Starting phenix.real_space_refine on Tue Feb 13 14:13:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/02_2024/6l48_0832_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/02_2024/6l48_0832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/02_2024/6l48_0832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/02_2024/6l48_0832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/02_2024/6l48_0832_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/02_2024/6l48_0832_updated.pdb" } resolution = 3.5 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4482 2.51 5 N 1000 2.21 5 O 1010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6528 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3236 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 17, 'TRANS': 379} Chain breaks: 2 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3236 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 17, 'TRANS': 379} Chain breaks: 2 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.50, per 1000 atoms: 0.69 Number of scatterers: 6528 At special positions: 0 Unit cell: (141.075, 74.195, 72.105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1010 8.00 N 1000 7.00 C 4482 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: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1532 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 0 sheets defined 73.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 136 through 163 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 181 through 212 Proline residue: A 199 - end of helix removed outlier: 4.113A pdb=" N THR A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 209 " --> pdb=" O HIS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 removed outlier: 3.865A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 Proline residue: A 239 - end of helix removed outlier: 3.702A pdb=" N VAL A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 283 removed outlier: 3.858A pdb=" N ILE A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 294 through 302 removed outlier: 4.182A pdb=" N PHE A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 343 Processing helix chain 'A' and resid 359 through 394 removed outlier: 4.234A pdb=" N ILE A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 413 through 419 removed outlier: 3.782A pdb=" N ARG A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 438 Processing helix chain 'A' and resid 445 through 468 Processing helix chain 'A' and resid 474 through 486 removed outlier: 3.672A pdb=" N PHE A 486 " --> pdb=" O PHE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 525 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 136 through 163 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 181 through 212 Proline residue: B 199 - end of helix removed outlier: 4.113A pdb=" N THR B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY B 209 " --> pdb=" O HIS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 231 removed outlier: 3.865A pdb=" N LEU B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 246 Proline residue: B 239 - end of helix removed outlier: 3.701A pdb=" N VAL B 243 " --> pdb=" O PRO B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 283 removed outlier: 3.858A pdb=" N ILE B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 294 through 302 removed outlier: 4.182A pdb=" N PHE B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 343 Processing helix chain 'B' and resid 359 through 394 removed outlier: 4.234A pdb=" N ILE B 370 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU B 371 " --> pdb=" O PHE B 367 " (cutoff:3.500A) Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 413 through 419 removed outlier: 3.781A pdb=" N ARG B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 438 Processing helix chain 'B' and resid 445 through 468 Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.672A pdb=" N PHE B 486 " --> pdb=" O PHE B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 525 418 hydrogen bonds defined for protein. 1254 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: 1.66 Time building geometry restraints manager: 2.74 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: 1831 1.34 - 1.46: 2056 1.46 - 1.58: 2835 1.58 - 1.70: 0 1.70 - 1.81: 58 Bond restraints: 6780 Sorted by residual: bond pdb=" CA ARG B 309 " pdb=" C ARG B 309 " ideal model delta sigma weight residual 1.523 1.551 -0.027 1.30e-02 5.92e+03 4.39e+00 bond pdb=" CA ARG A 309 " pdb=" C ARG A 309 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.30e-02 5.92e+03 4.38e+00 bond pdb=" C13 CLR B2001 " pdb=" C14 CLR B2001 " ideal model delta sigma weight residual 1.537 1.509 0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C13 CLR A2001 " pdb=" C14 CLR A2001 " ideal model delta sigma weight residual 1.537 1.510 0.027 2.00e-02 2.50e+03 1.87e+00 bond pdb=" N ASP A 310 " pdb=" CA ASP A 310 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.64e+00 ... (remaining 6775 not shown) Histogram of bond angle deviations from ideal: 100.87 - 107.50: 294 107.50 - 114.12: 3672 114.12 - 120.75: 3297 120.75 - 127.38: 1911 127.38 - 134.01: 98 Bond angle restraints: 9272 Sorted by residual: angle pdb=" N ARG B 309 " pdb=" CA ARG B 309 " pdb=" C ARG B 309 " ideal model delta sigma weight residual 111.28 104.58 6.70 1.09e+00 8.42e-01 3.78e+01 angle pdb=" N ARG A 309 " pdb=" CA ARG A 309 " pdb=" C ARG A 309 " ideal model delta sigma weight residual 111.28 104.59 6.69 1.09e+00 8.42e-01 3.76e+01 angle pdb=" C TRP A 388 " pdb=" N LEU A 389 " pdb=" CA LEU A 389 " ideal model delta sigma weight residual 122.38 113.90 8.48 1.81e+00 3.05e-01 2.19e+01 angle pdb=" C TRP B 388 " pdb=" N LEU B 389 " pdb=" CA LEU B 389 " ideal model delta sigma weight residual 122.38 113.92 8.46 1.81e+00 3.05e-01 2.19e+01 angle pdb=" N ASP A 310 " pdb=" CA ASP A 310 " pdb=" C ASP A 310 " ideal model delta sigma weight residual 110.80 119.11 -8.31 2.13e+00 2.20e-01 1.52e+01 ... (remaining 9267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.42: 3462 14.42 - 28.84: 297 28.84 - 43.26: 85 43.26 - 57.67: 10 57.67 - 72.09: 2 Dihedral angle restraints: 3856 sinusoidal: 1482 harmonic: 2374 Sorted by residual: dihedral pdb=" N ASP A 310 " pdb=" C ASP A 310 " pdb=" CA ASP A 310 " pdb=" CB ASP A 310 " ideal model delta harmonic sigma weight residual 122.80 134.29 -11.49 0 2.50e+00 1.60e-01 2.11e+01 dihedral pdb=" N ASP B 310 " pdb=" C ASP B 310 " pdb=" CA ASP B 310 " pdb=" CB ASP B 310 " ideal model delta harmonic sigma weight residual 122.80 134.29 -11.49 0 2.50e+00 1.60e-01 2.11e+01 dihedral pdb=" CA GLN A 354 " pdb=" C GLN A 354 " pdb=" N GLU A 355 " pdb=" CA GLU A 355 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 3853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 988 0.100 - 0.201: 30 0.201 - 0.301: 2 0.301 - 0.401: 0 0.401 - 0.502: 2 Chirality restraints: 1022 Sorted by residual: chirality pdb=" CA ASP A 310 " pdb=" N ASP A 310 " pdb=" C ASP A 310 " pdb=" CB ASP A 310 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.29e+00 chirality pdb=" CA ASP B 310 " pdb=" N ASP B 310 " pdb=" C ASP B 310 " pdb=" CB ASP B 310 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.28e+00 chirality pdb=" CA ARG B 309 " pdb=" N ARG B 309 " pdb=" C ARG B 309 " pdb=" CB ARG B 309 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1019 not shown) Planarity restraints: 1100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 308 " -0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C TYR B 308 " 0.069 2.00e-02 2.50e+03 pdb=" O TYR B 308 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG B 309 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 308 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C TYR A 308 " -0.068 2.00e-02 2.50e+03 pdb=" O TYR A 308 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG A 309 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 389 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C LEU A 389 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU A 389 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN A 390 " 0.017 2.00e-02 2.50e+03 ... (remaining 1097 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 852 2.75 - 3.29: 6827 3.29 - 3.83: 11259 3.83 - 4.36: 12462 4.36 - 4.90: 21552 Nonbonded interactions: 52952 Sorted by model distance: nonbonded pdb=" OD2 ASP B 130 " pdb=" OH TYR B 322 " model vdw 2.217 2.440 nonbonded pdb=" OD2 ASP A 130 " pdb=" OH TYR A 322 " model vdw 2.218 2.440 nonbonded pdb=" OH TYR B 299 " pdb=" O LEU B 396 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR A 299 " pdb=" O LEU A 396 " model vdw 2.283 2.440 nonbonded pdb=" O PHE A 237 " pdb=" N TYR A 241 " model vdw 2.284 2.520 ... (remaining 52947 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.980 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.840 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 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 0.035 6780 Z= 0.209 Angle : 0.762 9.490 9272 Z= 0.404 Chirality : 0.050 0.502 1022 Planarity : 0.006 0.040 1100 Dihedral : 12.004 72.093 2324 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.45 % Allowed : 7.34 % Favored : 90.21 % Cbeta Deviations : 0.26 % 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: -3.38 (0.26), residues: 782 helix: -1.58 (0.18), residues: 600 sheet: None (None), residues: 0 loop : -4.04 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 504 HIS 0.008 0.001 HIS A 425 PHE 0.015 0.001 PHE A 331 TYR 0.013 0.001 TYR B 433 ARG 0.003 0.000 ARG B 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 217 time to evaluate : 0.714 Fit side-chains REVERT: A 125 ARG cc_start: 0.7028 (pmt170) cc_final: 0.6720 (ptt-90) REVERT: A 151 LEU cc_start: 0.8834 (tt) cc_final: 0.8447 (mt) REVERT: A 205 HIS cc_start: 0.8220 (t70) cc_final: 0.7766 (t-170) REVERT: A 241 TYR cc_start: 0.7991 (t80) cc_final: 0.7616 (t80) REVERT: A 246 TYR cc_start: 0.8110 (m-10) cc_final: 0.7796 (m-80) REVERT: A 273 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7002 (tm-30) REVERT: A 293 THR cc_start: 0.8402 (p) cc_final: 0.7688 (t) REVERT: A 468 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7697 (mm) REVERT: A 511 ASN cc_start: 0.8285 (t0) cc_final: 0.7909 (m-40) REVERT: A 522 TRP cc_start: 0.7287 (t-100) cc_final: 0.5238 (t60) REVERT: B 125 ARG cc_start: 0.6984 (pmt170) cc_final: 0.6124 (ptt180) REVERT: B 241 TYR cc_start: 0.8001 (t80) cc_final: 0.7583 (t80) REVERT: B 246 TYR cc_start: 0.8094 (m-10) cc_final: 0.7787 (m-80) REVERT: B 273 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7178 (tm-30) REVERT: B 275 VAL cc_start: 0.8169 (t) cc_final: 0.7931 (t) REVERT: B 468 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7655 (mm) REVERT: B 522 TRP cc_start: 0.7409 (t-100) cc_final: 0.5196 (t60) outliers start: 16 outliers final: 6 residues processed: 233 average time/residue: 0.1880 time to fit residues: 56.6953 Evaluate side-chains 139 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 HIS A 274 ASN A 296 GLN B 204 GLN B 268 HIS B 274 ASN B 296 GLN B 511 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6780 Z= 0.225 Angle : 0.678 12.740 9272 Z= 0.340 Chirality : 0.041 0.162 1022 Planarity : 0.005 0.044 1100 Dihedral : 6.736 48.754 1016 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 6.12 % Allowed : 15.14 % Favored : 78.75 % 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: -1.91 (0.29), residues: 782 helix: -0.37 (0.21), residues: 590 sheet: None (None), residues: 0 loop : -3.95 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 188 HIS 0.006 0.001 HIS B 268 PHE 0.029 0.002 PHE A 398 TYR 0.011 0.001 TYR A 336 ARG 0.003 0.001 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 140 time to evaluate : 0.705 Fit side-chains REVERT: A 151 LEU cc_start: 0.8898 (tt) cc_final: 0.8456 (mt) REVERT: A 205 HIS cc_start: 0.8197 (t70) cc_final: 0.7868 (t-170) REVERT: A 212 LYS cc_start: 0.7861 (mmmt) cc_final: 0.7654 (mmmt) REVERT: A 241 TYR cc_start: 0.8073 (t80) cc_final: 0.7677 (t80) REVERT: A 291 ILE cc_start: 0.7816 (mp) cc_final: 0.7412 (tp) REVERT: A 522 TRP cc_start: 0.7345 (t-100) cc_final: 0.5109 (t60) REVERT: B 125 ARG cc_start: 0.6863 (pmt170) cc_final: 0.6105 (ptt180) REVERT: B 129 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8258 (mt) REVERT: B 241 TYR cc_start: 0.8052 (t80) cc_final: 0.7679 (t80) REVERT: B 273 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7434 (mm-30) REVERT: B 291 ILE cc_start: 0.8065 (mp) cc_final: 0.7762 (tp) REVERT: B 522 TRP cc_start: 0.7483 (t-100) cc_final: 0.5295 (t60) outliers start: 40 outliers final: 30 residues processed: 171 average time/residue: 0.1650 time to fit residues: 38.0966 Evaluate side-chains 156 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 474 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 ASN B 511 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6780 Z= 0.195 Angle : 0.650 12.312 9272 Z= 0.316 Chirality : 0.040 0.148 1022 Planarity : 0.005 0.058 1100 Dihedral : 6.221 55.200 1012 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 6.42 % Allowed : 16.82 % Favored : 76.76 % 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 (0.30), residues: 782 helix: 0.12 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -3.69 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 188 HIS 0.005 0.001 HIS B 425 PHE 0.017 0.001 PHE B 398 TYR 0.014 0.001 TYR B 433 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 142 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8132 (mt) REVERT: A 151 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8452 (mt) REVERT: A 241 TYR cc_start: 0.8061 (t80) cc_final: 0.7678 (t80) REVERT: A 476 PHE cc_start: 0.8088 (t80) cc_final: 0.7854 (t80) REVERT: A 478 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6701 (tm) REVERT: A 522 TRP cc_start: 0.7405 (t-100) cc_final: 0.5115 (t60) REVERT: B 125 ARG cc_start: 0.6868 (pmt170) cc_final: 0.6142 (ptt180) REVERT: B 129 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8135 (mt) REVERT: B 241 TYR cc_start: 0.8059 (t80) cc_final: 0.7696 (t80) REVERT: B 273 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7229 (mm-30) REVERT: B 291 ILE cc_start: 0.8026 (mp) cc_final: 0.7620 (tp) REVERT: B 522 TRP cc_start: 0.7599 (t-100) cc_final: 0.5115 (t60) outliers start: 42 outliers final: 28 residues processed: 170 average time/residue: 0.1614 time to fit residues: 37.2656 Evaluate side-chains 161 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 474 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 274 ASN A 511 ASN B 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6780 Z= 0.187 Angle : 0.645 12.211 9272 Z= 0.311 Chirality : 0.040 0.143 1022 Planarity : 0.005 0.046 1100 Dihedral : 5.838 50.739 1012 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.12 % Allowed : 18.50 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.31), residues: 782 helix: 0.34 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -3.41 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.007 0.001 HIS B 205 PHE 0.019 0.001 PHE B 481 TYR 0.016 0.001 TYR B 322 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 140 time to evaluate : 0.763 Fit side-chains REVERT: A 125 ARG cc_start: 0.6546 (ptt-90) cc_final: 0.5533 (ptt180) REVERT: A 151 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8469 (mt) REVERT: A 241 TYR cc_start: 0.8079 (t80) cc_final: 0.7687 (t80) REVERT: A 482 PHE cc_start: 0.6779 (m-80) cc_final: 0.6538 (m-80) REVERT: A 522 TRP cc_start: 0.7373 (t-100) cc_final: 0.5052 (t60) REVERT: B 125 ARG cc_start: 0.6769 (pmt170) cc_final: 0.5973 (ptt180) REVERT: B 129 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8075 (mt) REVERT: B 241 TYR cc_start: 0.8082 (t80) cc_final: 0.7703 (t80) REVERT: B 291 ILE cc_start: 0.8039 (mp) cc_final: 0.7619 (tp) REVERT: B 406 ASP cc_start: 0.7646 (p0) cc_final: 0.7377 (p0) REVERT: B 522 TRP cc_start: 0.7679 (t-100) cc_final: 0.5171 (t60) outliers start: 40 outliers final: 31 residues processed: 164 average time/residue: 0.1506 time to fit residues: 33.9701 Evaluate side-chains 165 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 474 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 274 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6780 Z= 0.202 Angle : 0.655 12.579 9272 Z= 0.315 Chirality : 0.041 0.144 1022 Planarity : 0.005 0.045 1100 Dihedral : 5.609 48.822 1012 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.81 % Allowed : 20.95 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.31), residues: 782 helix: 0.39 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -3.27 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 188 HIS 0.005 0.001 HIS A 425 PHE 0.025 0.001 PHE A 481 TYR 0.021 0.001 TYR A 210 ARG 0.006 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 138 time to evaluate : 0.695 Fit side-chains REVERT: A 125 ARG cc_start: 0.6494 (ptt-90) cc_final: 0.5451 (ptt180) REVERT: A 151 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8471 (mt) REVERT: A 522 TRP cc_start: 0.7410 (t-100) cc_final: 0.5050 (t60) REVERT: B 125 ARG cc_start: 0.6640 (pmt170) cc_final: 0.5729 (ptt180) REVERT: B 129 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8041 (mt) REVERT: B 161 TYR cc_start: 0.7315 (t80) cc_final: 0.7003 (t80) REVERT: B 291 ILE cc_start: 0.7997 (mp) cc_final: 0.7588 (tp) REVERT: B 406 ASP cc_start: 0.7669 (p0) cc_final: 0.7370 (p0) REVERT: B 522 TRP cc_start: 0.7721 (t-100) cc_final: 0.5148 (t60) outliers start: 38 outliers final: 27 residues processed: 167 average time/residue: 0.1405 time to fit residues: 32.9340 Evaluate side-chains 157 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 474 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6780 Z= 0.283 Angle : 0.712 12.083 9272 Z= 0.346 Chirality : 0.043 0.169 1022 Planarity : 0.005 0.048 1100 Dihedral : 5.887 44.030 1011 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 5.96 % Allowed : 22.32 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.30), residues: 782 helix: 0.22 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -3.19 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 188 HIS 0.007 0.001 HIS B 425 PHE 0.028 0.002 PHE A 481 TYR 0.024 0.002 TYR A 430 ARG 0.007 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 0.706 Fit side-chains REVERT: A 151 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8526 (mt) REVERT: A 241 TYR cc_start: 0.8188 (t80) cc_final: 0.7912 (t80) REVERT: A 291 ILE cc_start: 0.7935 (mp) cc_final: 0.7556 (tp) REVERT: A 522 TRP cc_start: 0.7464 (t-100) cc_final: 0.5124 (t60) REVERT: B 125 ARG cc_start: 0.6748 (pmt170) cc_final: 0.5822 (ptt180) REVERT: B 291 ILE cc_start: 0.8109 (mp) cc_final: 0.7699 (tp) REVERT: B 406 ASP cc_start: 0.7752 (p0) cc_final: 0.7493 (p0) REVERT: B 522 TRP cc_start: 0.7747 (t-100) cc_final: 0.5311 (t60) outliers start: 39 outliers final: 33 residues processed: 153 average time/residue: 0.1525 time to fit residues: 32.4043 Evaluate side-chains 155 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 474 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6780 Z= 0.282 Angle : 0.704 12.356 9272 Z= 0.344 Chirality : 0.043 0.165 1022 Planarity : 0.005 0.048 1100 Dihedral : 5.856 44.605 1011 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 6.88 % Allowed : 21.87 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.30), residues: 782 helix: 0.24 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -3.17 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 188 HIS 0.007 0.001 HIS B 425 PHE 0.033 0.002 PHE B 481 TYR 0.019 0.002 TYR A 430 ARG 0.006 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 119 time to evaluate : 0.719 Fit side-chains REVERT: A 151 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8531 (mt) REVERT: A 241 TYR cc_start: 0.8223 (t80) cc_final: 0.7984 (t80) REVERT: A 265 MET cc_start: 0.8702 (mtp) cc_final: 0.8492 (mtp) REVERT: A 390 ASN cc_start: 0.7547 (OUTLIER) cc_final: 0.7322 (t0) REVERT: A 522 TRP cc_start: 0.7464 (t-100) cc_final: 0.5121 (t60) REVERT: B 125 ARG cc_start: 0.6757 (pmt170) cc_final: 0.5867 (ptt180) REVERT: B 129 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8088 (mt) REVERT: B 406 ASP cc_start: 0.7806 (p0) cc_final: 0.7563 (p0) REVERT: B 522 TRP cc_start: 0.7788 (t-100) cc_final: 0.5317 (t60) outliers start: 45 outliers final: 38 residues processed: 150 average time/residue: 0.1506 time to fit residues: 31.6426 Evaluate side-chains 158 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 117 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 474 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 409 ASN B 390 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6780 Z= 0.204 Angle : 0.662 12.365 9272 Z= 0.317 Chirality : 0.041 0.145 1022 Planarity : 0.005 0.045 1100 Dihedral : 5.465 47.522 1011 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.20 % Allowed : 23.24 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.31), residues: 782 helix: 0.46 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -2.87 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 427 HIS 0.005 0.001 HIS B 425 PHE 0.025 0.001 PHE B 481 TYR 0.013 0.001 TYR A 308 ARG 0.004 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 0.707 Fit side-chains REVERT: A 151 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8480 (mt) REVERT: A 487 ASN cc_start: 0.7345 (t0) cc_final: 0.6918 (t0) REVERT: A 522 TRP cc_start: 0.7409 (t-100) cc_final: 0.5053 (t60) REVERT: B 125 ARG cc_start: 0.6696 (pmt170) cc_final: 0.5840 (ptt180) REVERT: B 129 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8005 (mt) REVERT: B 131 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7553 (pp20) REVERT: B 265 MET cc_start: 0.8723 (mtp) cc_final: 0.8462 (mtp) REVERT: B 406 ASP cc_start: 0.7729 (p0) cc_final: 0.7515 (p0) REVERT: B 522 TRP cc_start: 0.7823 (t-100) cc_final: 0.5328 (t60) outliers start: 34 outliers final: 30 residues processed: 154 average time/residue: 0.1505 time to fit residues: 32.1549 Evaluate side-chains 157 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 474 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 21 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6780 Z= 0.179 Angle : 0.648 12.782 9272 Z= 0.310 Chirality : 0.040 0.132 1022 Planarity : 0.005 0.044 1100 Dihedral : 5.284 49.987 1010 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.89 % Allowed : 23.85 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.31), residues: 782 helix: 0.54 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -2.78 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 427 HIS 0.004 0.001 HIS B 425 PHE 0.036 0.001 PHE B 481 TYR 0.014 0.001 TYR A 210 ARG 0.003 0.000 ARG B 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 0.784 Fit side-chains REVERT: A 151 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8478 (mt) REVERT: A 212 LYS cc_start: 0.6939 (mmmt) cc_final: 0.6696 (mttt) REVERT: A 241 TYR cc_start: 0.8056 (t80) cc_final: 0.7821 (t80) REVERT: A 522 TRP cc_start: 0.7393 (t-100) cc_final: 0.5092 (t60) REVERT: B 125 ARG cc_start: 0.6599 (pmt170) cc_final: 0.5720 (ptt180) REVERT: B 129 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.7902 (mt) REVERT: B 265 MET cc_start: 0.8602 (mtp) cc_final: 0.8331 (mtp) REVERT: B 406 ASP cc_start: 0.7679 (p0) cc_final: 0.7411 (p0) REVERT: B 522 TRP cc_start: 0.7780 (t-100) cc_final: 0.5272 (t60) outliers start: 32 outliers final: 28 residues processed: 160 average time/residue: 0.1507 time to fit residues: 33.6510 Evaluate side-chains 160 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.8980 chunk 71 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 9 optimal weight: 8.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6780 Z= 0.187 Angle : 0.656 12.602 9272 Z= 0.313 Chirality : 0.040 0.137 1022 Planarity : 0.005 0.045 1100 Dihedral : 5.263 50.470 1010 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.89 % Allowed : 24.31 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.31), residues: 782 helix: 0.57 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.64 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 427 HIS 0.004 0.001 HIS B 425 PHE 0.022 0.001 PHE B 398 TYR 0.013 0.001 TYR A 210 ARG 0.004 0.000 ARG A 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 0.645 Fit side-chains REVERT: A 151 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8484 (mt) REVERT: A 413 TYR cc_start: 0.5604 (OUTLIER) cc_final: 0.5138 (t80) REVERT: A 522 TRP cc_start: 0.7378 (t-100) cc_final: 0.5053 (t60) REVERT: B 125 ARG cc_start: 0.6601 (pmt170) cc_final: 0.5702 (ptt180) REVERT: B 129 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.7877 (mt) REVERT: B 406 ASP cc_start: 0.7669 (p0) cc_final: 0.7397 (p0) REVERT: B 522 TRP cc_start: 0.7744 (t-100) cc_final: 0.5214 (t60) outliers start: 32 outliers final: 29 residues processed: 151 average time/residue: 0.1470 time to fit residues: 31.0654 Evaluate side-chains 157 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.0670 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.215122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.193100 restraints weight = 7568.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.196268 restraints weight = 4856.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.198429 restraints weight = 3636.789| |-----------------------------------------------------------------------------| r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6780 Z= 0.200 Angle : 0.661 12.544 9272 Z= 0.317 Chirality : 0.041 0.141 1022 Planarity : 0.005 0.045 1100 Dihedral : 5.290 50.239 1010 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.20 % Allowed : 24.16 % Favored : 70.64 % 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: -0.20 (0.31), residues: 782 helix: 0.66 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -2.68 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 427 HIS 0.009 0.001 HIS A 205 PHE 0.023 0.001 PHE A 398 TYR 0.016 0.001 TYR A 430 ARG 0.005 0.000 ARG A 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1539.81 seconds wall clock time: 28 minutes 51.61 seconds (1731.61 seconds total)