Starting phenix.real_space_refine on Fri Jul 19 04:16:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyf_42804/07_2024/8uyf_42804.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyf_42804/07_2024/8uyf_42804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyf_42804/07_2024/8uyf_42804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyf_42804/07_2024/8uyf_42804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyf_42804/07_2024/8uyf_42804.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyf_42804/07_2024/8uyf_42804.cif" } resolution = 2.75 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= 0.007 sd= 0.044 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 2 5.49 5 S 44 5.16 5 C 4124 2.51 5 N 1090 2.21 5 O 1200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6460 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3231 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 381} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TPO:plan-1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3229 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 4.18, per 1000 atoms: 0.65 Number of scatterers: 6460 At special positions: 0 Unit cell: (115.544, 75.952, 76.76, 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 44 16.00 P 2 15.00 O 1200 8.00 N 1090 7.00 C 4124 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 - 3.50 Amino acid : False - 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: 2.46 Conformation dependent library (CDL) restraints added in 1.2 seconds 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1554 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 7 sheets defined 43.2% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 120 through 137 Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.533A pdb=" N HIS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 406 through 420 removed outlier: 3.750A pdb=" N TYR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 471 through 485 Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 498 through 515 Processing helix chain 'A' and resid 542 through 556 removed outlier: 3.701A pdb=" N ARG A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 574 removed outlier: 3.779A pdb=" N HIS A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 137 removed outlier: 4.242A pdb=" N GLY B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 Processing helix chain 'B' and resid 231 through 236 removed outlier: 4.416A pdb=" N ASP B 235 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 307 through 328 removed outlier: 3.556A pdb=" N HIS B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 4.542A pdb=" N CYS B 360 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 406 through 420 removed outlier: 3.979A pdb=" N TYR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 471 through 485 Processing helix chain 'B' and resid 486 through 491 removed outlier: 3.738A pdb=" N LEU B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 516 Processing helix chain 'B' and resid 542 through 555 removed outlier: 3.773A pdb=" N ARG B 555 " --> pdb=" O SER B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 574 removed outlier: 3.630A pdb=" N HIS B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 160 removed outlier: 3.597A pdb=" N SER A 251 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LYS A 291 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N MET A 249 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 254 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 296 removed outlier: 3.604A pdb=" N CYS A 295 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 372 Processing sheet with id=AA5, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.651A pdb=" N SER B 251 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LYS B 291 " --> pdb=" O MET B 249 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N MET B 249 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 295 through 296 removed outlier: 3.573A pdb=" N CYS B 295 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 370 through 372 290 hydrogen bonds defined for protein. 831 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: 1.78 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2089 1.34 - 1.46: 1405 1.46 - 1.58: 3019 1.58 - 1.69: 6 1.69 - 1.81: 68 Bond restraints: 6587 Sorted by residual: bond pdb=" OG1 TPO B 305 " pdb=" P TPO B 305 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" OG1 TPO A 305 " pdb=" P TPO A 305 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" O1P TPO B 305 " pdb=" P TPO B 305 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" O2P TPO A 305 " pdb=" P TPO A 305 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" O3P TPO A 305 " pdb=" P TPO A 305 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 6582 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.96: 196 106.96 - 113.71: 3701 113.71 - 120.46: 2345 120.46 - 127.21: 2602 127.21 - 133.96: 71 Bond angle restraints: 8915 Sorted by residual: angle pdb=" CB TPO B 305 " pdb=" OG1 TPO B 305 " pdb=" P TPO B 305 " ideal model delta sigma weight residual 119.31 106.41 12.90 3.00e+00 1.11e-01 1.85e+01 angle pdb=" CB TPO A 305 " pdb=" OG1 TPO A 305 " pdb=" P TPO A 305 " ideal model delta sigma weight residual 119.31 107.04 12.27 3.00e+00 1.11e-01 1.67e+01 angle pdb=" OG1 TPO A 305 " pdb=" P TPO A 305 " pdb=" O1P TPO A 305 " ideal model delta sigma weight residual 100.43 109.64 -9.21 3.00e+00 1.11e-01 9.42e+00 angle pdb=" OG1 TPO B 305 " pdb=" P TPO B 305 " pdb=" O1P TPO B 305 " ideal model delta sigma weight residual 100.43 109.40 -8.97 3.00e+00 1.11e-01 8.95e+00 angle pdb=" C THR A 215 " pdb=" N VAL A 216 " pdb=" CA VAL A 216 " ideal model delta sigma weight residual 120.33 122.15 -1.82 8.00e-01 1.56e+00 5.16e+00 ... (remaining 8910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.76: 3722 11.76 - 23.53: 232 23.53 - 35.29: 53 35.29 - 47.06: 16 47.06 - 58.82: 10 Dihedral angle restraints: 4033 sinusoidal: 1653 harmonic: 2380 Sorted by residual: dihedral pdb=" CB ARG B 554 " pdb=" CG ARG B 554 " pdb=" CD ARG B 554 " pdb=" NE ARG B 554 " ideal model delta sinusoidal sigma weight residual -60.00 -116.26 56.26 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" N GLU B 376 " pdb=" CA GLU B 376 " pdb=" CB GLU B 376 " pdb=" CG GLU B 376 " ideal model delta sinusoidal sigma weight residual -180.00 -124.69 -55.31 3 1.50e+01 4.44e-03 9.34e+00 dihedral pdb=" N LEU B 560 " pdb=" CA LEU B 560 " pdb=" CB LEU B 560 " pdb=" CG LEU B 560 " ideal model delta sinusoidal sigma weight residual -60.00 -114.70 54.70 3 1.50e+01 4.44e-03 9.30e+00 ... (remaining 4030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 640 0.028 - 0.055: 235 0.055 - 0.083: 77 0.083 - 0.110: 37 0.110 - 0.138: 12 Chirality restraints: 1001 Sorted by residual: chirality pdb=" CA ILE A 450 " pdb=" N ILE A 450 " pdb=" C ILE A 450 " pdb=" CB ILE A 450 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE B 450 " pdb=" N ILE B 450 " pdb=" C ILE B 450 " pdb=" CB ILE B 450 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA VAL B 172 " pdb=" N VAL B 172 " pdb=" C VAL B 172 " pdb=" CB VAL B 172 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 998 not shown) Planarity restraints: 1131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 450 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO B 451 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 451 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 451 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 450 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A 451 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 485 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 486 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 486 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 486 " 0.015 5.00e-02 4.00e+02 ... (remaining 1128 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 1894 2.82 - 3.34: 5921 3.34 - 3.86: 10404 3.86 - 4.38: 12995 4.38 - 4.90: 21551 Nonbonded interactions: 52765 Sorted by model distance: nonbonded pdb=" NZ LYS A 491 " pdb=" O ASN A 493 " model vdw 2.305 2.520 nonbonded pdb=" N ASP A 379 " pdb=" OD1 ASP A 379 " model vdw 2.322 2.520 nonbonded pdb=" O PHE B 452 " pdb=" ND2 ASN B 456 " model vdw 2.328 2.520 nonbonded pdb=" N ASP A 423 " pdb=" OD1 ASP A 423 " model vdw 2.336 2.520 nonbonded pdb=" O PRO A 389 " pdb=" ND2 ASN A 393 " model vdw 2.346 2.520 ... (remaining 52760 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 120 and (name N or name CA or name C or name O or name CB \ )) or resid 121 through 573 or (resid 574 and (name N or name CA or name C or n \ ame O or name CB )))) selection = (chain 'B' and (resid 120 through 515 or resid 540 through 574)) } 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: 0.780 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.470 Find NCS groups from input model: 0.310 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: 0.010 Load rotamer database and sin/cos tables:17.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.003 0.109 6587 Z= 0.181 Angle : 0.515 12.902 8915 Z= 0.264 Chirality : 0.037 0.138 1001 Planarity : 0.003 0.035 1131 Dihedral : 9.080 58.823 2479 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.12 % Allowed : 4.18 % Favored : 94.70 % 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: 1.14 (0.30), residues: 775 helix: 2.01 (0.29), residues: 317 sheet: -0.42 (0.48), residues: 123 loop : 0.10 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 484 HIS 0.002 0.001 HIS A 328 PHE 0.007 0.001 PHE A 253 TYR 0.008 0.001 TYR A 174 ARG 0.002 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 157 ASP cc_start: 0.7121 (m-30) cc_final: 0.6886 (m-30) REVERT: A 178 LEU cc_start: 0.8312 (mt) cc_final: 0.7799 (pp) REVERT: A 201 GLU cc_start: 0.8231 (mm-30) cc_final: 0.8031 (mm-30) REVERT: A 215 THR cc_start: 0.9419 (p) cc_final: 0.9182 (p) REVERT: A 232 ASN cc_start: 0.8509 (m-40) cc_final: 0.8184 (m110) REVERT: A 282 ARG cc_start: 0.7907 (mtp180) cc_final: 0.7395 (mpp-170) REVERT: A 384 ARG cc_start: 0.8488 (mtp-110) cc_final: 0.7923 (mtm110) REVERT: A 395 LYS cc_start: 0.8681 (mttt) cc_final: 0.8441 (mtpm) REVERT: A 500 ASN cc_start: 0.7923 (t0) cc_final: 0.7403 (t0) REVERT: A 563 LYS cc_start: 0.8363 (mttt) cc_final: 0.8035 (mptt) REVERT: A 570 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6865 (mp0) REVERT: B 133 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7638 (pp20) REVERT: B 178 LEU cc_start: 0.7388 (mt) cc_final: 0.7133 (pt) REVERT: B 179 LYS cc_start: 0.7529 (tttt) cc_final: 0.7248 (tppt) REVERT: B 209 LYS cc_start: 0.8523 (mmtp) cc_final: 0.8293 (mttp) REVERT: B 264 LYS cc_start: 0.6976 (mttt) cc_final: 0.6739 (mmmt) REVERT: B 338 ASP cc_start: 0.8435 (t0) cc_final: 0.8168 (t0) REVERT: B 366 GLN cc_start: 0.8720 (mt0) cc_final: 0.8508 (pt0) REVERT: B 379 ASP cc_start: 0.8282 (p0) cc_final: 0.8052 (OUTLIER) REVERT: B 558 LEU cc_start: 0.8735 (tp) cc_final: 0.8521 (tm) REVERT: B 559 HIS cc_start: 0.6704 (t70) cc_final: 0.6496 (t70) REVERT: B 563 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8408 (mtpp) outliers start: 8 outliers final: 2 residues processed: 179 average time/residue: 1.2668 time to fit residues: 237.6539 Evaluate side-chains 134 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 0.0980 chunk 32 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 367 ASN B 197 ASN B 339 ASN B 378 GLN B 467 ASN B 504 GLN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6587 Z= 0.214 Angle : 0.524 5.575 8915 Z= 0.273 Chirality : 0.040 0.141 1001 Planarity : 0.004 0.036 1131 Dihedral : 4.071 38.894 870 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.21 % Allowed : 11.58 % Favored : 85.22 % 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: 1.40 (0.30), residues: 775 helix: 2.19 (0.28), residues: 327 sheet: -0.16 (0.48), residues: 118 loop : 0.15 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 505 HIS 0.003 0.001 HIS A 328 PHE 0.014 0.001 PHE A 452 TYR 0.016 0.002 TYR A 494 ARG 0.005 0.001 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 0.904 Fit side-chains REVERT: A 178 LEU cc_start: 0.8117 (mt) cc_final: 0.7669 (pp) REVERT: A 215 THR cc_start: 0.9279 (p) cc_final: 0.9034 (p) REVERT: A 237 LYS cc_start: 0.8566 (ptpt) cc_final: 0.8226 (ptpp) REVERT: A 282 ARG cc_start: 0.7931 (mtp180) cc_final: 0.7296 (mtt90) REVERT: A 384 ARG cc_start: 0.8509 (mtp-110) cc_final: 0.7898 (mtm110) REVERT: A 395 LYS cc_start: 0.8670 (mttt) cc_final: 0.8447 (mtpm) REVERT: A 557 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7834 (mtm-85) REVERT: A 563 LYS cc_start: 0.8295 (mttt) cc_final: 0.7896 (mmtm) REVERT: B 121 ASP cc_start: 0.5864 (OUTLIER) cc_final: 0.5521 (OUTLIER) REVERT: B 133 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7537 (pp20) REVERT: B 178 LEU cc_start: 0.7411 (mt) cc_final: 0.7163 (pt) REVERT: B 179 LYS cc_start: 0.7657 (tttt) cc_final: 0.7368 (tppt) REVERT: B 284 MET cc_start: 0.8327 (tpp) cc_final: 0.7678 (tpp) REVERT: B 338 ASP cc_start: 0.8476 (t0) cc_final: 0.8170 (t0) REVERT: B 366 GLN cc_start: 0.8795 (mt0) cc_final: 0.8273 (pt0) REVERT: B 563 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8348 (mtpp) outliers start: 23 outliers final: 13 residues processed: 155 average time/residue: 1.1554 time to fit residues: 188.3264 Evaluate side-chains 139 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 379 ASP Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 515 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN B 339 ASN B 378 GLN B 504 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6587 Z= 0.167 Angle : 0.474 6.037 8915 Z= 0.245 Chirality : 0.038 0.140 1001 Planarity : 0.003 0.034 1131 Dihedral : 3.981 39.732 870 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.37 % Allowed : 14.50 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.30), residues: 775 helix: 2.38 (0.28), residues: 324 sheet: -0.10 (0.48), residues: 117 loop : 0.13 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.002 0.001 HIS A 328 PHE 0.010 0.001 PHE A 253 TYR 0.017 0.001 TYR A 494 ARG 0.006 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.854 Fit side-chains REVERT: A 178 LEU cc_start: 0.8023 (mt) cc_final: 0.7525 (pp) REVERT: A 215 THR cc_start: 0.9142 (p) cc_final: 0.8893 (p) REVERT: A 237 LYS cc_start: 0.8554 (ptpt) cc_final: 0.8225 (ptpp) REVERT: A 282 ARG cc_start: 0.7934 (mtp180) cc_final: 0.7391 (mpt90) REVERT: A 395 LYS cc_start: 0.8642 (mttt) cc_final: 0.8417 (mtpm) REVERT: A 431 MET cc_start: 0.4905 (OUTLIER) cc_final: 0.4694 (ttt) REVERT: A 440 GLU cc_start: 0.7834 (mt-10) cc_final: 0.6970 (mp0) REVERT: A 481 LEU cc_start: 0.8796 (mt) cc_final: 0.8578 (mp) REVERT: A 563 LYS cc_start: 0.8294 (mttt) cc_final: 0.7875 (mmtm) REVERT: B 178 LEU cc_start: 0.7402 (mt) cc_final: 0.7154 (pt) REVERT: B 179 LYS cc_start: 0.7476 (tttt) cc_final: 0.7220 (tppt) REVERT: B 284 MET cc_start: 0.8312 (tpp) cc_final: 0.7657 (tpp) REVERT: B 338 ASP cc_start: 0.8475 (t0) cc_final: 0.8131 (t0) REVERT: B 366 GLN cc_start: 0.8791 (mt0) cc_final: 0.8438 (pt0) REVERT: B 563 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8392 (mtpp) outliers start: 17 outliers final: 9 residues processed: 139 average time/residue: 1.2223 time to fit residues: 178.2106 Evaluate side-chains 126 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 515 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 0.0570 chunk 20 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN B 197 ASN B 339 ASN B 378 GLN B 504 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6587 Z= 0.139 Angle : 0.462 5.863 8915 Z= 0.237 Chirality : 0.038 0.141 1001 Planarity : 0.003 0.034 1131 Dihedral : 3.560 14.495 868 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.49 % Allowed : 14.50 % Favored : 82.01 % 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: 1.65 (0.30), residues: 775 helix: 2.55 (0.28), residues: 324 sheet: -0.09 (0.48), residues: 117 loop : 0.15 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.002 0.000 HIS A 328 PHE 0.011 0.001 PHE A 253 TYR 0.019 0.001 TYR A 494 ARG 0.006 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 0.738 Fit side-chains REVERT: A 178 LEU cc_start: 0.7930 (mt) cc_final: 0.7407 (pp) REVERT: A 215 THR cc_start: 0.9031 (p) cc_final: 0.8774 (p) REVERT: A 237 LYS cc_start: 0.8550 (ptpt) cc_final: 0.8221 (ptpp) REVERT: A 282 ARG cc_start: 0.7936 (mtp180) cc_final: 0.7387 (mpt90) REVERT: A 376 GLU cc_start: 0.8296 (mp0) cc_final: 0.8042 (mp0) REVERT: A 395 LYS cc_start: 0.8638 (mttt) cc_final: 0.8413 (mtpm) REVERT: A 440 GLU cc_start: 0.7838 (mt-10) cc_final: 0.6973 (mp0) REVERT: A 481 LEU cc_start: 0.8791 (mt) cc_final: 0.8579 (mp) REVERT: A 543 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8079 (tm) REVERT: A 563 LYS cc_start: 0.8339 (mttt) cc_final: 0.7921 (mmtm) REVERT: B 174 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.8098 (m-80) REVERT: B 338 ASP cc_start: 0.8469 (t0) cc_final: 0.8124 (t0) REVERT: B 366 GLN cc_start: 0.8803 (mt0) cc_final: 0.8231 (pt0) REVERT: B 377 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7361 (t0) REVERT: B 563 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8384 (mtpp) outliers start: 25 outliers final: 11 residues processed: 137 average time/residue: 1.1482 time to fit residues: 165.4591 Evaluate side-chains 133 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 379 ASP Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 515 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.4980 chunk 1 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 0 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN B 197 ASN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6587 Z= 0.156 Angle : 0.462 5.565 8915 Z= 0.236 Chirality : 0.038 0.140 1001 Planarity : 0.003 0.034 1131 Dihedral : 3.556 14.485 868 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.07 % Allowed : 15.48 % Favored : 81.45 % 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: 1.68 (0.30), residues: 775 helix: 2.59 (0.28), residues: 324 sheet: -0.01 (0.48), residues: 117 loop : 0.13 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 505 HIS 0.006 0.001 HIS A 572 PHE 0.011 0.001 PHE A 253 TYR 0.021 0.001 TYR A 494 ARG 0.006 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 0.772 Fit side-chains REVERT: A 178 LEU cc_start: 0.7871 (mt) cc_final: 0.7361 (pp) REVERT: A 215 THR cc_start: 0.9036 (p) cc_final: 0.8776 (p) REVERT: A 237 LYS cc_start: 0.8554 (ptpt) cc_final: 0.8222 (ptpp) REVERT: A 282 ARG cc_start: 0.7946 (mtp180) cc_final: 0.7400 (mpt90) REVERT: A 376 GLU cc_start: 0.8297 (mp0) cc_final: 0.8082 (mp0) REVERT: A 395 LYS cc_start: 0.8661 (mttt) cc_final: 0.8431 (mtpm) REVERT: A 440 GLU cc_start: 0.7833 (mt-10) cc_final: 0.6966 (mp0) REVERT: A 481 LEU cc_start: 0.8809 (mt) cc_final: 0.8606 (mp) REVERT: A 543 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8071 (tm) REVERT: A 563 LYS cc_start: 0.8341 (mttt) cc_final: 0.7921 (mmtm) REVERT: B 174 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8138 (m-80) REVERT: B 284 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7589 (tpp) REVERT: B 338 ASP cc_start: 0.8479 (t0) cc_final: 0.8124 (t0) REVERT: B 366 GLN cc_start: 0.8810 (mt0) cc_final: 0.8441 (pt0) REVERT: B 504 GLN cc_start: 0.7614 (mt0) cc_final: 0.7394 (mt0) REVERT: B 563 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8408 (mtpp) outliers start: 22 outliers final: 15 residues processed: 136 average time/residue: 1.2515 time to fit residues: 178.7939 Evaluate side-chains 136 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 379 ASP Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 488 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 74 optimal weight: 0.0070 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN B 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6587 Z= 0.212 Angle : 0.487 6.555 8915 Z= 0.247 Chirality : 0.039 0.139 1001 Planarity : 0.003 0.034 1131 Dihedral : 3.659 14.401 868 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.07 % Allowed : 16.04 % Favored : 80.89 % 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: 1.61 (0.30), residues: 775 helix: 2.55 (0.28), residues: 324 sheet: 0.02 (0.48), residues: 117 loop : 0.03 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.005 0.001 HIS A 572 PHE 0.012 0.001 PHE A 253 TYR 0.020 0.001 TYR A 494 ARG 0.006 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 0.857 Fit side-chains REVERT: A 178 LEU cc_start: 0.7935 (mt) cc_final: 0.7470 (pp) REVERT: A 215 THR cc_start: 0.9109 (p) cc_final: 0.8851 (p) REVERT: A 237 LYS cc_start: 0.8563 (ptpt) cc_final: 0.8223 (ptpp) REVERT: A 261 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6559 (mm-40) REVERT: A 282 ARG cc_start: 0.7959 (mtp180) cc_final: 0.7386 (mpt90) REVERT: A 376 GLU cc_start: 0.8283 (mp0) cc_final: 0.8074 (mp0) REVERT: A 395 LYS cc_start: 0.8671 (mttt) cc_final: 0.8441 (mtpm) REVERT: A 440 GLU cc_start: 0.7862 (mt-10) cc_final: 0.6980 (mp0) REVERT: A 504 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: A 543 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8097 (tm) REVERT: A 563 LYS cc_start: 0.8348 (mttt) cc_final: 0.7934 (mmtm) REVERT: B 121 ASP cc_start: 0.5809 (OUTLIER) cc_final: 0.5320 (t0) REVERT: B 174 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: B 284 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7559 (tpp) REVERT: B 338 ASP cc_start: 0.8496 (t0) cc_final: 0.8108 (t0) REVERT: B 366 GLN cc_start: 0.8859 (mt0) cc_final: 0.8285 (pt0) REVERT: B 563 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8417 (mtpp) outliers start: 22 outliers final: 12 residues processed: 131 average time/residue: 1.2706 time to fit residues: 174.8996 Evaluate side-chains 134 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 379 ASP Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 488 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6587 Z= 0.146 Angle : 0.485 11.629 8915 Z= 0.241 Chirality : 0.038 0.141 1001 Planarity : 0.003 0.032 1131 Dihedral : 3.573 14.690 868 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.07 % Allowed : 16.32 % Favored : 80.61 % 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: 1.71 (0.30), residues: 775 helix: 2.66 (0.28), residues: 324 sheet: 0.04 (0.48), residues: 117 loop : 0.05 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 505 HIS 0.002 0.001 HIS A 572 PHE 0.010 0.001 PHE A 253 TYR 0.021 0.001 TYR A 494 ARG 0.006 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 0.775 Fit side-chains REVERT: A 178 LEU cc_start: 0.7852 (mt) cc_final: 0.7362 (pp) REVERT: A 215 THR cc_start: 0.9035 (p) cc_final: 0.8777 (p) REVERT: A 235 ASP cc_start: 0.7884 (m-30) cc_final: 0.7649 (m-30) REVERT: A 237 LYS cc_start: 0.8570 (ptpt) cc_final: 0.8230 (ptpp) REVERT: A 261 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6557 (mm-40) REVERT: A 282 ARG cc_start: 0.7960 (mtp180) cc_final: 0.7372 (mpt90) REVERT: A 395 LYS cc_start: 0.8657 (mttt) cc_final: 0.8428 (mtpm) REVERT: A 440 GLU cc_start: 0.7835 (mt-10) cc_final: 0.6959 (mp0) REVERT: A 504 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: A 543 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8089 (tm) REVERT: A 563 LYS cc_start: 0.8332 (mttt) cc_final: 0.7914 (mmtm) REVERT: B 121 ASP cc_start: 0.5726 (OUTLIER) cc_final: 0.5255 (t0) REVERT: B 133 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7500 (mt-10) REVERT: B 174 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8137 (m-80) REVERT: B 179 LYS cc_start: 0.7082 (tppt) cc_final: 0.6664 (mttm) REVERT: B 284 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7582 (tpp) REVERT: B 338 ASP cc_start: 0.8495 (t0) cc_final: 0.8148 (t0) REVERT: B 366 GLN cc_start: 0.8844 (mt0) cc_final: 0.8277 (pt0) REVERT: B 504 GLN cc_start: 0.7617 (mt0) cc_final: 0.7395 (mt0) REVERT: B 563 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8392 (mtpp) outliers start: 22 outliers final: 15 residues processed: 139 average time/residue: 1.2092 time to fit residues: 176.5159 Evaluate side-chains 137 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 488 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 0.3980 chunk 14 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 HIS B 197 ASN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6587 Z= 0.165 Angle : 0.523 18.025 8915 Z= 0.254 Chirality : 0.039 0.157 1001 Planarity : 0.003 0.032 1131 Dihedral : 3.561 15.066 868 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.07 % Allowed : 17.02 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.67 (0.30), residues: 775 helix: 2.63 (0.28), residues: 324 sheet: 0.05 (0.48), residues: 117 loop : 0.03 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 505 HIS 0.003 0.001 HIS A 572 PHE 0.011 0.001 PHE A 253 TYR 0.021 0.001 TYR A 494 ARG 0.007 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 0.782 Fit side-chains REVERT: A 178 LEU cc_start: 0.7846 (mt) cc_final: 0.7375 (pp) REVERT: A 215 THR cc_start: 0.9043 (p) cc_final: 0.8781 (p) REVERT: A 235 ASP cc_start: 0.7877 (m-30) cc_final: 0.7636 (m-30) REVERT: A 237 LYS cc_start: 0.8573 (ptpt) cc_final: 0.8229 (ptpp) REVERT: A 261 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6529 (mm-40) REVERT: A 282 ARG cc_start: 0.7963 (mtp180) cc_final: 0.7370 (mpt90) REVERT: A 376 GLU cc_start: 0.8243 (mp0) cc_final: 0.8011 (mp0) REVERT: A 395 LYS cc_start: 0.8660 (mttt) cc_final: 0.8431 (mtpm) REVERT: A 440 GLU cc_start: 0.7842 (mt-10) cc_final: 0.6949 (mp0) REVERT: A 504 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: A 543 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8113 (tm) REVERT: A 563 LYS cc_start: 0.8350 (mttt) cc_final: 0.7934 (mmtm) REVERT: B 121 ASP cc_start: 0.5744 (OUTLIER) cc_final: 0.5266 (t0) REVERT: B 133 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7535 (mt-10) REVERT: B 174 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: B 179 LYS cc_start: 0.7004 (tppt) cc_final: 0.6611 (mttm) REVERT: B 284 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7592 (tpp) REVERT: B 338 ASP cc_start: 0.8502 (t0) cc_final: 0.8137 (t0) REVERT: B 366 GLN cc_start: 0.8846 (mt0) cc_final: 0.8453 (pt0) REVERT: B 563 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8409 (mtpp) outliers start: 22 outliers final: 13 residues processed: 133 average time/residue: 1.3090 time to fit residues: 182.9516 Evaluate side-chains 136 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 488 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 0.0050 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 572 HIS B 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6587 Z= 0.150 Angle : 0.517 17.273 8915 Z= 0.251 Chirality : 0.038 0.139 1001 Planarity : 0.003 0.032 1131 Dihedral : 3.494 15.026 868 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.93 % Allowed : 17.29 % Favored : 79.78 % 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: 1.73 (0.30), residues: 775 helix: 2.69 (0.29), residues: 324 sheet: 0.06 (0.48), residues: 117 loop : 0.05 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 505 HIS 0.002 0.001 HIS A 572 PHE 0.011 0.001 PHE A 253 TYR 0.019 0.001 TYR A 494 ARG 0.007 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.783 Fit side-chains REVERT: A 178 LEU cc_start: 0.7772 (mt) cc_final: 0.7311 (pp) REVERT: A 215 THR cc_start: 0.8982 (p) cc_final: 0.8717 (p) REVERT: A 261 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6585 (mm-40) REVERT: A 282 ARG cc_start: 0.7974 (mtp180) cc_final: 0.7283 (mtt90) REVERT: A 376 GLU cc_start: 0.8260 (mp0) cc_final: 0.8041 (mp0) REVERT: A 395 LYS cc_start: 0.8617 (mttt) cc_final: 0.8381 (mtpm) REVERT: A 440 GLU cc_start: 0.7836 (mt-10) cc_final: 0.6934 (mp0) REVERT: A 504 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7555 (mp10) REVERT: A 543 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8108 (tm) REVERT: A 563 LYS cc_start: 0.8330 (mttt) cc_final: 0.7923 (mmtm) REVERT: B 121 ASP cc_start: 0.5805 (OUTLIER) cc_final: 0.5311 (t0) REVERT: B 174 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.8120 (m-80) REVERT: B 179 LYS cc_start: 0.6831 (tppt) cc_final: 0.6464 (mttm) REVERT: B 284 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7589 (tpp) REVERT: B 338 ASP cc_start: 0.8479 (t0) cc_final: 0.8093 (t0) REVERT: B 366 GLN cc_start: 0.8886 (mt0) cc_final: 0.8399 (pt0) REVERT: B 563 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8347 (mtpp) outliers start: 21 outliers final: 15 residues processed: 132 average time/residue: 1.1992 time to fit residues: 166.2500 Evaluate side-chains 139 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 379 ASP Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 488 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 73 optimal weight: 0.0370 chunk 63 optimal weight: 4.9990 chunk 6 optimal weight: 0.0470 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 572 HIS B 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6587 Z= 0.138 Angle : 0.519 17.378 8915 Z= 0.252 Chirality : 0.038 0.140 1001 Planarity : 0.003 0.032 1131 Dihedral : 3.456 15.115 868 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.93 % Allowed : 17.43 % Favored : 79.64 % 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: 1.79 (0.30), residues: 775 helix: 2.86 (0.29), residues: 317 sheet: 0.06 (0.48), residues: 117 loop : 0.03 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 567 HIS 0.003 0.001 HIS A 572 PHE 0.010 0.001 PHE A 253 TYR 0.021 0.001 TYR A 494 ARG 0.007 0.000 ARG A 248 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 0.858 Fit side-chains REVERT: A 178 LEU cc_start: 0.7695 (mt) cc_final: 0.7256 (pp) REVERT: A 215 THR cc_start: 0.8929 (p) cc_final: 0.8661 (p) REVERT: A 261 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6628 (mm-40) REVERT: A 282 ARG cc_start: 0.7969 (mtp180) cc_final: 0.7283 (mtt90) REVERT: A 395 LYS cc_start: 0.8600 (mttt) cc_final: 0.8364 (mtpm) REVERT: A 440 GLU cc_start: 0.7871 (mt-10) cc_final: 0.6967 (mp0) REVERT: A 504 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7544 (mp10) REVERT: A 543 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8102 (tm) REVERT: A 563 LYS cc_start: 0.8327 (mttt) cc_final: 0.7921 (mmtm) REVERT: B 121 ASP cc_start: 0.5774 (OUTLIER) cc_final: 0.5296 (t0) REVERT: B 133 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7546 (mt-10) REVERT: B 174 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.8015 (m-80) REVERT: B 284 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7590 (tpp) REVERT: B 338 ASP cc_start: 0.8466 (t0) cc_final: 0.8085 (t0) REVERT: B 563 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8346 (mtpp) outliers start: 21 outliers final: 13 residues processed: 134 average time/residue: 1.2400 time to fit residues: 174.5726 Evaluate side-chains 137 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 379 ASP Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 488 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 572 HIS B 197 ASN B 366 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.120765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.107537 restraints weight = 9681.669| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.25 r_work: 0.3312 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6587 Z= 0.170 Angle : 0.535 17.244 8915 Z= 0.259 Chirality : 0.039 0.139 1001 Planarity : 0.003 0.032 1131 Dihedral : 3.487 15.035 868 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.65 % Allowed : 17.99 % Favored : 79.36 % 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: 1.77 (0.30), residues: 775 helix: 2.82 (0.29), residues: 317 sheet: 0.09 (0.48), residues: 117 loop : 0.01 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 567 HIS 0.003 0.001 HIS A 572 PHE 0.012 0.001 PHE A 228 TYR 0.021 0.001 TYR A 494 ARG 0.007 0.000 ARG A 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3329.42 seconds wall clock time: 58 minutes 53.10 seconds (3533.10 seconds total)