 0.004 0.001 HIS B 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 7126) covalent geometry : angle 0.58278 / 0.29 ( 9648) hydrogen bonds : bond 0.03273 / 2.20 ( 438) hydrogen bonds : angle 4.71982 / 3.41 ( 1308) Misc. bond : bond 0.00022 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.309 Fit side-chains REVERT: A 73 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7987 (t0) REVERT: A 250 ARG cc_start: 0.7562 (mtp85) cc_final: 0.7338 (mtp85) REVERT: A 389 PHE cc_start: 0.9041 (t80) cc_final: 0.8814 (t80) REVERT: A 400 LYS cc_start: 0.7368 (ttmt) cc_final: 0.7054 (ttmt) REVERT: A 404 ARG cc_start: 0.7158 (mtt-85) cc_final: 0.6148 (mtm110) REVERT: A 435 MET cc_start: 0.8325 (tpp) cc_final: 0.7254 (tmm) REVERT: B 250 ARG cc_start: 0.7562 (mtp85) cc_final: 0.7344 (mtp85) REVERT: B 389 PHE cc_start: 0.9044 (t80) cc_final: 0.8839 (t80) REVERT: B 404 ARG cc_start: 0.7191 (mtt-85) cc_final: 0.6481 (mtt90) REVERT: B 435 MET cc_start: 0.8348 (tpp) cc_final: 0.7312 (tmm) outliers start: 19 outliers final: 14 residues processed: 120 average time/residue: 0.4541 time to fit residues: 57.8571 Evaluate side-chains 121 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.143327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111057 restraints weight = 9156.851| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.15 r_work: 0.3194 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7128 Z= 0.118 Angle : 0.579 8.868 9648 Z= 0.286 Chirality : 0.041 0.338 1032 Planarity : 0.004 0.030 1172 Dihedral : 11.829 151.752 1038 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.80 % Allowed : 22.69 % Favored : 74.51 % 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 are not related in a simple way. whole: 1.23 (0.31), residues: 804 helix: 1.90 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.73 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 427 TYR 0.009 0.001 TYR B 211 PHE 0.031 0.001 PHE A 443 TRP 0.025 0.001 TRP B 340 HIS 0.003 0.001 HIS B 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 7126) covalent geometry : angle 0.57904 / 0.29 ( 9648) hydrogen bonds : bond 0.03129 / 2.10 ( 438) hydrogen bonds : angle 4.69455 / 3.39 ( 1308) Misc. bond : bond 0.00026 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2398.02 seconds wall clock time: 41 minutes 40.18 seconds (2500.18 seconds total)