Starting phenix.real_space_refine on Tue Sep 24 02:16:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/09_2024/6l48_0832.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/09_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_0832/09_2024/6l48_0832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/09_2024/6l48_0832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/09_2024/6l48_0832.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l48_0832/09_2024/6l48_0832.cif" } 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. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6528 Number of models: 1 Model: "" Number of chains: 2 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: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 5.50, per 1000 atoms: 0.84 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 893.0 milliseconds 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... Secondary structure from input PDB file: 34 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 127 through 133 removed outlier: 3.552A pdb=" N GLU A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 165 Processing helix chain 'A' and resid 171 through 178 removed outlier: 3.625A pdb=" N SER A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 213 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 215 through 232 removed outlier: 4.116A pdb=" N ARG A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 247 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 249 through 284 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 293 through 301 Processing helix chain 'A' and resid 319 through 344 Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.521A pdb=" N PHE A 349 " --> pdb=" O CYS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'A' and resid 369 through 395 Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.782A pdb=" N ARG A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 439 Processing helix chain 'A' and resid 444 through 469 removed outlier: 4.030A pdb=" N ALA A 448 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 487 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 526 Processing helix chain 'B' and resid 127 through 133 removed outlier: 3.552A pdb=" N GLU B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 165 Processing helix chain 'B' and resid 171 through 178 removed outlier: 3.625A pdb=" N SER B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 213 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 215 through 232 removed outlier: 4.116A pdb=" N ARG B 219 " --> pdb=" O HIS B 215 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 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 249 through 284 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 293 through 301 Processing helix chain 'B' and resid 319 through 344 Processing helix chain 'B' and resid 345 through 350 removed outlier: 3.520A pdb=" N PHE B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'B' and resid 369 through 395 Processing helix chain 'B' and resid 412 through 418 removed outlier: 3.781A pdb=" N ARG B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 439 Processing helix chain 'B' and resid 444 through 469 removed outlier: 4.029A pdb=" N ALA B 448 " --> pdb=" O PHE B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 487 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 526 472 hydrogen bonds defined for protein. 1416 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: 1.86 Time building geometry restraints manager: 1.86 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: 0.00 - 1.90: 9011 1.90 - 3.80: 194 3.80 - 5.69: 47 5.69 - 7.59: 10 7.59 - 9.49: 10 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: 848 2.75 - 3.29: 6781 3.29 - 3.83: 11195 3.83 - 4.36: 12372 4.36 - 4.90: 21540 Nonbonded interactions: 52736 Sorted by model distance: nonbonded pdb=" OD2 ASP B 130 " pdb=" OH TYR B 322 " model vdw 2.217 3.040 nonbonded pdb=" OD2 ASP A 130 " pdb=" OH TYR A 322 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR B 299 " pdb=" O LEU B 396 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 299 " pdb=" O LEU A 396 " model vdw 2.283 3.040 nonbonded pdb=" O PHE A 237 " pdb=" N TYR A 241 " model vdw 2.284 3.120 ... (remaining 52731 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.360 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.220 ------------------------------------------------------------------------------- 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= 0.212 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 : 0.709 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: 0.1994 time to fit residues: 60.0755 Evaluate side-chains 139 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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: 0.8980 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 B 268 HIS B 296 GLN B 511 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6780 Z= 0.227 Angle : 0.695 13.063 9272 Z= 0.349 Chirality : 0.041 0.163 1022 Planarity : 0.005 0.037 1100 Dihedral : 6.749 50.407 1016 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.96 % Allowed : 14.37 % Favored : 79.66 % 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: -1.95 (0.28), residues: 782 helix: -0.53 (0.20), residues: 606 sheet: None (None), residues: 0 loop : -3.70 (0.41), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 188 HIS 0.006 0.001 HIS B 425 PHE 0.027 0.002 PHE A 398 TYR 0.011 0.001 TYR B 299 ARG 0.003 0.001 ARG B 350 *********************** 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 185 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 146 time to evaluate : 0.721 Fit side-chains REVERT: A 125 ARG cc_start: 0.6902 (pmt170) cc_final: 0.6587 (ptt-90) REVERT: A 129 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8143 (mt) REVERT: A 151 LEU cc_start: 0.8916 (tt) cc_final: 0.8481 (mt) REVERT: A 161 TYR cc_start: 0.7245 (t80) cc_final: 0.6979 (t80) REVERT: A 205 HIS cc_start: 0.8240 (t70) cc_final: 0.7881 (t-170) REVERT: A 273 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6969 (tm-30) REVERT: A 291 ILE cc_start: 0.7921 (mp) cc_final: 0.7500 (tp) REVERT: A 297 TYR cc_start: 0.8649 (t80) cc_final: 0.8027 (t80) REVERT: A 439 PHE cc_start: 0.4744 (m-10) cc_final: 0.4527 (m-10) REVERT: A 468 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8149 (mm) REVERT: A 511 ASN cc_start: 0.8017 (t0) cc_final: 0.7726 (m-40) REVERT: A 522 TRP cc_start: 0.7323 (t-100) cc_final: 0.5125 (t60) REVERT: B 125 ARG cc_start: 0.7015 (pmt170) cc_final: 0.6100 (ptt180) REVERT: B 129 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8153 (mt) REVERT: B 291 ILE cc_start: 0.8109 (mp) cc_final: 0.7780 (tp) REVERT: B 297 TYR cc_start: 0.8619 (t80) cc_final: 0.8052 (t80) REVERT: B 299 TYR cc_start: 0.6910 (t80) cc_final: 0.6695 (t80) REVERT: B 402 MET cc_start: 0.6571 (ptt) cc_final: 0.6349 (ptt) REVERT: B 522 TRP cc_start: 0.7354 (t-100) cc_final: 0.5153 (t60) outliers start: 39 outliers final: 26 residues processed: 177 average time/residue: 0.1665 time to fit residues: 40.3093 Evaluate side-chains 158 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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 371 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 436 PHE Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 468 LEU 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 167 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 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: 0.9990 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 0.0470 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- 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 296 GLN B 204 GLN B 260 GLN B 511 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6780 Z= 0.190 Angle : 0.667 13.354 9272 Z= 0.328 Chirality : 0.041 0.191 1022 Planarity : 0.005 0.059 1100 Dihedral : 6.417 52.635 1014 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % 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: -1.08 (0.30), residues: 782 helix: 0.21 (0.21), residues: 588 sheet: None (None), residues: 0 loop : -3.55 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 188 HIS 0.004 0.001 HIS A 425 PHE 0.022 0.001 PHE B 481 TYR 0.012 0.001 TYR B 404 ARG 0.003 0.000 ARG B 350 *********************** 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 185 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 143 time to evaluate : 0.836 Fit side-chains REVERT: A 125 ARG cc_start: 0.6764 (pmt170) cc_final: 0.5793 (ptt180) REVERT: A 129 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8065 (mt) REVERT: A 161 TYR cc_start: 0.7316 (t80) cc_final: 0.6983 (t80) REVERT: A 291 ILE cc_start: 0.7875 (mp) cc_final: 0.7439 (tp) REVERT: A 297 TYR cc_start: 0.8589 (t80) cc_final: 0.8042 (t80) REVERT: A 439 PHE cc_start: 0.4704 (m-10) cc_final: 0.4488 (m-10) REVERT: A 468 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7782 (mp) REVERT: A 478 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6484 (tm) REVERT: A 482 PHE cc_start: 0.6131 (m-80) cc_final: 0.5839 (m-80) REVERT: A 511 ASN cc_start: 0.7982 (t0) cc_final: 0.7714 (m-40) REVERT: A 522 TRP cc_start: 0.7392 (t-100) cc_final: 0.5206 (t60) REVERT: B 125 ARG cc_start: 0.6725 (pmt170) cc_final: 0.5784 (ptt180) REVERT: B 129 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8079 (mt) REVERT: B 231 GLN cc_start: 0.7015 (pt0) cc_final: 0.6770 (pt0) REVERT: B 291 ILE cc_start: 0.7964 (mp) cc_final: 0.7656 (tp) REVERT: B 293 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8218 (p) REVERT: B 297 TYR cc_start: 0.8570 (t80) cc_final: 0.8060 (t80) REVERT: B 522 TRP cc_start: 0.7334 (t-100) cc_final: 0.5103 (t60) outliers start: 42 outliers final: 27 residues processed: 175 average time/residue: 0.1681 time to fit residues: 39.6853 Evaluate side-chains 161 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 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 390 ASN Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 468 LEU 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 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 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 467 CYS 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: 3.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6780 Z= 0.271 Angle : 0.730 13.117 9272 Z= 0.356 Chirality : 0.044 0.169 1022 Planarity : 0.005 0.049 1100 Dihedral : 6.649 55.832 1014 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 6.12 % Allowed : 17.89 % Favored : 75.99 % 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: -1.15 (0.30), residues: 782 helix: 0.12 (0.21), residues: 606 sheet: None (None), residues: 0 loop : -3.77 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 427 HIS 0.006 0.001 HIS A 425 PHE 0.019 0.002 PHE A 398 TYR 0.017 0.002 TYR B 430 ARG 0.005 0.001 ARG A 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 178 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 0.785 Fit side-chains REVERT: A 125 ARG cc_start: 0.6821 (pmt170) cc_final: 0.5776 (ptt180) REVERT: A 161 TYR cc_start: 0.7359 (t80) cc_final: 0.7055 (t80) REVERT: A 291 ILE cc_start: 0.8041 (mp) cc_final: 0.7565 (tp) REVERT: A 297 TYR cc_start: 0.8731 (t80) cc_final: 0.8483 (t80) REVERT: A 299 TYR cc_start: 0.7080 (t80) cc_final: 0.6862 (t80) REVERT: A 406 ASP cc_start: 0.7718 (p0) cc_final: 0.7499 (p0) REVERT: A 468 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7689 (mp) REVERT: A 478 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6674 (tm) REVERT: A 511 ASN cc_start: 0.8142 (t0) cc_final: 0.7805 (m-40) REVERT: A 522 TRP cc_start: 0.7517 (t-100) cc_final: 0.5140 (t60) REVERT: B 125 ARG cc_start: 0.6838 (pmt170) cc_final: 0.5913 (ptt180) REVERT: B 129 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.7976 (mt) REVERT: B 291 ILE cc_start: 0.8160 (mp) cc_final: 0.7806 (tp) REVERT: B 293 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8211 (p) REVERT: B 297 TYR cc_start: 0.8712 (t80) cc_final: 0.8468 (t80) REVERT: B 406 ASP cc_start: 0.7769 (p0) cc_final: 0.7535 (p0) REVERT: B 522 TRP cc_start: 0.7568 (t-100) cc_final: 0.5247 (t60) outliers start: 40 outliers final: 29 residues processed: 170 average time/residue: 0.1618 time to fit residues: 37.4939 Evaluate side-chains 164 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 167 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 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 422 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 154 LEU 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 293 THR 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 467 CYS 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: 0.6980 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7371 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6780 Z= 0.193 Angle : 0.664 13.534 9272 Z= 0.320 Chirality : 0.041 0.146 1022 Planarity : 0.005 0.045 1100 Dihedral : 6.020 49.938 1014 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 6.12 % Allowed : 19.11 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.71 (0.31), residues: 782 helix: 0.42 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -3.60 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 427 HIS 0.005 0.001 HIS A 425 PHE 0.022 0.001 PHE B 481 TYR 0.013 0.001 TYR B 210 ARG 0.004 0.000 ARG B 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 182 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 142 time to evaluate : 0.726 Fit side-chains REVERT: A 125 ARG cc_start: 0.6717 (pmt170) cc_final: 0.5663 (ptt180) REVERT: A 129 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.7923 (mt) REVERT: A 291 ILE cc_start: 0.7815 (mp) cc_final: 0.7409 (tp) REVERT: A 297 TYR cc_start: 0.8572 (t80) cc_final: 0.8050 (t80) REVERT: A 406 ASP cc_start: 0.7733 (p0) cc_final: 0.7455 (p0) REVERT: A 468 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7731 (mp) REVERT: A 511 ASN cc_start: 0.7932 (t0) cc_final: 0.7662 (m-40) REVERT: A 522 TRP cc_start: 0.7557 (t-100) cc_final: 0.5192 (t60) REVERT: B 125 ARG cc_start: 0.6785 (pmt170) cc_final: 0.5823 (ptt180) REVERT: B 129 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.7959 (mt) REVERT: B 291 ILE cc_start: 0.7976 (mp) cc_final: 0.7576 (tp) REVERT: B 293 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8245 (p) REVERT: B 297 TYR cc_start: 0.8574 (t80) cc_final: 0.8048 (t80) REVERT: B 406 ASP cc_start: 0.7746 (p0) cc_final: 0.7499 (p0) REVERT: B 468 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7649 (mp) REVERT: B 522 TRP cc_start: 0.7540 (t-100) cc_final: 0.5166 (t60) outliers start: 40 outliers final: 29 residues processed: 174 average time/residue: 0.1408 time to fit residues: 34.5182 Evaluate side-chains 170 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 154 LEU 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 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 380 THR Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 154 LEU 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 293 THR Chi-restraints excluded: chain B residue 301 LEU 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 422 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 468 LEU 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: 1.9990 chunk 75 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.7430 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6780 Z= 0.245 Angle : 0.702 13.308 9272 Z= 0.338 Chirality : 0.043 0.158 1022 Planarity : 0.005 0.042 1100 Dihedral : 6.037 46.436 1014 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 6.27 % Allowed : 20.03 % Favored : 73.70 % 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: -0.69 (0.31), residues: 782 helix: 0.43 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -3.58 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 188 HIS 0.006 0.001 HIS A 425 PHE 0.022 0.002 PHE A 481 TYR 0.013 0.001 TYR A 210 ARG 0.003 0.000 ARG A 319 *********************** 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 182 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 141 time to evaluate : 0.724 Fit side-chains REVERT: A 125 ARG cc_start: 0.6792 (pmt170) cc_final: 0.5732 (ptt180) REVERT: A 291 ILE cc_start: 0.7964 (mp) cc_final: 0.7576 (tp) REVERT: A 297 TYR cc_start: 0.8660 (t80) cc_final: 0.8427 (t80) REVERT: A 406 ASP cc_start: 0.7784 (p0) cc_final: 0.7482 (p0) REVERT: A 468 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7817 (mp) REVERT: A 511 ASN cc_start: 0.8062 (t0) cc_final: 0.7795 (m-40) REVERT: A 522 TRP cc_start: 0.7593 (t-100) cc_final: 0.5215 (t60) REVERT: B 125 ARG cc_start: 0.6875 (pmt170) cc_final: 0.5869 (ptt180) REVERT: B 129 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.7912 (mt) REVERT: B 291 ILE cc_start: 0.8042 (mp) cc_final: 0.7614 (tp) REVERT: B 293 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8250 (p) REVERT: B 406 ASP cc_start: 0.7765 (p0) cc_final: 0.7528 (p0) REVERT: B 468 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7726 (mp) REVERT: B 522 TRP cc_start: 0.7637 (t-100) cc_final: 0.5137 (t60) outliers start: 41 outliers final: 32 residues processed: 173 average time/residue: 0.1432 time to fit residues: 34.9147 Evaluate side-chains 168 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 154 LEU 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 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 380 THR Chi-restraints excluded: chain A residue 390 ASN 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 467 CYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 154 LEU 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 293 THR Chi-restraints excluded: chain B residue 301 LEU 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 422 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 506 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 0.0010 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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: 0.7346 moved from start: 0.4273 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= 0.176 Angle : 0.654 13.714 9272 Z= 0.312 Chirality : 0.040 0.141 1022 Planarity : 0.005 0.041 1100 Dihedral : 5.685 50.639 1014 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.50 % Allowed : 20.18 % Favored : 74.31 % 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: -0.26 (0.31), residues: 782 helix: 0.69 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -3.27 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 427 HIS 0.003 0.001 HIS A 205 PHE 0.019 0.001 PHE A 482 TYR 0.016 0.001 TYR B 297 ARG 0.003 0.000 ARG A 319 *********************** 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 174 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 0.676 Fit side-chains REVERT: A 125 ARG cc_start: 0.6659 (pmt170) cc_final: 0.5589 (ptt180) REVERT: A 273 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: A 297 TYR cc_start: 0.8526 (t80) cc_final: 0.8111 (t80) REVERT: A 406 ASP cc_start: 0.7689 (p0) cc_final: 0.7391 (p0) REVERT: A 413 TYR cc_start: 0.5501 (OUTLIER) cc_final: 0.5012 (t80) REVERT: A 468 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7826 (mp) REVERT: A 511 ASN cc_start: 0.7924 (t0) cc_final: 0.7690 (m-40) REVERT: A 522 TRP cc_start: 0.7617 (t-100) cc_final: 0.5199 (t60) REVERT: B 125 ARG cc_start: 0.6712 (pmt170) cc_final: 0.5677 (ptt180) REVERT: B 129 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.7745 (mt) REVERT: B 272 ARG cc_start: 0.8011 (tpt-90) cc_final: 0.7686 (mmm160) REVERT: B 293 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8261 (p) REVERT: B 406 ASP cc_start: 0.7681 (p0) cc_final: 0.7449 (p0) REVERT: B 449 MET cc_start: 0.4861 (OUTLIER) cc_final: 0.3303 (tpt) REVERT: B 468 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7619 (mp) REVERT: B 503 MET cc_start: 0.8204 (tmm) cc_final: 0.7903 (ttp) REVERT: B 522 TRP cc_start: 0.7617 (t-100) cc_final: 0.5009 (t60) outliers start: 36 outliers final: 26 residues processed: 165 average time/residue: 0.1399 time to fit residues: 32.5165 Evaluate side-chains 164 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 154 LEU 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 330 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 468 LEU 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 167 LEU 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 301 LEU 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 449 MET Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 506 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS B 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4348 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= 0.216 Angle : 0.671 13.333 9272 Z= 0.323 Chirality : 0.042 0.149 1022 Planarity : 0.005 0.043 1100 Dihedral : 5.739 49.196 1012 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 6.12 % Allowed : 20.34 % Favored : 73.55 % 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: -0.35 (0.31), residues: 782 helix: 0.63 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -3.26 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 188 HIS 0.006 0.001 HIS A 425 PHE 0.022 0.001 PHE B 254 TYR 0.013 0.001 TYR B 431 ARG 0.003 0.000 ARG A 319 *********************** 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 182 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 142 time to evaluate : 1.571 Fit side-chains REVERT: A 193 LEU cc_start: 0.7279 (mt) cc_final: 0.7060 (mt) REVERT: A 273 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: A 406 ASP cc_start: 0.7736 (p0) cc_final: 0.7470 (p0) REVERT: A 413 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.5266 (t80) REVERT: A 468 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7870 (mp) REVERT: A 511 ASN cc_start: 0.8043 (t0) cc_final: 0.7792 (m-40) REVERT: A 522 TRP cc_start: 0.7647 (t-100) cc_final: 0.5205 (t60) REVERT: B 125 ARG cc_start: 0.6783 (pmt170) cc_final: 0.5714 (ptt180) REVERT: B 129 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.7715 (mt) REVERT: B 293 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8245 (p) REVERT: B 406 ASP cc_start: 0.7716 (p0) cc_final: 0.7504 (p0) REVERT: B 413 TYR cc_start: 0.5752 (OUTLIER) cc_final: 0.5422 (t80) REVERT: B 449 MET cc_start: 0.4754 (OUTLIER) cc_final: 0.3138 (tpt) REVERT: B 468 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7648 (mp) REVERT: B 522 TRP cc_start: 0.7724 (t-100) cc_final: 0.5072 (t60) outliers start: 40 outliers final: 32 residues processed: 170 average time/residue: 0.1654 time to fit residues: 40.2394 Evaluate side-chains 171 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 131 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 154 LEU 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 380 THR 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 467 CYS Chi-restraints excluded: chain A residue 468 LEU 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 167 LEU 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 301 LEU 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 411 THR Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 468 LEU 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: 0.6980 chunk 55 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.7393 moved from start: 0.4451 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= 0.218 Angle : 0.674 13.686 9272 Z= 0.325 Chirality : 0.042 0.149 1022 Planarity : 0.005 0.043 1100 Dihedral : 5.727 48.541 1012 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.96 % Allowed : 20.49 % Favored : 73.55 % 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: -0.30 (0.31), residues: 782 helix: 0.64 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -3.14 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 188 HIS 0.005 0.001 HIS A 425 PHE 0.021 0.001 PHE A 398 TYR 0.020 0.001 TYR A 297 ARG 0.002 0.000 ARG A 319 *********************** 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 174 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 0.729 Fit side-chains REVERT: A 125 ARG cc_start: 0.6291 (ptt-90) cc_final: 0.5251 (ptt180) REVERT: A 273 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: A 406 ASP cc_start: 0.7733 (p0) cc_final: 0.7486 (p0) REVERT: A 413 TYR cc_start: 0.5659 (OUTLIER) cc_final: 0.5242 (t80) REVERT: A 511 ASN cc_start: 0.8035 (t0) cc_final: 0.7815 (m-40) REVERT: A 522 TRP cc_start: 0.7765 (t-100) cc_final: 0.5370 (t60) REVERT: B 125 ARG cc_start: 0.6794 (pmt170) cc_final: 0.5761 (ptt180) REVERT: B 129 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.7701 (mt) REVERT: B 293 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8197 (p) REVERT: B 406 ASP cc_start: 0.7731 (p0) cc_final: 0.7514 (p0) REVERT: B 413 TYR cc_start: 0.5799 (OUTLIER) cc_final: 0.5536 (t80) REVERT: B 449 MET cc_start: 0.4747 (OUTLIER) cc_final: 0.3141 (tpt) REVERT: B 468 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7625 (mp) outliers start: 39 outliers final: 29 residues processed: 163 average time/residue: 0.1395 time to fit residues: 31.9015 Evaluate side-chains 169 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 133 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 154 LEU 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 330 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 380 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 467 CYS 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 167 LEU 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 301 LEU 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 411 THR Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 474 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.0000 chunk 57 optimal weight: 0.3980 chunk 9 optimal weight: 5.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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: 0.7347 moved from start: 0.4661 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= 0.185 Angle : 0.666 13.522 9272 Z= 0.317 Chirality : 0.041 0.139 1022 Planarity : 0.005 0.042 1100 Dihedral : 5.338 50.668 1010 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.35 % Allowed : 21.10 % Favored : 73.55 % 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: -0.06 (0.31), residues: 782 helix: 0.78 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -2.93 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 188 HIS 0.004 0.001 HIS B 386 PHE 0.021 0.001 PHE A 398 TYR 0.017 0.001 TYR A 297 ARG 0.002 0.000 ARG A 350 ********************** 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 176 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 0.701 Fit side-chains REVERT: A 125 ARG cc_start: 0.6255 (ptt-90) cc_final: 0.5290 (ptt180) REVERT: A 273 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: A 406 ASP cc_start: 0.7688 (p0) cc_final: 0.7443 (p0) REVERT: A 413 TYR cc_start: 0.5586 (OUTLIER) cc_final: 0.5158 (t80) REVERT: A 511 ASN cc_start: 0.7965 (t0) cc_final: 0.7719 (m-40) REVERT: A 522 TRP cc_start: 0.7657 (t-100) cc_final: 0.5241 (t60) REVERT: B 125 ARG cc_start: 0.6696 (pmt170) cc_final: 0.5690 (ptt180) REVERT: B 129 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.7620 (mt) REVERT: B 293 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8196 (p) REVERT: B 406 ASP cc_start: 0.7623 (p0) cc_final: 0.7410 (p0) REVERT: B 413 TYR cc_start: 0.5794 (OUTLIER) cc_final: 0.5533 (t80) REVERT: B 449 MET cc_start: 0.4881 (OUTLIER) cc_final: 0.3357 (tpt) REVERT: B 468 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7617 (mp) outliers start: 35 outliers final: 27 residues processed: 169 average time/residue: 0.1422 time to fit residues: 33.8556 Evaluate side-chains 168 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 154 LEU 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 330 VAL Chi-restraints excluded: chain A residue 379 LEU 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 467 CYS 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 167 LEU 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 301 LEU 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 413 TYR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 474 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.0570 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.219392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.197868 restraints weight = 7584.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.200919 restraints weight = 4941.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.202722 restraints weight = 3742.015| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.4720 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= 0.185 Angle : 0.665 13.678 9272 Z= 0.317 Chirality : 0.041 0.136 1022 Planarity : 0.005 0.045 1100 Dihedral : 5.304 52.689 1010 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.50 % Allowed : 21.10 % Favored : 73.39 % 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: 0.06 (0.31), residues: 782 helix: 0.86 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -2.90 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 427 HIS 0.005 0.001 HIS B 386 PHE 0.021 0.001 PHE A 398 TYR 0.016 0.001 TYR A 297 ARG 0.002 0.000 ARG A 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1621.99 seconds wall clock time: 30 minutes 0.37 seconds (1800.37 seconds total)