Starting phenix.real_space_refine on Tue Feb 13 18:09:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qv6_4645/02_2024/6qv6_4645.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qv6_4645/02_2024/6qv6_4645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qv6_4645/02_2024/6qv6_4645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qv6_4645/02_2024/6qv6_4645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qv6_4645/02_2024/6qv6_4645.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qv6_4645/02_2024/6qv6_4645.pdb" } resolution = 3.63 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 58 5.16 5 C 4814 2.51 5 N 1138 2.21 5 O 1198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A PHE 547": "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: 7208 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3604 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 25, 'TRANS': 443} Chain breaks: 1 Chain: "A" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3604 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 25, 'TRANS': 443} Chain breaks: 1 Time building chain proxies: 4.25, per 1000 atoms: 0.59 Number of scatterers: 7208 At special positions: 0 Unit cell: (105.93, 82.39, 75.97, 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 58 16.00 O 1198 8.00 N 1138 7.00 C 4814 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: 2.93 Conformation dependent library (CDL) restraints added in 1.2 seconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 2 sheets defined 74.8% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'B' and resid 116 through 153 removed outlier: 4.096A pdb=" N PHE B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 181 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 190 through 198 removed outlier: 4.209A pdb=" N MET B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 207 removed outlier: 3.852A pdb=" N LEU B 207 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 204 through 207' Processing helix chain 'B' and resid 208 through 224 removed outlier: 3.962A pdb=" N PHE B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 213 " --> pdb=" O MET B 209 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 217 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 250 removed outlier: 3.644A pdb=" N PHE B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 280 Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 298 through 323 removed outlier: 3.879A pdb=" N ALA B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 377 removed outlier: 3.899A pdb=" N PHE B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N CYS B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY B 375 " --> pdb=" O GLN B 371 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 removed outlier: 3.585A pdb=" N HIS B 389 " --> pdb=" O PHE B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 404 removed outlier: 3.645A pdb=" N GLY B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B 397 " --> pdb=" O TYR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 434 through 438 removed outlier: 3.806A pdb=" N GLY B 438 " --> pdb=" O LYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 450 removed outlier: 3.682A pdb=" N ALA B 447 " --> pdb=" O GLY B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 477 removed outlier: 3.597A pdb=" N ILE B 459 " --> pdb=" O ASN B 455 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE B 472 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 473 " --> pdb=" O TRP B 469 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET B 477 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 506 Processing helix chain 'B' and resid 521 through 537 removed outlier: 4.761A pdb=" N THR B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 551 removed outlier: 3.903A pdb=" N ILE B 545 " --> pdb=" O SER B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 574 removed outlier: 3.731A pdb=" N GLN B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 586 Processing helix chain 'A' and resid 116 through 153 removed outlier: 4.097A pdb=" N PHE A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 181 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 190 through 198 removed outlier: 4.209A pdb=" N MET A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 207 removed outlier: 3.852A pdb=" N LEU A 207 " --> pdb=" O LYS A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 207' Processing helix chain 'A' and resid 208 through 224 removed outlier: 3.963A pdb=" N PHE A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.644A pdb=" N PHE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 280 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 298 through 323 removed outlier: 3.879A pdb=" N ALA A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 377 removed outlier: 3.900A pdb=" N PHE A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N CYS A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY A 375 " --> pdb=" O GLN A 371 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 removed outlier: 3.585A pdb=" N HIS A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 404 removed outlier: 3.645A pdb=" N GLY A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.807A pdb=" N GLY A 438 " --> pdb=" O LYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.681A pdb=" N ALA A 447 " --> pdb=" O GLY A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 477 removed outlier: 3.598A pdb=" N ILE A 459 " --> pdb=" O ASN A 455 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 472 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 473 " --> pdb=" O TRP A 469 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET A 477 " --> pdb=" O VAL A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 506 Processing helix chain 'A' and resid 521 through 537 removed outlier: 4.761A pdb=" N THR A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 551 removed outlier: 3.904A pdb=" N ILE A 545 " --> pdb=" O SER A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 574 removed outlier: 3.732A pdb=" N GLN A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 586 Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 512 Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 512 486 hydrogen bonds defined for protein. 1422 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: 2.01 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2036 1.34 - 1.46: 1662 1.46 - 1.58: 3614 1.58 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 7410 Sorted by residual: bond pdb=" CB PRO B 408 " pdb=" CG PRO B 408 " ideal model delta sigma weight residual 1.492 1.400 0.092 5.00e-02 4.00e+02 3.37e+00 bond pdb=" CB PRO A 408 " pdb=" CG PRO A 408 " ideal model delta sigma weight residual 1.492 1.401 0.091 5.00e-02 4.00e+02 3.31e+00 bond pdb=" CB GLU B 347 " pdb=" CG GLU B 347 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.30e+00 bond pdb=" CB GLU A 347 " pdb=" CG GLU A 347 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.26e+00 bond pdb=" CG1 ILE A 564 " pdb=" CD1 ILE A 564 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.24e+00 ... (remaining 7405 not shown) Histogram of bond angle deviations from ideal: 94.29 - 103.28: 102 103.28 - 112.28: 3685 112.28 - 121.27: 4771 121.27 - 130.26: 1472 130.26 - 139.25: 54 Bond angle restraints: 10084 Sorted by residual: angle pdb=" CA GLU B 347 " pdb=" CB GLU B 347 " pdb=" CG GLU B 347 " ideal model delta sigma weight residual 114.10 129.10 -15.00 2.00e+00 2.50e-01 5.62e+01 angle pdb=" CA GLU A 347 " pdb=" CB GLU A 347 " pdb=" CG GLU A 347 " ideal model delta sigma weight residual 114.10 129.07 -14.97 2.00e+00 2.50e-01 5.60e+01 angle pdb=" CB GLU A 347 " pdb=" CG GLU A 347 " pdb=" CD GLU A 347 " ideal model delta sigma weight residual 112.60 122.08 -9.48 1.70e+00 3.46e-01 3.11e+01 angle pdb=" CB GLU B 347 " pdb=" CG GLU B 347 " pdb=" CD GLU B 347 " ideal model delta sigma weight residual 112.60 122.03 -9.43 1.70e+00 3.46e-01 3.08e+01 angle pdb=" N VAL A 252 " pdb=" CA VAL A 252 " pdb=" C VAL A 252 " ideal model delta sigma weight residual 113.20 107.91 5.29 9.60e-01 1.09e+00 3.03e+01 ... (remaining 10079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.85: 3848 13.85 - 27.70: 328 27.70 - 41.56: 86 41.56 - 55.41: 16 55.41 - 69.26: 4 Dihedral angle restraints: 4282 sinusoidal: 1600 harmonic: 2682 Sorted by residual: dihedral pdb=" CA ALA A 326 " pdb=" C ALA A 326 " pdb=" N VAL A 327 " pdb=" CA VAL A 327 " ideal model delta harmonic sigma weight residual -180.00 -134.24 -45.76 0 5.00e+00 4.00e-02 8.37e+01 dihedral pdb=" CA ALA B 326 " pdb=" C ALA B 326 " pdb=" N VAL B 327 " pdb=" CA VAL B 327 " ideal model delta harmonic sigma weight residual -180.00 -134.27 -45.73 0 5.00e+00 4.00e-02 8.36e+01 dihedral pdb=" CA ILE A 290 " pdb=" C ILE A 290 " pdb=" N GLU A 291 " pdb=" CA GLU A 291 " ideal model delta harmonic sigma weight residual -180.00 -151.85 -28.15 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 4279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 718 0.053 - 0.107: 318 0.107 - 0.160: 101 0.160 - 0.214: 37 0.214 - 0.267: 4 Chirality restraints: 1178 Sorted by residual: chirality pdb=" CB ILE A 329 " pdb=" CA ILE A 329 " pdb=" CG1 ILE A 329 " pdb=" CG2 ILE A 329 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE B 329 " pdb=" CA ILE B 329 " pdb=" CG1 ILE B 329 " pdb=" CG2 ILE B 329 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA LEU B 557 " pdb=" N LEU B 557 " pdb=" C LEU B 557 " pdb=" CB LEU B 557 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1175 not shown) Planarity restraints: 1234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 365 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.26e+00 pdb=" C PHE B 365 " -0.053 2.00e-02 2.50e+03 pdb=" O PHE B 365 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL B 366 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 365 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.21e+00 pdb=" C PHE A 365 " 0.052 2.00e-02 2.50e+03 pdb=" O PHE A 365 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL A 366 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 370 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C ARG A 370 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG A 370 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN A 371 " 0.017 2.00e-02 2.50e+03 ... (remaining 1231 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2041 2.81 - 3.33: 7042 3.33 - 3.85: 12078 3.85 - 4.38: 12824 4.38 - 4.90: 22442 Nonbonded interactions: 56427 Sorted by model distance: nonbonded pdb=" O ILE A 472 " pdb=" OG1 THR A 476 " model vdw 2.282 2.440 nonbonded pdb=" O ILE B 472 " pdb=" OG1 THR B 476 " model vdw 2.283 2.440 nonbonded pdb=" OE2 GLU B 193 " pdb=" OH TYR B 206 " model vdw 2.283 2.440 nonbonded pdb=" OE2 GLU A 193 " pdb=" OH TYR A 206 " model vdw 2.284 2.440 nonbonded pdb=" OE2 GLU B 291 " pdb=" OG SER B 541 " model vdw 2.296 2.440 ... (remaining 56422 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: 1.390 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: 5.350 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.420 Find NCS groups from input model: 0.390 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 : 0.010 0.092 7410 Z= 0.624 Angle : 1.309 14.996 10084 Z= 0.693 Chirality : 0.070 0.267 1178 Planarity : 0.011 0.059 1234 Dihedral : 11.643 69.261 2562 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.96 % Favored : 91.61 % Rotamer: Outliers : 1.04 % Allowed : 6.77 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.57 (0.21), residues: 930 helix: -2.34 (0.16), residues: 672 sheet: None (None), residues: 0 loop : -4.55 (0.28), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 133 HIS 0.009 0.002 HIS B 237 PHE 0.026 0.004 PHE B 547 TYR 0.035 0.003 TYR B 146 ARG 0.008 0.001 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 0.838 Fit side-chains REVERT: B 194 MET cc_start: 0.8534 (ppp) cc_final: 0.8309 (ppp) REVERT: B 209 MET cc_start: 0.8955 (tmt) cc_final: 0.8635 (tmm) REVERT: B 291 GLU cc_start: 0.8040 (pm20) cc_final: 0.7626 (pm20) REVERT: B 417 GLU cc_start: 0.8383 (tt0) cc_final: 0.8007 (tm-30) REVERT: B 571 GLN cc_start: 0.8664 (tt0) cc_final: 0.8003 (tp40) REVERT: B 589 TYR cc_start: 0.8083 (t80) cc_final: 0.7697 (t80) REVERT: A 206 TYR cc_start: 0.6453 (t80) cc_final: 0.6240 (t80) REVERT: A 209 MET cc_start: 0.8905 (tmt) cc_final: 0.8545 (tmm) REVERT: A 589 TYR cc_start: 0.8060 (t80) cc_final: 0.7589 (t80) outliers start: 8 outliers final: 4 residues processed: 162 average time/residue: 0.1791 time to fit residues: 39.3134 Evaluate side-chains 108 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 347 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 0.0170 chunk 83 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7410 Z= 0.213 Angle : 0.768 10.364 10084 Z= 0.385 Chirality : 0.044 0.154 1178 Planarity : 0.006 0.049 1234 Dihedral : 6.386 40.096 996 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.81 % Favored : 93.98 % Rotamer: Outliers : 3.65 % Allowed : 16.02 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.27), residues: 930 helix: -0.10 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -3.78 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 469 HIS 0.004 0.001 HIS A 237 PHE 0.034 0.002 PHE A 547 TYR 0.014 0.001 TYR B 206 ARG 0.004 0.001 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: B 194 MET cc_start: 0.8419 (ppp) cc_final: 0.8182 (ppp) REVERT: B 209 MET cc_start: 0.8866 (tmt) cc_final: 0.8388 (tmm) REVERT: B 277 CYS cc_start: 0.7951 (t) cc_final: 0.7749 (t) REVERT: B 340 ASP cc_start: 0.7602 (m-30) cc_final: 0.7304 (m-30) REVERT: B 344 ASP cc_start: 0.8773 (p0) cc_final: 0.8440 (p0) REVERT: B 571 GLN cc_start: 0.8549 (tt0) cc_final: 0.7942 (tp40) REVERT: A 209 MET cc_start: 0.8860 (tmt) cc_final: 0.8377 (tmm) REVERT: A 340 ASP cc_start: 0.8056 (m-30) cc_final: 0.7850 (m-30) REVERT: A 344 ASP cc_start: 0.8899 (p0) cc_final: 0.8540 (p0) REVERT: A 373 MET cc_start: 0.8629 (mmt) cc_final: 0.8426 (mmt) REVERT: A 466 MET cc_start: 0.7574 (mmt) cc_final: 0.7175 (mmt) REVERT: A 571 GLN cc_start: 0.8403 (tt0) cc_final: 0.7848 (tp40) outliers start: 28 outliers final: 14 residues processed: 175 average time/residue: 0.1451 time to fit residues: 36.8454 Evaluate side-chains 126 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 389 HIS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 567 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7410 Z= 0.268 Angle : 0.786 12.138 10084 Z= 0.387 Chirality : 0.044 0.165 1178 Planarity : 0.005 0.045 1234 Dihedral : 5.426 37.498 986 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.45 % Favored : 93.44 % Rotamer: Outliers : 6.12 % Allowed : 18.75 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.81 (0.28), residues: 930 helix: 0.72 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -4.00 (0.32), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 164 HIS 0.013 0.002 HIS B 379 PHE 0.031 0.002 PHE B 547 TYR 0.015 0.001 TYR A 146 ARG 0.003 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 121 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8914 (tp) REVERT: B 178 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7931 (t80) REVERT: B 209 MET cc_start: 0.8808 (tmt) cc_final: 0.8308 (tmm) REVERT: B 277 CYS cc_start: 0.7909 (t) cc_final: 0.7673 (t) REVERT: B 391 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8797 (pp) REVERT: B 419 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8262 (mmm) REVERT: B 571 GLN cc_start: 0.8556 (tt0) cc_final: 0.7947 (tp40) REVERT: A 127 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8939 (tp) REVERT: A 178 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7911 (t80) REVERT: A 209 MET cc_start: 0.8877 (tmt) cc_final: 0.8468 (tmm) REVERT: A 303 TRP cc_start: 0.8314 (m-10) cc_final: 0.8094 (m-10) REVERT: A 391 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8515 (pp) REVERT: A 466 MET cc_start: 0.7752 (mmt) cc_final: 0.7371 (mmt) REVERT: A 571 GLN cc_start: 0.8496 (tt0) cc_final: 0.7883 (tp40) outliers start: 47 outliers final: 27 residues processed: 150 average time/residue: 0.1319 time to fit residues: 29.3918 Evaluate side-chains 142 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 108 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 389 HIS Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 0.0570 chunk 23 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7410 Z= 0.192 Angle : 0.724 11.526 10084 Z= 0.353 Chirality : 0.042 0.174 1178 Planarity : 0.005 0.048 1234 Dihedral : 5.066 33.488 986 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 6.25 % Allowed : 18.88 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 (0.29), residues: 930 helix: 1.15 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -3.88 (0.31), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 469 HIS 0.008 0.001 HIS A 379 PHE 0.029 0.001 PHE A 547 TYR 0.012 0.001 TYR B 206 ARG 0.003 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 118 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: B 127 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8840 (tp) REVERT: B 178 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7959 (t80) REVERT: B 209 MET cc_start: 0.8818 (tmt) cc_final: 0.8323 (tmm) REVERT: B 277 CYS cc_start: 0.7911 (t) cc_final: 0.7670 (t) REVERT: B 302 TYR cc_start: 0.9099 (t80) cc_final: 0.8371 (t80) REVERT: B 368 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9206 (mm) REVERT: B 389 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7850 (m-70) REVERT: B 391 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8693 (pp) REVERT: B 524 TYR cc_start: 0.7982 (m-10) cc_final: 0.7725 (m-10) REVERT: B 571 GLN cc_start: 0.8561 (tt0) cc_final: 0.7949 (tp40) REVERT: A 127 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8863 (tp) REVERT: A 178 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7927 (t80) REVERT: A 209 MET cc_start: 0.8861 (tmt) cc_final: 0.8419 (tmm) REVERT: A 302 TYR cc_start: 0.9160 (t80) cc_final: 0.8448 (t80) REVERT: A 391 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8450 (pp) REVERT: A 571 GLN cc_start: 0.8477 (tt0) cc_final: 0.7847 (tp40) outliers start: 48 outliers final: 26 residues processed: 151 average time/residue: 0.1490 time to fit residues: 33.1434 Evaluate side-chains 142 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 108 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 389 HIS Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.0470 chunk 79 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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: 0.8028 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7410 Z= 0.183 Angle : 0.719 11.546 10084 Z= 0.347 Chirality : 0.042 0.172 1178 Planarity : 0.005 0.047 1234 Dihedral : 4.888 29.443 986 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 6.25 % Allowed : 19.79 % Favored : 73.96 % 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: 0.02 (0.29), residues: 930 helix: 1.31 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -3.59 (0.33), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 469 HIS 0.007 0.001 HIS A 379 PHE 0.029 0.001 PHE A 547 TYR 0.011 0.001 TYR B 137 ARG 0.002 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 123 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: B 178 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7975 (t80) REVERT: B 209 MET cc_start: 0.8815 (tmt) cc_final: 0.8299 (tmm) REVERT: B 302 TYR cc_start: 0.9104 (t80) cc_final: 0.8291 (t80) REVERT: B 303 TRP cc_start: 0.8391 (m-10) cc_final: 0.7940 (m100) REVERT: B 368 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9228 (mm) REVERT: B 389 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7892 (m-70) REVERT: B 391 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8701 (pp) REVERT: B 466 MET cc_start: 0.7642 (mmt) cc_final: 0.7238 (mmp) REVERT: B 571 GLN cc_start: 0.8528 (tt0) cc_final: 0.7936 (tp40) REVERT: A 127 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8833 (tp) REVERT: A 178 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7878 (t80) REVERT: A 209 MET cc_start: 0.8867 (tmt) cc_final: 0.8425 (tmm) REVERT: A 302 TYR cc_start: 0.9176 (t80) cc_final: 0.8371 (t80) REVERT: A 368 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9138 (mm) REVERT: A 391 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8526 (pp) REVERT: A 571 GLN cc_start: 0.8504 (tt0) cc_final: 0.7826 (tp40) outliers start: 48 outliers final: 25 residues processed: 157 average time/residue: 0.1462 time to fit residues: 34.0619 Evaluate side-chains 147 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 389 HIS Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 0.0770 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.0170 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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: 0.8021 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7410 Z= 0.178 Angle : 0.717 12.590 10084 Z= 0.341 Chirality : 0.042 0.179 1178 Planarity : 0.005 0.050 1234 Dihedral : 4.730 25.622 986 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.60 % Allowed : 20.70 % 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: 0.21 (0.29), residues: 930 helix: 1.45 (0.21), residues: 666 sheet: None (None), residues: 0 loop : -3.51 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 469 HIS 0.007 0.001 HIS A 379 PHE 0.029 0.001 PHE B 547 TYR 0.011 0.001 TYR B 137 ARG 0.002 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8790 (tp) REVERT: B 178 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7943 (t80) REVERT: B 209 MET cc_start: 0.8792 (tmt) cc_final: 0.8301 (tmm) REVERT: B 302 TYR cc_start: 0.9117 (t80) cc_final: 0.8203 (t80) REVERT: B 368 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9220 (mm) REVERT: B 391 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8701 (pp) REVERT: B 466 MET cc_start: 0.7694 (mmt) cc_final: 0.7326 (mmp) REVERT: B 571 GLN cc_start: 0.8521 (tt0) cc_final: 0.7929 (tp40) REVERT: A 178 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7861 (t80) REVERT: A 209 MET cc_start: 0.8852 (tmt) cc_final: 0.8415 (tmm) REVERT: A 302 TYR cc_start: 0.9191 (t80) cc_final: 0.8231 (t80) REVERT: A 391 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8531 (pp) REVERT: A 571 GLN cc_start: 0.8484 (tt0) cc_final: 0.7908 (tp40) outliers start: 43 outliers final: 27 residues processed: 149 average time/residue: 0.1407 time to fit residues: 30.7293 Evaluate side-chains 144 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 54 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 0.0770 chunk 52 optimal weight: 4.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7410 Z= 0.171 Angle : 0.722 16.330 10084 Z= 0.338 Chirality : 0.042 0.205 1178 Planarity : 0.005 0.049 1234 Dihedral : 4.570 21.333 986 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.73 % Allowed : 20.18 % Favored : 74.09 % 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: 0.46 (0.29), residues: 930 helix: 1.60 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -3.24 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 469 HIS 0.006 0.001 HIS A 379 PHE 0.027 0.001 PHE B 547 TYR 0.010 0.001 TYR B 137 ARG 0.002 0.000 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: B 178 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7983 (t80) REVERT: B 209 MET cc_start: 0.8819 (tmt) cc_final: 0.8378 (tmm) REVERT: B 302 TYR cc_start: 0.9108 (t80) cc_final: 0.8197 (t80) REVERT: B 368 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9204 (mm) REVERT: B 391 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8701 (pp) REVERT: B 436 HIS cc_start: 0.8020 (m-70) cc_final: 0.7696 (m-70) REVERT: B 524 TYR cc_start: 0.7460 (m-10) cc_final: 0.7215 (m-10) REVERT: B 557 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8130 (mt) REVERT: B 571 GLN cc_start: 0.8514 (tt0) cc_final: 0.7923 (tp40) REVERT: A 127 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8699 (tt) REVERT: A 209 MET cc_start: 0.8830 (tmt) cc_final: 0.8406 (tmm) REVERT: A 302 TYR cc_start: 0.9178 (t80) cc_final: 0.8250 (t80) REVERT: A 391 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8538 (pp) REVERT: A 571 GLN cc_start: 0.8363 (tt0) cc_final: 0.7852 (tp40) outliers start: 44 outliers final: 27 residues processed: 155 average time/residue: 0.1396 time to fit residues: 31.9891 Evaluate side-chains 149 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.0470 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7410 Z= 0.197 Angle : 0.720 16.042 10084 Z= 0.346 Chirality : 0.042 0.183 1178 Planarity : 0.005 0.048 1234 Dihedral : 4.628 21.474 986 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.99 % Allowed : 20.70 % Favored : 73.31 % 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: 0.62 (0.29), residues: 930 helix: 1.73 (0.21), residues: 666 sheet: None (None), residues: 0 loop : -3.26 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 469 HIS 0.007 0.001 HIS B 379 PHE 0.041 0.002 PHE B 333 TYR 0.010 0.001 TYR B 137 ARG 0.002 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 121 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 178 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7988 (t80) REVERT: B 209 MET cc_start: 0.8791 (tmt) cc_final: 0.8360 (tmm) REVERT: B 302 TYR cc_start: 0.9140 (t80) cc_final: 0.8199 (t80) REVERT: B 303 TRP cc_start: 0.8394 (m-10) cc_final: 0.7983 (m100) REVERT: B 344 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8440 (p0) REVERT: B 368 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9191 (mm) REVERT: B 391 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8691 (pp) REVERT: B 422 GLU cc_start: 0.8424 (pm20) cc_final: 0.7980 (pm20) REVERT: B 436 HIS cc_start: 0.8045 (m-70) cc_final: 0.7710 (m-70) REVERT: B 466 MET cc_start: 0.7699 (mmt) cc_final: 0.7353 (mmp) REVERT: B 557 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8185 (mt) REVERT: B 571 GLN cc_start: 0.8520 (tt0) cc_final: 0.7887 (tp40) REVERT: A 209 MET cc_start: 0.8798 (tmt) cc_final: 0.8368 (tmm) REVERT: A 302 TYR cc_start: 0.9184 (t80) cc_final: 0.8303 (t80) REVERT: A 303 TRP cc_start: 0.8429 (m-10) cc_final: 0.8066 (m100) REVERT: A 339 MET cc_start: 0.8663 (ptt) cc_final: 0.8427 (ptp) REVERT: A 391 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8526 (pp) REVERT: A 498 VAL cc_start: 0.8642 (p) cc_final: 0.8330 (m) REVERT: A 571 GLN cc_start: 0.8407 (tt0) cc_final: 0.7817 (tp40) outliers start: 46 outliers final: 32 residues processed: 151 average time/residue: 0.1456 time to fit residues: 32.5966 Evaluate side-chains 155 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 117 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.0670 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 379 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7410 Z= 0.184 Angle : 0.695 13.480 10084 Z= 0.336 Chirality : 0.041 0.180 1178 Planarity : 0.005 0.050 1234 Dihedral : 4.578 21.760 986 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.21 % Allowed : 21.61 % Favored : 73.18 % 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: 0.66 (0.29), residues: 930 helix: 1.75 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -3.19 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 469 HIS 0.007 0.001 HIS A 379 PHE 0.035 0.002 PHE B 333 TYR 0.010 0.001 TYR A 137 ARG 0.002 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.8860 (tpp) cc_final: 0.8530 (tpt) REVERT: B 178 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.8003 (t80) REVERT: B 209 MET cc_start: 0.8790 (tmt) cc_final: 0.8373 (tmm) REVERT: B 302 TYR cc_start: 0.9153 (t80) cc_final: 0.8218 (t80) REVERT: B 303 TRP cc_start: 0.8385 (m-10) cc_final: 0.7987 (m100) REVERT: B 368 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9188 (mm) REVERT: B 391 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8684 (pp) REVERT: B 422 GLU cc_start: 0.8464 (pm20) cc_final: 0.8066 (pm20) REVERT: B 436 HIS cc_start: 0.8015 (m-70) cc_final: 0.7694 (m-70) REVERT: B 557 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8152 (mt) REVERT: B 571 GLN cc_start: 0.8389 (tt0) cc_final: 0.7874 (tp40) REVERT: A 128 MET cc_start: 0.8817 (tpp) cc_final: 0.8556 (tpt) REVERT: A 209 MET cc_start: 0.8796 (tmt) cc_final: 0.8384 (tmm) REVERT: A 291 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7831 (pm20) REVERT: A 302 TYR cc_start: 0.9181 (t80) cc_final: 0.8255 (t80) REVERT: A 391 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8529 (pp) REVERT: A 498 VAL cc_start: 0.8629 (p) cc_final: 0.8320 (m) REVERT: A 571 GLN cc_start: 0.8279 (tt0) cc_final: 0.7791 (tp40) outliers start: 40 outliers final: 30 residues processed: 148 average time/residue: 0.1377 time to fit residues: 30.5034 Evaluate side-chains 159 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 123 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 84 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.8047 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7410 Z= 0.220 Angle : 0.733 13.077 10084 Z= 0.355 Chirality : 0.042 0.182 1178 Planarity : 0.005 0.048 1234 Dihedral : 4.682 25.831 986 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 5.60 % Allowed : 21.35 % Favored : 73.05 % 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: 0.67 (0.29), residues: 930 helix: 1.75 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -3.22 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 148 HIS 0.007 0.001 HIS A 379 PHE 0.030 0.002 PHE B 333 TYR 0.011 0.001 TYR B 137 ARG 0.002 0.000 ARG B 496 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.8896 (tpp) cc_final: 0.8613 (tpt) REVERT: B 178 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7969 (t80) REVERT: B 209 MET cc_start: 0.8795 (tmt) cc_final: 0.8383 (tmm) REVERT: B 302 TYR cc_start: 0.9157 (t80) cc_final: 0.8135 (t80) REVERT: B 303 TRP cc_start: 0.8418 (m-10) cc_final: 0.7975 (m100) REVERT: B 344 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8424 (p0) REVERT: B 368 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9210 (mm) REVERT: B 391 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8646 (pp) REVERT: B 422 GLU cc_start: 0.8513 (pm20) cc_final: 0.8087 (pm20) REVERT: B 436 HIS cc_start: 0.8059 (m-70) cc_final: 0.7766 (m-70) REVERT: B 466 MET cc_start: 0.7734 (mmt) cc_final: 0.7378 (mmp) REVERT: B 557 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8140 (mt) REVERT: B 571 GLN cc_start: 0.8456 (tt0) cc_final: 0.7928 (tp40) REVERT: A 128 MET cc_start: 0.8773 (tpp) cc_final: 0.8495 (tpt) REVERT: A 209 MET cc_start: 0.8802 (tmt) cc_final: 0.8383 (tmm) REVERT: A 302 TYR cc_start: 0.9184 (t80) cc_final: 0.8235 (t80) REVERT: A 328 THR cc_start: 0.6685 (m) cc_final: 0.6373 (t) REVERT: A 391 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8544 (pp) REVERT: A 498 VAL cc_start: 0.8665 (p) cc_final: 0.8352 (m) REVERT: A 571 GLN cc_start: 0.8376 (tt0) cc_final: 0.7824 (tp40) outliers start: 43 outliers final: 32 residues processed: 148 average time/residue: 0.1323 time to fit residues: 29.0590 Evaluate side-chains 156 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 118 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.091049 restraints weight = 14450.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.094645 restraints weight = 6710.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097024 restraints weight = 4018.237| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7410 Z= 0.221 Angle : 0.730 13.178 10084 Z= 0.354 Chirality : 0.042 0.184 1178 Planarity : 0.005 0.052 1234 Dihedral : 4.776 29.071 986 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.34 % Allowed : 20.83 % Favored : 73.83 % 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: 0.66 (0.29), residues: 930 helix: 1.77 (0.21), residues: 666 sheet: None (None), residues: 0 loop : -3.27 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 469 HIS 0.006 0.001 HIS A 379 PHE 0.030 0.002 PHE B 174 TYR 0.010 0.001 TYR A 137 ARG 0.002 0.000 ARG B 496 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1633.06 seconds wall clock time: 30 minutes 42.37 seconds (1842.37 seconds total)