Starting phenix.real_space_refine on Tue May 7 01:53:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyf_42804/05_2024/8uyf_42804_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyf_42804/05_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_42804/05_2024/8uyf_42804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyf_42804/05_2024/8uyf_42804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyf_42804/05_2024/8uyf_42804_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyf_42804/05_2024/8uyf_42804_updated.pdb" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 4.13, per 1000 atoms: 0.64 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: 2.38 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... running ksdssp... Secondary structure from input PDB file: 28 helices and 6 sheets defined 37.5% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 121 through 136 Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.940A pdb=" N VAL A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Proline residue: A 217 - end of helix Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'A' and resid 308 through 327 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 389 through 392 No H-bonds generated for 'chain 'A' and resid 389 through 392' Processing helix chain 'A' and resid 407 through 419 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 452 through 461 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 499 through 514 Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 558 through 573 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 136 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 204 through 214 Processing helix chain 'B' and resid 232 through 235 removed outlier: 4.416A pdb=" N ASP B 235 " --> pdb=" O ASN B 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 308 through 327 Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 389 through 392 No H-bonds generated for 'chain 'B' and resid 389 through 392' Processing helix chain 'B' and resid 407 through 419 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 440 through 442 No H-bonds generated for 'chain 'B' and resid 440 through 442' Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 487 through 490 No H-bonds generated for 'chain 'B' and resid 487 through 490' Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 558 through 573 removed outlier: 3.630A pdb=" N HIS B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 171 through 176 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) Processing sheet with id= B, first strand: chain 'A' and resid 340 through 343 Processing sheet with id= C, first strand: chain 'A' and resid 370 through 372 Processing sheet with id= D, first strand: chain 'B' and resid 171 through 176 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= E, first strand: chain 'B' and resid 340 through 343 Processing sheet with id= F, first strand: chain 'B' and resid 370 through 372 232 hydrogen bonds defined for protein. 684 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: 1.64 Time building geometry restraints manager: 2.58 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: 1901 2.82 - 3.34: 5959 3.34 - 3.86: 10471 3.86 - 4.38: 13092 4.38 - 4.90: 21566 Nonbonded interactions: 52989 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 52984 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: 1.030 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: 3.710 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.330 Find NCS groups from input model: 0.390 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:15.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.830 ------------------------------------------------------------------------------- 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= 0.224 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 : 0.679 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: 1.2914 time to fit residues: 241.4383 Evaluate side-chains 134 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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: 4.9990 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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: 0.8350 moved from start: 0.1711 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= 0.261 Angle : 0.526 5.076 8915 Z= 0.275 Chirality : 0.040 0.139 1001 Planarity : 0.004 0.036 1131 Dihedral : 4.126 38.590 870 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.07 % Allowed : 11.72 % 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: 1.32 (0.30), residues: 775 helix: 2.22 (0.29), residues: 316 sheet: -0.18 (0.48), residues: 118 loop : 0.06 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 505 HIS 0.004 0.001 HIS A 328 PHE 0.012 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 161 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 0.813 Fit side-chains REVERT: A 178 LEU cc_start: 0.8177 (mt) cc_final: 0.7717 (pp) REVERT: A 215 THR cc_start: 0.9299 (p) cc_final: 0.9065 (p) REVERT: A 237 LYS cc_start: 0.8573 (ptpt) cc_final: 0.8229 (ptpp) REVERT: A 282 ARG cc_start: 0.7942 (mtp180) cc_final: 0.7376 (mpt90) REVERT: A 384 ARG cc_start: 0.8517 (mtp-110) cc_final: 0.7899 (mtm110) REVERT: A 395 LYS cc_start: 0.8694 (mttt) cc_final: 0.8450 (mtpp) REVERT: A 563 LYS cc_start: 0.8304 (mttt) cc_final: 0.7933 (mptt) REVERT: B 121 ASP cc_start: 0.5910 (OUTLIER) cc_final: 0.5548 (OUTLIER) REVERT: B 178 LEU cc_start: 0.7417 (mt) cc_final: 0.7171 (pt) REVERT: B 179 LYS cc_start: 0.7725 (tttt) cc_final: 0.7381 (tppt) REVERT: B 284 MET cc_start: 0.8324 (tpp) cc_final: 0.7671 (tpp) REVERT: B 338 ASP cc_start: 0.8473 (t0) cc_final: 0.8159 (t0) REVERT: B 366 GLN cc_start: 0.8816 (mt0) cc_final: 0.8309 (pt0) REVERT: B 563 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8352 (mtpp) outliers start: 22 outliers final: 13 residues processed: 152 average time/residue: 1.3094 time to fit residues: 208.6419 Evaluate side-chains 135 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 267 TYR 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 24 optimal weight: 0.0870 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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: 0.8317 moved from start: 0.2042 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= 0.139 Angle : 0.464 5.341 8915 Z= 0.239 Chirality : 0.038 0.140 1001 Planarity : 0.003 0.034 1131 Dihedral : 3.889 39.366 870 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.09 % Allowed : 14.64 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.30), residues: 775 helix: 2.40 (0.29), residues: 319 sheet: -0.08 (0.47), residues: 117 loop : 0.18 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.001 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 141 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 0.831 Fit side-chains REVERT: A 178 LEU cc_start: 0.8079 (mt) cc_final: 0.7583 (pp) REVERT: A 195 MET cc_start: 0.8903 (mtp) cc_final: 0.8588 (mtp) REVERT: A 215 THR cc_start: 0.9075 (p) cc_final: 0.8828 (p) REVERT: A 237 LYS cc_start: 0.8558 (ptpt) cc_final: 0.8231 (ptpp) REVERT: A 282 ARG cc_start: 0.7926 (mtp180) cc_final: 0.7363 (mpt90) REVERT: A 384 ARG cc_start: 0.8504 (mtp-110) cc_final: 0.7930 (mtm110) REVERT: A 395 LYS cc_start: 0.8634 (mttt) cc_final: 0.8400 (mtpp) REVERT: A 440 GLU cc_start: 0.7830 (mt-10) cc_final: 0.6976 (mp0) REVERT: A 566 LYS cc_start: 0.7929 (mmmt) cc_final: 0.7573 (mmmt) REVERT: A 570 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6844 (mp0) REVERT: B 133 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7593 (mt-10) REVERT: B 178 LEU cc_start: 0.7384 (mt) cc_final: 0.7133 (pt) REVERT: B 179 LYS cc_start: 0.7457 (tttt) cc_final: 0.7207 (tppt) REVERT: B 284 MET cc_start: 0.8286 (tpp) cc_final: 0.7625 (tpp) REVERT: B 338 ASP cc_start: 0.8455 (t0) cc_final: 0.8115 (t0) REVERT: B 366 GLN cc_start: 0.8786 (mt0) cc_final: 0.8424 (pt0) outliers start: 15 outliers final: 9 residues processed: 135 average time/residue: 1.3264 time to fit residues: 187.7567 Evaluate side-chains 127 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 267 TYR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 504 GLN 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: 2.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 64 optimal weight: 0.0370 overall best weight: 1.5264 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6587 Z= 0.227 Angle : 0.489 5.870 8915 Z= 0.251 Chirality : 0.039 0.142 1001 Planarity : 0.004 0.034 1131 Dihedral : 3.788 15.981 868 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.63 % Allowed : 14.23 % Favored : 82.15 % 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: 2.33 (0.29), residues: 320 sheet: -0.03 (0.48), residues: 117 loop : 0.02 (0.32), residues: 338 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 0.012 0.001 PHE A 253 TYR 0.018 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 144 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 0.837 Fit side-chains REVERT: A 178 LEU cc_start: 0.8096 (mt) cc_final: 0.7635 (pp) REVERT: A 215 THR cc_start: 0.9186 (p) cc_final: 0.8935 (p) REVERT: A 237 LYS cc_start: 0.8563 (ptpt) cc_final: 0.8217 (ptpp) REVERT: A 282 ARG cc_start: 0.7963 (mtp180) cc_final: 0.7402 (mpt90) REVERT: A 376 GLU cc_start: 0.8319 (mp0) cc_final: 0.8059 (mp0) REVERT: A 384 ARG cc_start: 0.8509 (mtp-110) cc_final: 0.7911 (mtm110) REVERT: A 395 LYS cc_start: 0.8676 (mttt) cc_final: 0.8450 (mtpm) REVERT: A 440 GLU cc_start: 0.7860 (mt-10) cc_final: 0.6984 (mp0) REVERT: A 481 LEU cc_start: 0.8796 (mt) cc_final: 0.8592 (mp) REVERT: A 543 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8210 (tm) REVERT: A 563 LYS cc_start: 0.8334 (mttt) cc_final: 0.7920 (mmtm) REVERT: A 570 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6739 (mp0) REVERT: B 133 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7572 (mt-10) REVERT: B 178 LEU cc_start: 0.7330 (mt) cc_final: 0.7125 (pt) REVERT: B 179 LYS cc_start: 0.7516 (tttt) cc_final: 0.7279 (tppt) REVERT: B 338 ASP cc_start: 0.8496 (t0) cc_final: 0.8115 (t0) REVERT: B 366 GLN cc_start: 0.8845 (mt0) cc_final: 0.8285 (pt0) REVERT: B 563 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8361 (mtpp) outliers start: 26 outliers final: 19 residues processed: 136 average time/residue: 1.2099 time to fit residues: 173.2278 Evaluate side-chains 136 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 267 TYR 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 495 THR 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 161 LEU Chi-restraints excluded: chain B residue 235 ASP 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 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: 0.0000 chunk 1 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 0 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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: 0.8324 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6587 Z= 0.150 Angle : 0.459 5.589 8915 Z= 0.236 Chirality : 0.038 0.142 1001 Planarity : 0.003 0.031 1131 Dihedral : 3.641 15.973 868 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.07 % Allowed : 14.78 % Favored : 82.15 % 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: 1.57 (0.30), residues: 775 helix: 2.47 (0.29), residues: 320 sheet: -0.06 (0.48), residues: 117 loop : 0.12 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 505 HIS 0.002 0.001 HIS B 559 PHE 0.014 0.001 PHE B 236 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 140 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 0.773 Fit side-chains REVERT: A 178 LEU cc_start: 0.8054 (mt) cc_final: 0.7535 (pp) REVERT: A 195 MET cc_start: 0.8881 (mtp) cc_final: 0.8554 (mtp) REVERT: A 215 THR cc_start: 0.9082 (p) cc_final: 0.8833 (p) REVERT: A 237 LYS cc_start: 0.8565 (ptpt) cc_final: 0.8226 (ptpp) REVERT: A 261 GLN cc_start: 0.7106 (OUTLIER) cc_final: 0.6575 (mm-40) REVERT: A 282 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7363 (mpt90) REVERT: A 376 GLU cc_start: 0.8316 (mp0) cc_final: 0.8091 (mp0) REVERT: A 384 ARG cc_start: 0.8496 (mtp-110) cc_final: 0.7914 (mtm110) REVERT: A 395 LYS cc_start: 0.8642 (mttt) cc_final: 0.8406 (mtpm) REVERT: A 440 GLU cc_start: 0.7851 (mt-10) cc_final: 0.6970 (mp0) REVERT: A 543 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8201 (tm) REVERT: A 563 LYS cc_start: 0.8310 (mttt) cc_final: 0.7883 (mmtm) REVERT: A 570 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6756 (mp0) REVERT: B 121 ASP cc_start: 0.5824 (OUTLIER) cc_final: 0.5346 (t0) REVERT: B 133 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7540 (mt-10) REVERT: B 178 LEU cc_start: 0.7469 (mt) cc_final: 0.7210 (pt) REVERT: B 179 LYS cc_start: 0.7404 (tttt) cc_final: 0.7178 (tppt) REVERT: B 284 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7590 (tpp) REVERT: B 338 ASP cc_start: 0.8492 (t0) cc_final: 0.8110 (t0) REVERT: B 366 GLN cc_start: 0.8835 (mt0) cc_final: 0.8457 (pt0) REVERT: B 563 LYS cc_start: 0.8637 (mtpt) cc_final: 0.8332 (mtpp) outliers start: 22 outliers final: 14 residues processed: 133 average time/residue: 1.3400 time to fit residues: 187.5750 Evaluate side-chains 132 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 261 GLN Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 423 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 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 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: 4.9990 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 0.0870 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.1960 ------------------------------------------------------------------------------- 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: 0.8332 moved from start: 0.2297 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= 0.190 Angle : 0.484 10.904 8915 Z= 0.243 Chirality : 0.039 0.141 1001 Planarity : 0.003 0.032 1131 Dihedral : 3.662 16.172 868 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.49 % Allowed : 15.20 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.54 (0.30), residues: 775 helix: 2.44 (0.29), residues: 320 sheet: -0.02 (0.48), residues: 117 loop : 0.08 (0.33), residues: 338 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 0.021 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 141 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 0.783 Fit side-chains REVERT: A 122 ASP cc_start: 0.6559 (OUTLIER) cc_final: 0.6356 (p0) REVERT: A 178 LEU cc_start: 0.8048 (mt) cc_final: 0.7557 (pp) REVERT: A 215 THR cc_start: 0.9101 (p) cc_final: 0.8851 (p) REVERT: A 237 LYS cc_start: 0.8578 (ptpt) cc_final: 0.8227 (ptpp) REVERT: A 282 ARG cc_start: 0.7962 (mtp180) cc_final: 0.7363 (mpt90) REVERT: A 376 GLU cc_start: 0.8290 (mp0) cc_final: 0.8082 (mp0) REVERT: A 384 ARG cc_start: 0.8502 (mtp-110) cc_final: 0.7941 (mtm110) REVERT: A 395 LYS cc_start: 0.8656 (mttt) cc_final: 0.8435 (mtpm) REVERT: A 440 GLU cc_start: 0.7868 (mt-10) cc_final: 0.6999 (mp0) REVERT: A 543 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8210 (tm) REVERT: A 563 LYS cc_start: 0.8329 (mttt) cc_final: 0.7914 (mmtm) REVERT: A 570 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6700 (mp0) REVERT: B 121 ASP cc_start: 0.5841 (OUTLIER) cc_final: 0.5356 (t0) REVERT: B 133 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7546 (mt-10) REVERT: B 178 LEU cc_start: 0.7502 (mt) cc_final: 0.7220 (pt) REVERT: B 179 LYS cc_start: 0.7393 (tttt) cc_final: 0.7102 (tppt) REVERT: B 284 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7589 (tpp) REVERT: B 338 ASP cc_start: 0.8498 (t0) cc_final: 0.8106 (t0) REVERT: B 366 GLN cc_start: 0.8879 (mt0) cc_final: 0.8300 (pt0) REVERT: B 563 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8357 (mtpp) outliers start: 25 outliers final: 15 residues processed: 133 average time/residue: 1.2294 time to fit residues: 171.6895 Evaluate side-chains 132 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 267 TYR Chi-restraints excluded: chain A residue 379 ASP 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 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 Chi-restraints excluded: chain B residue 515 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.0060 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 46 optimal weight: 4.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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: 0.8315 moved from start: 0.2378 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= 0.137 Angle : 0.470 9.452 8915 Z= 0.235 Chirality : 0.038 0.142 1001 Planarity : 0.003 0.031 1131 Dihedral : 3.545 16.058 868 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.65 % Allowed : 16.04 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.58 (0.29), residues: 320 sheet: -0.00 (0.48), residues: 117 loop : 0.15 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 505 HIS 0.002 0.001 HIS B 559 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 137 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.761 Fit side-chains REVERT: A 178 LEU cc_start: 0.8008 (mt) cc_final: 0.7481 (pp) REVERT: A 215 THR cc_start: 0.9007 (p) cc_final: 0.8745 (p) REVERT: A 282 ARG cc_start: 0.7956 (mtp180) cc_final: 0.7356 (mpt90) REVERT: A 384 ARG cc_start: 0.8489 (mtp-110) cc_final: 0.7937 (mtm110) REVERT: A 395 LYS cc_start: 0.8628 (mttt) cc_final: 0.8398 (mtpm) REVERT: A 440 GLU cc_start: 0.7845 (mt-10) cc_final: 0.6976 (mp0) REVERT: A 543 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8207 (tm) REVERT: A 563 LYS cc_start: 0.8297 (mttt) cc_final: 0.7862 (mmtm) REVERT: B 121 ASP cc_start: 0.5785 (OUTLIER) cc_final: 0.5305 (t0) REVERT: B 133 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7546 (mt-10) REVERT: B 179 LYS cc_start: 0.7297 (tttt) cc_final: 0.7074 (tppt) REVERT: B 284 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7550 (tpp) REVERT: B 338 ASP cc_start: 0.8503 (t0) cc_final: 0.8141 (t0) REVERT: B 366 GLN cc_start: 0.8852 (mt0) cc_final: 0.8272 (pt0) REVERT: B 563 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8311 (mtpp) outliers start: 19 outliers final: 13 residues processed: 131 average time/residue: 1.2415 time to fit residues: 170.8533 Evaluate side-chains 127 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS 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 407 SER Chi-restraints excluded: chain A residue 423 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 284 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.0980 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 229 ASN B 197 ASN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6587 Z= 0.187 Angle : 0.519 17.979 8915 Z= 0.252 Chirality : 0.039 0.171 1001 Planarity : 0.003 0.032 1131 Dihedral : 3.592 16.320 868 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.93 % Allowed : 17.15 % 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: 1.60 (0.30), residues: 775 helix: 2.52 (0.29), residues: 320 sheet: 0.04 (0.48), residues: 117 loop : 0.08 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 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 135 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 0.746 Fit side-chains REVERT: A 178 LEU cc_start: 0.8020 (mt) cc_final: 0.7520 (pp) REVERT: A 215 THR cc_start: 0.9057 (p) cc_final: 0.8799 (p) REVERT: A 235 ASP cc_start: 0.7891 (m-30) cc_final: 0.7667 (m-30) REVERT: A 237 LYS cc_start: 0.8575 (ptpt) cc_final: 0.8230 (ptpp) REVERT: A 282 ARG cc_start: 0.7966 (mtp180) cc_final: 0.7356 (mpt90) REVERT: A 376 GLU cc_start: 0.8226 (mp0) cc_final: 0.8023 (mp0) REVERT: A 384 ARG cc_start: 0.8498 (mtp-110) cc_final: 0.7939 (mtm110) REVERT: A 395 LYS cc_start: 0.8633 (mttt) cc_final: 0.8404 (mtpm) REVERT: A 440 GLU cc_start: 0.7848 (mt-10) cc_final: 0.6992 (mp0) REVERT: A 543 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8224 (tm) REVERT: A 563 LYS cc_start: 0.8312 (mttt) cc_final: 0.7898 (mmtm) REVERT: B 133 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7559 (mt-10) REVERT: B 179 LYS cc_start: 0.7365 (tttt) cc_final: 0.7156 (tppt) REVERT: B 284 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7554 (tpp) REVERT: B 338 ASP cc_start: 0.8502 (t0) cc_final: 0.8126 (t0) REVERT: B 366 GLN cc_start: 0.8873 (mt0) cc_final: 0.8329 (pt0) REVERT: B 563 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8354 (mtpp) outliers start: 21 outliers final: 14 residues processed: 127 average time/residue: 1.2033 time to fit residues: 160.5888 Evaluate side-chains 129 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 267 TYR 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 496 LEU 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 161 LEU Chi-restraints excluded: chain B residue 284 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 0.0570 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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: 0.8307 moved from start: 0.2519 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= 0.143 Angle : 0.500 15.786 8915 Z= 0.245 Chirality : 0.038 0.141 1001 Planarity : 0.003 0.031 1131 Dihedral : 3.455 16.200 868 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.09 % Allowed : 18.13 % 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: 1.75 (0.30), residues: 775 helix: 2.62 (0.29), residues: 320 sheet: 0.34 (0.49), residues: 112 loop : 0.08 (0.33), residues: 343 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 0.019 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 128 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 0.950 Fit side-chains REVERT: A 178 LEU cc_start: 0.7912 (mt) cc_final: 0.7401 (pp) REVERT: A 215 THR cc_start: 0.8930 (p) cc_final: 0.8665 (p) REVERT: A 282 ARG cc_start: 0.7974 (mtp180) cc_final: 0.7259 (mtt90) REVERT: A 384 ARG cc_start: 0.8485 (mtp-110) cc_final: 0.7926 (mtm110) REVERT: A 395 LYS cc_start: 0.8627 (mttt) cc_final: 0.8399 (mtpm) REVERT: A 440 GLU cc_start: 0.7824 (mt-10) cc_final: 0.6943 (mp0) REVERT: A 543 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8203 (tm) REVERT: A 563 LYS cc_start: 0.8286 (mttt) cc_final: 0.7855 (mmtm) REVERT: B 133 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7565 (mt-10) REVERT: B 179 LYS cc_start: 0.7237 (tttt) cc_final: 0.6997 (tppt) REVERT: B 284 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7549 (tpp) REVERT: B 338 ASP cc_start: 0.8474 (t0) cc_final: 0.8090 (t0) REVERT: B 366 GLN cc_start: 0.8868 (mt0) cc_final: 0.8475 (pt0) REVERT: B 480 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8380 (mm-40) outliers start: 15 outliers final: 9 residues processed: 124 average time/residue: 1.1881 time to fit residues: 155.0810 Evaluate side-chains 123 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 407 SER 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 284 MET 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=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: 5.9990 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 229 ASN ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 6587 Z= 0.377 Angle : 0.608 17.564 8915 Z= 0.301 Chirality : 0.042 0.148 1001 Planarity : 0.004 0.035 1131 Dihedral : 4.050 16.046 868 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.65 % Allowed : 17.85 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.29), residues: 775 helix: 2.19 (0.29), residues: 318 sheet: 0.04 (0.48), residues: 116 loop : -0.19 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 489 HIS 0.004 0.001 HIS A 328 PHE 0.016 0.001 PHE A 452 TYR 0.017 0.002 TYR A 482 ARG 0.007 0.001 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 135 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.903 Fit side-chains REVERT: A 178 LEU cc_start: 0.8167 (mt) cc_final: 0.7738 (pp) REVERT: A 215 THR cc_start: 0.9304 (p) cc_final: 0.9059 (p) REVERT: A 237 LYS cc_start: 0.8590 (ptpt) cc_final: 0.8225 (ptpp) REVERT: A 261 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6622 (mm-40) REVERT: A 282 ARG cc_start: 0.7965 (mtp180) cc_final: 0.7260 (mtt90) REVERT: A 384 ARG cc_start: 0.8509 (mtp-110) cc_final: 0.7888 (mtm110) REVERT: A 395 LYS cc_start: 0.8687 (mttt) cc_final: 0.8456 (mtpm) REVERT: A 440 GLU cc_start: 0.7887 (mt-10) cc_final: 0.6994 (mp0) REVERT: A 563 LYS cc_start: 0.8350 (mttt) cc_final: 0.7943 (mptt) REVERT: B 121 ASP cc_start: 0.6064 (OUTLIER) cc_final: 0.5575 (t0) REVERT: B 133 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7573 (mt-10) REVERT: B 179 LYS cc_start: 0.7615 (tttt) cc_final: 0.7303 (tttp) REVERT: B 338 ASP cc_start: 0.8546 (t0) cc_final: 0.8114 (t0) REVERT: B 377 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7253 (t70) REVERT: B 563 LYS cc_start: 0.8670 (mtpt) cc_final: 0.8395 (mtpp) outliers start: 19 outliers final: 11 residues processed: 129 average time/residue: 1.2615 time to fit residues: 171.3406 Evaluate side-chains 129 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS 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 423 ASP Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 377 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: 0.9990 chunk 9 optimal weight: 0.0070 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 366 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.105778 restraints weight = 9775.498| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.25 r_work: 0.3278 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2533 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= 0.152 Angle : 0.541 16.186 8915 Z= 0.262 Chirality : 0.039 0.142 1001 Planarity : 0.003 0.032 1131 Dihedral : 3.628 16.228 868 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.39 % Allowed : 18.97 % 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: 1.55 (0.30), residues: 775 helix: 2.48 (0.29), residues: 320 sheet: 0.07 (0.48), residues: 116 loop : 0.02 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 505 HIS 0.001 0.001 HIS B 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: 3280.48 seconds wall clock time: 59 minutes 20.16 seconds (3560.16 seconds total)