Starting phenix.real_space_refine on Sat Aug 3 00:55:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyf_42804/08_2024/8uyf_42804.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyf_42804/08_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_42804/08_2024/8uyf_42804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyf_42804/08_2024/8uyf_42804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyf_42804/08_2024/8uyf_42804.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyf_42804/08_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-5409/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: 4.43, per 1000 atoms: 0.69 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 1.1 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: 0.75 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: 1.74 Time building geometry restraints manager: 2.70 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 3.120 nonbonded pdb=" N ASP A 379 " pdb=" OD1 ASP A 379 " model vdw 2.322 3.120 nonbonded pdb=" O PHE B 452 " pdb=" ND2 ASN B 456 " model vdw 2.328 3.120 nonbonded pdb=" N ASP A 423 " pdb=" OD1 ASP A 423 " model vdw 2.336 3.120 nonbonded pdb=" O PRO A 389 " pdb=" ND2 ASN A 393 " model vdw 2.346 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.870 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.700 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- 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 : 0.799 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: 1.1958 time to fit residues: 224.1902 Evaluate side-chains 134 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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: 0.5980 chunk 32 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN B 197 ASN B 339 ASN B 378 GLN B 467 ASN B 504 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6587 Z= 0.181 Angle : 0.521 4.829 8915 Z= 0.275 Chirality : 0.040 0.141 1001 Planarity : 0.004 0.034 1131 Dihedral : 3.990 38.448 870 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.65 % Allowed : 11.44 % Favored : 85.91 % 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: 1.43 (0.30), residues: 775 helix: 2.23 (0.28), residues: 328 sheet: -0.31 (0.46), residues: 124 loop : 0.22 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.003 0.001 HIS B 559 PHE 0.012 0.001 PHE A 452 TYR 0.016 0.001 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 157 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 0.812 Fit side-chains REVERT: A 178 LEU cc_start: 0.8112 (mt) cc_final: 0.7589 (pp) REVERT: A 201 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 237 LYS cc_start: 0.8472 (ptpt) cc_final: 0.8150 (ptpp) REVERT: A 282 ARG cc_start: 0.7914 (mtp180) cc_final: 0.7289 (mtt90) REVERT: A 384 ARG cc_start: 0.8484 (mtp-110) cc_final: 0.7885 (mtm110) REVERT: A 395 LYS cc_start: 0.8753 (mttt) cc_final: 0.8508 (mtpp) REVERT: A 563 LYS cc_start: 0.8296 (mttt) cc_final: 0.7888 (mmtm) REVERT: B 133 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7539 (pp20) REVERT: B 174 TYR cc_start: 0.8870 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: B 178 LEU cc_start: 0.7376 (mt) cc_final: 0.7138 (pt) REVERT: B 179 LYS cc_start: 0.7596 (tttt) cc_final: 0.7329 (tppt) REVERT: B 209 LYS cc_start: 0.8475 (mmtp) cc_final: 0.8266 (mtmm) REVERT: B 264 LYS cc_start: 0.7038 (mttt) cc_final: 0.6797 (mmmt) REVERT: B 284 MET cc_start: 0.8322 (tpp) cc_final: 0.7664 (tpp) REVERT: B 338 ASP cc_start: 0.8463 (t0) cc_final: 0.8167 (t0) REVERT: B 366 GLN cc_start: 0.8762 (mt0) cc_final: 0.8200 (pt0) REVERT: B 563 LYS cc_start: 0.8619 (mtpt) cc_final: 0.8353 (mtpp) outliers start: 19 outliers final: 10 residues processed: 150 average time/residue: 1.1452 time to fit residues: 180.4383 Evaluate side-chains 130 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 TYR 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: 3.9990 chunk 22 optimal weight: 0.1980 chunk 60 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.8309 moved from start: 0.2211 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= 0.155 Angle : 0.479 5.332 8915 Z= 0.249 Chirality : 0.039 0.141 1001 Planarity : 0.003 0.033 1131 Dihedral : 3.944 37.989 870 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.67 % Allowed : 13.81 % Favored : 84.52 % 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: 1.50 (0.30), residues: 775 helix: 2.36 (0.28), residues: 323 sheet: -0.15 (0.47), residues: 117 loop : 0.15 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.003 0.001 HIS A 572 PHE 0.010 0.001 PHE A 253 TYR 0.020 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 141 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.167 Fit side-chains REVERT: A 178 LEU cc_start: 0.7990 (mt) cc_final: 0.7475 (pp) REVERT: A 201 GLU cc_start: 0.8214 (mm-30) cc_final: 0.8005 (mm-30) REVERT: A 237 LYS cc_start: 0.8460 (ptpt) cc_final: 0.8143 (ptpp) REVERT: A 282 ARG cc_start: 0.7917 (mtp180) cc_final: 0.7391 (mpt90) REVERT: A 395 LYS cc_start: 0.8729 (mttt) cc_final: 0.8502 (mtpm) REVERT: A 431 MET cc_start: 0.4834 (OUTLIER) cc_final: 0.4608 (ttt) REVERT: A 440 GLU cc_start: 0.7729 (mt-10) cc_final: 0.6995 (mp0) REVERT: A 481 LEU cc_start: 0.8746 (mt) cc_final: 0.8529 (mp) REVERT: A 563 LYS cc_start: 0.8340 (mttt) cc_final: 0.7920 (mmtm) REVERT: B 178 LEU cc_start: 0.7341 (mt) cc_final: 0.7134 (pt) REVERT: B 179 LYS cc_start: 0.7442 (tttt) cc_final: 0.7176 (tppt) REVERT: B 209 LYS cc_start: 0.8473 (mmtp) cc_final: 0.8184 (mtmm) REVERT: B 264 LYS cc_start: 0.6999 (mttt) cc_final: 0.6777 (mmmt) REVERT: B 284 MET cc_start: 0.8309 (tpp) cc_final: 0.7641 (tpp) REVERT: B 338 ASP cc_start: 0.8452 (t0) cc_final: 0.8123 (t0) REVERT: B 366 GLN cc_start: 0.8733 (mt0) cc_final: 0.8415 (pt0) REVERT: B 563 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8390 (mtpp) outliers start: 12 outliers final: 5 residues processed: 135 average time/residue: 1.2998 time to fit residues: 183.4918 Evaluate side-chains 128 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain B residue 488 SER 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: 2.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6587 Z= 0.354 Angle : 0.549 6.601 8915 Z= 0.285 Chirality : 0.041 0.137 1001 Planarity : 0.004 0.035 1131 Dihedral : 4.035 15.774 868 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.63 % Allowed : 12.83 % Favored : 83.54 % 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: 1.24 (0.29), residues: 775 helix: 2.17 (0.28), residues: 323 sheet: -0.05 (0.48), residues: 117 loop : -0.13 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.004 0.001 HIS A 328 PHE 0.016 0.002 PHE A 452 TYR 0.017 0.002 TYR A 494 ARG 0.006 0.001 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 146 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 0.905 Fit side-chains REVERT: A 178 LEU cc_start: 0.8127 (mt) cc_final: 0.7748 (pp) REVERT: A 237 LYS cc_start: 0.8554 (ptpt) cc_final: 0.8203 (ptpp) REVERT: A 282 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7405 (mpt90) REVERT: A 395 LYS cc_start: 0.8752 (mttt) cc_final: 0.8516 (mtpm) REVERT: A 431 MET cc_start: 0.4913 (ttt) cc_final: 0.4646 (ttt) REVERT: A 439 LYS cc_start: 0.7827 (mttt) cc_final: 0.7611 (mtpt) REVERT: A 440 GLU cc_start: 0.7802 (mt-10) cc_final: 0.6989 (mp0) REVERT: A 481 LEU cc_start: 0.8785 (mt) cc_final: 0.8564 (mp) REVERT: A 543 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8123 (tm) REVERT: A 563 LYS cc_start: 0.8329 (mttt) cc_final: 0.7937 (mptt) REVERT: B 155 ASN cc_start: 0.7405 (OUTLIER) cc_final: 0.7198 (p0) REVERT: B 174 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: B 178 LEU cc_start: 0.7358 (mt) cc_final: 0.7148 (pt) REVERT: B 179 LYS cc_start: 0.7621 (tttt) cc_final: 0.7336 (tppt) REVERT: B 213 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.6884 (mtp85) REVERT: B 264 LYS cc_start: 0.7018 (mttt) cc_final: 0.6818 (mmmt) REVERT: B 338 ASP cc_start: 0.8509 (t0) cc_final: 0.8148 (t0) REVERT: B 366 GLN cc_start: 0.8866 (mt0) cc_final: 0.8303 (pt0) REVERT: B 563 LYS cc_start: 0.8663 (mtpt) cc_final: 0.8298 (mtmm) outliers start: 26 outliers final: 17 residues processed: 135 average time/residue: 1.2078 time to fit residues: 170.8978 Evaluate side-chains 135 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 267 TYR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 327 ILE 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: 3.9990 chunk 1 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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: 0.8352 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6587 Z= 0.275 Angle : 0.521 6.605 8915 Z= 0.270 Chirality : 0.040 0.139 1001 Planarity : 0.004 0.034 1131 Dihedral : 4.023 15.150 868 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.77 % Allowed : 13.81 % Favored : 82.43 % 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: 1.20 (0.29), residues: 775 helix: 2.19 (0.28), residues: 323 sheet: -0.04 (0.48), residues: 117 loop : -0.23 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.003 0.001 HIS A 328 PHE 0.013 0.001 PHE A 452 TYR 0.018 0.001 TYR A 494 ARG 0.006 0.001 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 146 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 0.719 Fit side-chains REVERT: A 174 TYR cc_start: 0.8700 (m-80) cc_final: 0.8486 (m-80) REVERT: A 178 LEU cc_start: 0.8094 (mt) cc_final: 0.7709 (pp) REVERT: A 261 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6511 (mm-40) REVERT: A 282 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7369 (mpt90) REVERT: A 379 ASP cc_start: 0.8080 (p0) cc_final: 0.7512 (p0) REVERT: A 395 LYS cc_start: 0.8742 (mttt) cc_final: 0.8508 (mtpm) REVERT: A 440 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7013 (mp0) REVERT: A 441 GLU cc_start: 0.8253 (pm20) cc_final: 0.7869 (pm20) REVERT: A 481 LEU cc_start: 0.8777 (mt) cc_final: 0.8552 (mp) REVERT: A 543 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8116 (tm) REVERT: A 563 LYS cc_start: 0.8344 (mttt) cc_final: 0.7924 (mmtm) REVERT: B 174 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: B 178 LEU cc_start: 0.7386 (mt) cc_final: 0.7160 (pt) REVERT: B 179 LYS cc_start: 0.7585 (tttt) cc_final: 0.7310 (tppt) REVERT: B 213 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.6906 (mtp85) REVERT: B 264 LYS cc_start: 0.7038 (mttt) cc_final: 0.6836 (mmmt) REVERT: B 284 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7620 (tpp) REVERT: B 338 ASP cc_start: 0.8518 (t0) cc_final: 0.8140 (t0) REVERT: B 366 GLN cc_start: 0.8875 (mt0) cc_final: 0.8465 (pt0) REVERT: B 377 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7223 (t70) REVERT: B 563 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8345 (mtpp) outliers start: 27 outliers final: 11 residues processed: 135 average time/residue: 1.2159 time to fit residues: 172.4192 Evaluate side-chains 133 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 504 GLN 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 213 ARG Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 515 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6587 Z= 0.180 Angle : 0.492 6.099 8915 Z= 0.254 Chirality : 0.039 0.141 1001 Planarity : 0.003 0.032 1131 Dihedral : 3.824 14.565 868 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.51 % Allowed : 15.20 % Favored : 82.29 % 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: 2.38 (0.28), residues: 323 sheet: -0.03 (0.48), residues: 117 loop : -0.11 (0.32), residues: 335 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 0.011 0.001 PHE A 253 TYR 0.019 0.001 TYR A 494 ARG 0.007 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 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 134 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 0.788 Fit side-chains REVERT: A 178 LEU cc_start: 0.8047 (mt) cc_final: 0.7594 (pp) REVERT: A 282 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7355 (mpt90) REVERT: A 395 LYS cc_start: 0.8697 (mttt) cc_final: 0.8471 (mtpm) REVERT: A 440 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7004 (mp0) REVERT: A 481 LEU cc_start: 0.8779 (mt) cc_final: 0.8571 (mp) REVERT: A 543 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8100 (tm) REVERT: A 563 LYS cc_start: 0.8342 (mttt) cc_final: 0.7925 (mmtm) REVERT: B 174 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.8078 (m-80) REVERT: B 178 LEU cc_start: 0.7345 (mt) cc_final: 0.7136 (pt) REVERT: B 179 LYS cc_start: 0.7454 (tttt) cc_final: 0.7140 (tppt) REVERT: B 264 LYS cc_start: 0.7041 (mttt) cc_final: 0.6833 (mmmt) REVERT: B 284 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7602 (tpp) REVERT: B 338 ASP cc_start: 0.8512 (t0) cc_final: 0.8125 (t0) REVERT: B 366 GLN cc_start: 0.8900 (mt0) cc_final: 0.8300 (pt0) REVERT: B 504 GLN cc_start: 0.7621 (mt0) cc_final: 0.7419 (mt0) REVERT: B 563 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8350 (mtpp) outliers start: 18 outliers final: 7 residues processed: 126 average time/residue: 1.2235 time to fit residues: 161.7778 Evaluate side-chains 121 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 504 GLN 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 284 MET Chi-restraints excluded: chain B residue 327 ILE 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: 2.9990 chunk 44 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6587 Z= 0.231 Angle : 0.510 6.207 8915 Z= 0.263 Chirality : 0.039 0.140 1001 Planarity : 0.004 0.033 1131 Dihedral : 3.878 14.616 868 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.23 % Allowed : 16.32 % 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: 1.36 (0.30), residues: 775 helix: 2.36 (0.28), residues: 323 sheet: 0.00 (0.48), residues: 117 loop : -0.16 (0.32), residues: 335 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 0.011 0.001 PHE A 253 TYR 0.020 0.001 TYR A 494 ARG 0.007 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 128 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.8015 (mt) cc_final: 0.7594 (pp) REVERT: A 282 ARG cc_start: 0.7985 (mtp180) cc_final: 0.7269 (mtt90) REVERT: A 384 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8064 (mtm110) REVERT: A 395 LYS cc_start: 0.8705 (mttt) cc_final: 0.8477 (mtpm) REVERT: A 440 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7003 (mp0) REVERT: A 481 LEU cc_start: 0.8780 (mt) cc_final: 0.8571 (mp) REVERT: A 543 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8112 (tm) REVERT: A 563 LYS cc_start: 0.8334 (mttt) cc_final: 0.7903 (mmtm) REVERT: B 174 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.8124 (m-80) REVERT: B 178 LEU cc_start: 0.7464 (mt) cc_final: 0.7215 (pt) REVERT: B 179 LYS cc_start: 0.7501 (tttt) cc_final: 0.7174 (tppt) REVERT: B 264 LYS cc_start: 0.7044 (mttt) cc_final: 0.6843 (mmmt) REVERT: B 284 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7610 (tpp) REVERT: B 338 ASP cc_start: 0.8526 (t0) cc_final: 0.8119 (t0) REVERT: B 366 GLN cc_start: 0.8898 (mt0) cc_final: 0.8301 (pt0) REVERT: B 504 GLN cc_start: 0.7627 (mt0) cc_final: 0.7424 (mt0) REVERT: B 563 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8380 (mtpp) outliers start: 16 outliers final: 8 residues processed: 122 average time/residue: 1.2457 time to fit residues: 159.5824 Evaluate side-chains 120 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 504 GLN 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 284 MET Chi-restraints excluded: chain B residue 327 ILE 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: 5.9990 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6587 Z= 0.158 Angle : 0.491 5.802 8915 Z= 0.252 Chirality : 0.038 0.141 1001 Planarity : 0.003 0.032 1131 Dihedral : 3.714 14.530 868 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.95 % Allowed : 17.02 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.30), residues: 775 helix: 2.55 (0.28), residues: 323 sheet: -0.01 (0.47), residues: 118 loop : -0.04 (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 0.011 0.001 PHE A 253 TYR 0.018 0.001 TYR A 494 ARG 0.006 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 132 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 174 TYR cc_start: 0.8716 (m-80) cc_final: 0.8505 (m-80) REVERT: A 178 LEU cc_start: 0.7947 (mt) cc_final: 0.7469 (pp) REVERT: A 235 ASP cc_start: 0.7946 (m-30) cc_final: 0.7719 (m-30) REVERT: A 282 ARG cc_start: 0.7959 (mtp180) cc_final: 0.7248 (mtt90) REVERT: A 395 LYS cc_start: 0.8705 (mttt) cc_final: 0.8483 (mtpm) REVERT: A 440 GLU cc_start: 0.7816 (mt-10) cc_final: 0.6977 (mp0) REVERT: A 481 LEU cc_start: 0.8779 (mt) cc_final: 0.8576 (mp) REVERT: A 504 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: A 543 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8092 (tm) REVERT: A 563 LYS cc_start: 0.8346 (mttt) cc_final: 0.7915 (mmtm) REVERT: B 174 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: B 179 LYS cc_start: 0.7314 (tttt) cc_final: 0.7023 (tppt) REVERT: B 264 LYS cc_start: 0.7026 (mttt) cc_final: 0.6820 (mmmt) REVERT: B 284 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7629 (tpp) REVERT: B 338 ASP cc_start: 0.8516 (t0) cc_final: 0.8095 (t0) REVERT: B 366 GLN cc_start: 0.8883 (mt0) cc_final: 0.8458 (pt0) REVERT: B 504 GLN cc_start: 0.7600 (mt0) cc_final: 0.7392 (mt0) REVERT: B 563 LYS cc_start: 0.8648 (mtpt) cc_final: 0.8347 (mtpp) outliers start: 14 outliers final: 8 residues processed: 127 average time/residue: 1.1806 time to fit residues: 157.5418 Evaluate side-chains 122 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 504 GLN 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 284 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 379 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: 4.9990 chunk 73 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 0.0030 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 64 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.4948 ------------------------------------------------------------------------------- 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: 0.8304 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6587 Z= 0.148 Angle : 0.509 7.410 8915 Z= 0.256 Chirality : 0.039 0.141 1001 Planarity : 0.003 0.031 1131 Dihedral : 3.633 14.530 868 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.23 % Allowed : 17.02 % Favored : 80.75 % 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: 2.60 (0.28), residues: 323 sheet: 0.01 (0.46), residues: 124 loop : -0.02 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 505 HIS 0.001 0.000 HIS A 328 PHE 0.010 0.001 PHE A 253 TYR 0.020 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 128 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 0.723 Fit side-chains REVERT: A 178 LEU cc_start: 0.7840 (mt) cc_final: 0.7387 (pp) REVERT: A 235 ASP cc_start: 0.7916 (m-30) cc_final: 0.7692 (m-30) REVERT: A 261 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6581 (mm-40) REVERT: A 282 ARG cc_start: 0.7962 (mtp180) cc_final: 0.7237 (mtt90) REVERT: A 395 LYS cc_start: 0.8698 (mttt) cc_final: 0.8478 (mtpm) REVERT: A 440 GLU cc_start: 0.7841 (mt-10) cc_final: 0.6985 (mp0) REVERT: A 481 LEU cc_start: 0.8804 (mt) cc_final: 0.8599 (mp) REVERT: A 543 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8106 (tm) REVERT: A 563 LYS cc_start: 0.8337 (mttt) cc_final: 0.7908 (mmtm) REVERT: B 174 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: B 179 LYS cc_start: 0.7276 (tttt) cc_final: 0.7060 (tppt) REVERT: B 264 LYS cc_start: 0.7011 (mttt) cc_final: 0.6807 (mmmt) REVERT: B 284 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7619 (tpp) REVERT: B 338 ASP cc_start: 0.8486 (t0) cc_final: 0.8078 (t0) REVERT: B 366 GLN cc_start: 0.8903 (mt0) cc_final: 0.8308 (pt0) REVERT: B 504 GLN cc_start: 0.7584 (mt0) cc_final: 0.7372 (mt0) REVERT: B 563 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8346 (mtpp) REVERT: B 569 GLN cc_start: 0.7881 (mm110) cc_final: 0.7372 (tp40) REVERT: B 573 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.7092 (mp) outliers start: 16 outliers final: 9 residues processed: 121 average time/residue: 1.1760 time to fit residues: 149.5729 Evaluate side-chains 125 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 473 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 543 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 379 ASP Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 573 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 73 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- 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: 0.8316 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6587 Z= 0.187 Angle : 0.523 6.654 8915 Z= 0.265 Chirality : 0.039 0.140 1001 Planarity : 0.003 0.032 1131 Dihedral : 3.665 14.564 868 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.09 % Allowed : 16.74 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.59 (0.30), residues: 775 helix: 2.59 (0.28), residues: 323 sheet: 0.03 (0.46), residues: 124 loop : -0.04 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 505 HIS 0.002 0.001 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 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 127 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 0.747 Fit side-chains REVERT: A 178 LEU cc_start: 0.7912 (mt) cc_final: 0.7449 (pp) REVERT: A 235 ASP cc_start: 0.7932 (m-30) cc_final: 0.7711 (m-30) REVERT: A 261 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6560 (mm-40) REVERT: A 282 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7239 (mtt90) REVERT: A 376 GLU cc_start: 0.8166 (mp0) cc_final: 0.7808 (mp0) REVERT: A 395 LYS cc_start: 0.8705 (mttt) cc_final: 0.8484 (mtpm) REVERT: A 440 GLU cc_start: 0.7835 (mt-10) cc_final: 0.6973 (mp0) REVERT: A 543 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8121 (tm) REVERT: A 563 LYS cc_start: 0.8347 (mttt) cc_final: 0.7919 (mmtm) REVERT: B 174 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: B 179 LYS cc_start: 0.7327 (tttt) cc_final: 0.7072 (tppt) REVERT: B 213 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7543 (mtp180) REVERT: B 264 LYS cc_start: 0.7014 (mttt) cc_final: 0.6804 (mmmt) REVERT: B 284 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7641 (tpp) REVERT: B 338 ASP cc_start: 0.8499 (t0) cc_final: 0.8080 (t0) REVERT: B 366 GLN cc_start: 0.8910 (mt0) cc_final: 0.8309 (pt0) REVERT: B 504 GLN cc_start: 0.7597 (mt0) cc_final: 0.7386 (mt0) REVERT: B 563 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8354 (mtpp) REVERT: B 573 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7135 (mp) outliers start: 15 outliers final: 10 residues processed: 122 average time/residue: 1.2602 time to fit residues: 161.1644 Evaluate side-chains 125 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP 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 473 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 379 ASP Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 573 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.119464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.106146 restraints weight = 9722.668| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.28 r_work: 0.3279 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6587 Z= 0.178 Angle : 0.539 13.066 8915 Z= 0.269 Chirality : 0.039 0.140 1001 Planarity : 0.003 0.032 1131 Dihedral : 3.668 14.929 868 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.95 % Allowed : 17.02 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.30), residues: 775 helix: 2.61 (0.28), residues: 323 sheet: 0.02 (0.46), residues: 124 loop : -0.06 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 505 HIS 0.002 0.001 HIS A 328 PHE 0.010 0.001 PHE A 253 TYR 0.020 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: 3195.88 seconds wall clock time: 56 minutes 17.74 seconds (3377.74 seconds total)