Starting phenix.real_space_refine on Mon Mar 11 01:38:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dv1_27730/03_2024/8dv1_27730.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dv1_27730/03_2024/8dv1_27730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dv1_27730/03_2024/8dv1_27730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dv1_27730/03_2024/8dv1_27730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dv1_27730/03_2024/8dv1_27730.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dv1_27730/03_2024/8dv1_27730.pdb" } resolution = 3.4 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= 0.001 sd= 0.038 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 37 5.16 5 C 4183 2.51 5 N 1074 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "D ARG 219": "NH1" <-> "NH2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 393": "NH1" <-> "NH2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "D ARG 482": "NH1" <-> "NH2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D ARG 582": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6543 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1590 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "D" Number of atoms: 4855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4855 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.04, per 1000 atoms: 0.62 Number of scatterers: 6543 At special positions: 0 Unit cell: (76.311, 87.57, 126.351, 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 37 16.00 O 1249 8.00 N 1074 7.00 C 4183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG D1001 " - " ASN D 322 " " NAG D1002 " - " ASN D 103 " " NAG D1003 " - " ASN D 432 " " NAG D1004 " - " ASN D 546 " " NAG D1005 " - " ASN D 90 " " NAG D1006 " - " ASN D 53 " Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.3 seconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1498 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 6 sheets defined 58.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.677A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.589A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.108A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.969A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASP D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.736A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 Processing helix chain 'D' and resid 172 through 194 Proline residue: D 178 - end of helix removed outlier: 4.486A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 Proline residue: D 235 - end of helix removed outlier: 3.996A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.078A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.881A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 598 Proline residue: D 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.915A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.072A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 350 323 hydrogen bonds defined for protein. 906 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: 1.75 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1266 1.32 - 1.45: 2072 1.45 - 1.58: 3320 1.58 - 1.71: 9 1.71 - 1.84: 58 Bond restraints: 6725 Sorted by residual: bond pdb=" CD2 TRP D 477 " pdb=" CE3 TRP D 477 " ideal model delta sigma weight residual 1.398 1.306 0.092 1.60e-02 3.91e+03 3.28e+01 bond pdb=" CB SER D 44 " pdb=" OG SER D 44 " ideal model delta sigma weight residual 1.417 1.313 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" CB TYR A 421 " pdb=" CG TYR A 421 " ideal model delta sigma weight residual 1.512 1.402 0.110 2.20e-02 2.07e+03 2.48e+01 bond pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 1.516 1.392 0.124 2.50e-02 1.60e+03 2.45e+01 bond pdb=" CB HIS D 540 " pdb=" CG HIS D 540 " ideal model delta sigma weight residual 1.497 1.430 0.067 1.40e-02 5.10e+03 2.29e+01 ... (remaining 6720 not shown) Histogram of bond angle deviations from ideal: 95.90 - 103.71: 92 103.71 - 111.52: 2559 111.52 - 119.32: 2954 119.32 - 127.13: 3444 127.13 - 134.94: 91 Bond angle restraints: 9140 Sorted by residual: angle pdb=" C GLY D 537 " pdb=" N PRO D 538 " pdb=" CA PRO D 538 " ideal model delta sigma weight residual 119.78 128.55 -8.77 1.03e+00 9.43e-01 7.24e+01 angle pdb=" C ALA A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta sigma weight residual 119.47 129.12 -9.65 1.16e+00 7.43e-01 6.93e+01 angle pdb=" C ASN D 137 " pdb=" N PRO D 138 " pdb=" CA PRO D 138 " ideal model delta sigma weight residual 119.56 127.64 -8.08 1.02e+00 9.61e-01 6.28e+01 angle pdb=" C VAL D 283 " pdb=" N PRO D 284 " pdb=" CA PRO D 284 " ideal model delta sigma weight residual 119.24 127.24 -8.00 1.04e+00 9.25e-01 5.91e+01 angle pdb=" C SER D 611 " pdb=" N PRO D 612 " pdb=" CA PRO D 612 " ideal model delta sigma weight residual 119.82 127.13 -7.31 9.80e-01 1.04e+00 5.57e+01 ... (remaining 9135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3870 17.80 - 35.59: 146 35.59 - 53.39: 29 53.39 - 71.19: 12 71.19 - 88.98: 5 Dihedral angle restraints: 4062 sinusoidal: 1727 harmonic: 2335 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -140.80 54.80 1 1.00e+01 1.00e-02 4.07e+01 dihedral pdb=" C TYR A 421 " pdb=" N TYR A 421 " pdb=" CA TYR A 421 " pdb=" CB TYR A 421 " ideal model delta harmonic sigma weight residual -122.60 -135.05 12.45 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" CA ALA D 153 " pdb=" C ALA D 153 " pdb=" N ASN D 154 " pdb=" CA ASN D 154 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 4059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 838 0.137 - 0.274: 124 0.274 - 0.412: 10 0.412 - 0.549: 3 0.549 - 0.686: 1 Chirality restraints: 976 Sorted by residual: chirality pdb=" CA TYR A 421 " pdb=" N TYR A 421 " pdb=" C TYR A 421 " pdb=" CB TYR A 421 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" C1 NAG D1002 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG D1002 " pdb=" O5 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.93 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" C2 NAG D1002 " pdb=" C1 NAG D1002 " pdb=" C3 NAG D1002 " pdb=" N2 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.49 -3.00 0.50 2.00e-01 2.50e+01 6.35e+00 ... (remaining 973 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 90 " 0.217 2.00e-02 2.50e+03 2.54e-01 8.05e+02 pdb=" CG ASN D 90 " -0.123 2.00e-02 2.50e+03 pdb=" OD1 ASN D 90 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN D 90 " -0.403 2.00e-02 2.50e+03 pdb=" C1 NAG D1005 " 0.312 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 163 " 0.287 2.00e-02 2.50e+03 1.39e-01 4.80e+02 pdb=" CG TRP D 163 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP D 163 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP D 163 " -0.148 2.00e-02 2.50e+03 pdb=" NE1 TRP D 163 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TRP D 163 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP D 163 " -0.174 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 163 " 0.148 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 163 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP D 163 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.135 2.00e-02 2.50e+03 1.44e-01 2.59e+02 pdb=" CG ASN A 343 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.225 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " -0.171 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1716 2.80 - 3.33: 6477 3.33 - 3.85: 11592 3.85 - 4.38: 14234 4.38 - 4.90: 22417 Nonbonded interactions: 56436 Sorted by model distance: nonbonded pdb=" O4 NAG D1004 " pdb=" O6 NAG D1004 " model vdw 2.277 2.440 nonbonded pdb=" N ASN D 103 " pdb=" OD1 ASN D 103 " model vdw 2.318 2.520 nonbonded pdb=" N ASN D 432 " pdb=" OD1 ASN D 432 " model vdw 2.327 2.520 nonbonded pdb=" N ASN D 546 " pdb=" OD1 ASN D 546 " model vdw 2.356 2.520 nonbonded pdb=" N ASN D 322 " pdb=" OD1 ASN D 322 " model vdw 2.411 2.520 ... (remaining 56431 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.820 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: 16.700 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.150 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.018 0.125 6725 Z= 1.160 Angle : 1.709 10.789 9140 Z= 1.169 Chirality : 0.101 0.686 976 Planarity : 0.011 0.139 1177 Dihedral : 10.891 88.982 2543 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.43 % Allowed : 1.57 % Favored : 98.00 % Cbeta Deviations : 0.27 % 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: -0.24 (0.28), residues: 792 helix: -0.33 (0.23), residues: 378 sheet: 0.33 (0.67), residues: 58 loop : 0.18 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.287 0.015 TRP D 163 HIS 0.010 0.002 HIS D 241 PHE 0.069 0.008 PHE D 32 TYR 0.070 0.011 TYR D 180 ARG 0.016 0.001 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 198 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 ASN cc_start: 0.7661 (m-40) cc_final: 0.7098 (p0) REVERT: A 472 ILE cc_start: 0.7249 (mm) cc_final: 0.7040 (mm) REVERT: A 500 THR cc_start: 0.8413 (p) cc_final: 0.8103 (p) REVERT: D 476 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8347 (mptt) outliers start: 3 outliers final: 1 residues processed: 200 average time/residue: 0.2357 time to fit residues: 59.4289 Evaluate side-chains 121 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 322 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 0.0040 chunk 71 optimal weight: 0.9980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 ASN D 96 GLN D 401 HIS D 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6725 Z= 0.222 Angle : 0.671 9.850 9140 Z= 0.347 Chirality : 0.052 0.629 976 Planarity : 0.004 0.038 1177 Dihedral : 7.301 81.869 1013 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.29 % Allowed : 8.58 % Favored : 89.13 % 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: 792 helix: 1.39 (0.27), residues: 373 sheet: 0.06 (0.67), residues: 60 loop : 0.35 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 165 HIS 0.005 0.001 HIS D 374 PHE 0.020 0.002 PHE D 369 TYR 0.021 0.002 TYR D 183 ARG 0.004 0.001 ARG D 559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7955 (pt) cc_final: 0.7507 (pt) REVERT: A 355 ARG cc_start: 0.8498 (tpt170) cc_final: 0.8200 (tpt170) REVERT: D 26 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8176 (ttmt) REVERT: D 56 GLU cc_start: 0.8065 (pm20) cc_final: 0.7495 (pm20) REVERT: D 60 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7617 (mm-40) REVERT: D 115 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.7333 (mmm-85) REVERT: D 168 TRP cc_start: 0.7208 (t-100) cc_final: 0.6754 (t-100) REVERT: D 206 ASP cc_start: 0.8817 (t70) cc_final: 0.8578 (t0) REVERT: D 210 ASN cc_start: 0.7182 (m-40) cc_final: 0.6899 (m-40) outliers start: 16 outliers final: 8 residues processed: 153 average time/residue: 0.1910 time to fit residues: 38.0435 Evaluate side-chains 128 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 599 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 ASN D 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6725 Z= 0.282 Angle : 0.686 14.611 9140 Z= 0.346 Chirality : 0.052 0.629 976 Planarity : 0.004 0.030 1177 Dihedral : 6.756 63.680 1011 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.29 % Allowed : 9.87 % Favored : 86.84 % 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: 792 helix: 1.38 (0.27), residues: 381 sheet: -0.25 (0.66), residues: 59 loop : 0.30 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 478 HIS 0.008 0.001 HIS D 378 PHE 0.016 0.002 PHE D 230 TYR 0.017 0.001 TYR D 385 ARG 0.004 0.001 ARG D 518 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 117 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 469 SER cc_start: 0.8693 (t) cc_final: 0.8477 (p) REVERT: A 498 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8062 (mt0) REVERT: D 26 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8385 (ttmt) REVERT: D 56 GLU cc_start: 0.8048 (pm20) cc_final: 0.7542 (pm20) REVERT: D 115 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7561 (mmm-85) REVERT: D 168 TRP cc_start: 0.7330 (t-100) cc_final: 0.6705 (t-100) REVERT: D 174 LYS cc_start: 0.8537 (ttmt) cc_final: 0.8291 (mttp) REVERT: D 210 ASN cc_start: 0.7415 (m-40) cc_final: 0.7004 (m-40) REVERT: D 366 MET cc_start: 0.7105 (ppp) cc_final: 0.6872 (ppp) REVERT: D 401 HIS cc_start: 0.8605 (OUTLIER) cc_final: 0.7627 (t-90) REVERT: D 472 GLN cc_start: 0.7232 (mp10) cc_final: 0.6585 (mp10) REVERT: D 475 LYS cc_start: 0.8986 (ttpp) cc_final: 0.8765 (ttpt) outliers start: 23 outliers final: 11 residues processed: 130 average time/residue: 0.2239 time to fit residues: 38.7169 Evaluate side-chains 126 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 401 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6725 Z= 0.240 Angle : 0.610 10.163 9140 Z= 0.311 Chirality : 0.050 0.563 976 Planarity : 0.003 0.027 1177 Dihedral : 5.946 50.659 1011 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.43 % Allowed : 10.73 % Favored : 85.84 % 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: 1.07 (0.30), residues: 792 helix: 1.52 (0.27), residues: 381 sheet: -0.43 (0.64), residues: 61 loop : 0.13 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 165 HIS 0.006 0.001 HIS D 378 PHE 0.015 0.002 PHE D 369 TYR 0.017 0.001 TYR D 385 ARG 0.003 0.000 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 423 TYR cc_start: 0.8519 (t80) cc_final: 0.8316 (t80) REVERT: A 469 SER cc_start: 0.8646 (t) cc_final: 0.8420 (p) REVERT: A 498 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7972 (mt0) REVERT: D 56 GLU cc_start: 0.7974 (pm20) cc_final: 0.7490 (pm20) REVERT: D 168 TRP cc_start: 0.7348 (t-100) cc_final: 0.6740 (t-100) REVERT: D 210 ASN cc_start: 0.7527 (m-40) cc_final: 0.7253 (m-40) REVERT: D 249 MET cc_start: 0.7963 (tpt) cc_final: 0.7713 (tpt) REVERT: D 355 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7811 (m-30) REVERT: D 366 MET cc_start: 0.7187 (ppp) cc_final: 0.6916 (ppp) REVERT: D 401 HIS cc_start: 0.8560 (OUTLIER) cc_final: 0.7664 (t-90) REVERT: D 472 GLN cc_start: 0.7024 (mp10) cc_final: 0.6399 (mp10) outliers start: 24 outliers final: 12 residues processed: 137 average time/residue: 0.1931 time to fit residues: 34.7365 Evaluate side-chains 131 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 530 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 44 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6725 Z= 0.199 Angle : 0.582 9.323 9140 Z= 0.295 Chirality : 0.048 0.539 976 Planarity : 0.003 0.027 1177 Dihedral : 5.546 51.455 1011 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.58 % Allowed : 11.87 % Favored : 85.55 % 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: 1.18 (0.31), residues: 792 helix: 1.68 (0.27), residues: 381 sheet: -0.47 (0.63), residues: 61 loop : 0.13 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 165 HIS 0.005 0.001 HIS D 378 PHE 0.014 0.001 PHE D 369 TYR 0.016 0.001 TYR D 385 ARG 0.003 0.000 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.6285 (t70) cc_final: 0.5775 (m-30) REVERT: A 498 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: D 56 GLU cc_start: 0.7941 (pm20) cc_final: 0.7481 (pm20) REVERT: D 63 ASN cc_start: 0.7914 (m-40) cc_final: 0.7655 (m-40) REVERT: D 115 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7724 (mmm-85) REVERT: D 163 TRP cc_start: 0.6194 (t60) cc_final: 0.5958 (t60) REVERT: D 210 ASN cc_start: 0.7735 (m-40) cc_final: 0.7465 (m-40) REVERT: D 472 GLN cc_start: 0.7213 (mp10) cc_final: 0.6977 (mp10) outliers start: 18 outliers final: 11 residues processed: 129 average time/residue: 0.2070 time to fit residues: 34.5085 Evaluate side-chains 121 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 530 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6725 Z= 0.357 Angle : 0.670 8.806 9140 Z= 0.343 Chirality : 0.052 0.628 976 Planarity : 0.004 0.030 1177 Dihedral : 5.876 49.529 1011 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.86 % Allowed : 13.45 % Favored : 83.69 % 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: 0.86 (0.30), residues: 792 helix: 1.40 (0.26), residues: 383 sheet: -0.50 (0.62), residues: 61 loop : -0.07 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 477 HIS 0.006 0.002 HIS D 378 PHE 0.018 0.002 PHE A 374 TYR 0.015 0.002 TYR D 385 ARG 0.003 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: D 63 ASN cc_start: 0.8102 (m-40) cc_final: 0.7861 (m-40) REVERT: D 115 ARG cc_start: 0.8061 (mmm-85) cc_final: 0.7686 (mmm-85) REVERT: D 210 ASN cc_start: 0.7731 (m-40) cc_final: 0.7476 (m-40) REVERT: D 401 HIS cc_start: 0.8673 (OUTLIER) cc_final: 0.7696 (t-90) outliers start: 20 outliers final: 16 residues processed: 121 average time/residue: 0.2033 time to fit residues: 32.4120 Evaluate side-chains 123 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 599 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8168 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6725 Z= 0.246 Angle : 0.630 9.971 9140 Z= 0.317 Chirality : 0.050 0.546 976 Planarity : 0.003 0.029 1177 Dihedral : 5.696 51.545 1011 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.15 % Allowed : 13.88 % Favored : 82.98 % 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: 0.92 (0.31), residues: 792 helix: 1.53 (0.27), residues: 382 sheet: -0.01 (0.68), residues: 52 loop : -0.24 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 168 HIS 0.004 0.001 HIS D 378 PHE 0.013 0.001 PHE A 374 TYR 0.016 0.001 TYR D 385 ARG 0.003 0.000 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 484 GLU cc_start: 0.6430 (tp30) cc_final: 0.5823 (mt-10) REVERT: A 498 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: D 63 ASN cc_start: 0.7990 (m-40) cc_final: 0.7766 (m-40) REVERT: D 210 ASN cc_start: 0.7739 (m-40) cc_final: 0.7481 (m-40) REVERT: D 401 HIS cc_start: 0.8600 (OUTLIER) cc_final: 0.7627 (t-90) outliers start: 22 outliers final: 16 residues processed: 129 average time/residue: 0.2187 time to fit residues: 37.6078 Evaluate side-chains 126 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 599 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 51 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8155 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 6725 Z= 0.243 Angle : 0.636 10.749 9140 Z= 0.321 Chirality : 0.049 0.537 976 Planarity : 0.003 0.029 1177 Dihedral : 5.724 51.709 1011 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.72 % Allowed : 15.45 % Favored : 81.83 % 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: 0.95 (0.30), residues: 792 helix: 1.59 (0.26), residues: 382 sheet: 0.01 (0.67), residues: 52 loop : -0.28 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 163 HIS 0.004 0.001 HIS D 378 PHE 0.012 0.001 PHE D 523 TYR 0.016 0.001 TYR D 385 ARG 0.003 0.000 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 484 GLU cc_start: 0.6408 (tp30) cc_final: 0.5776 (mt-10) REVERT: A 498 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7870 (mt0) REVERT: D 115 ARG cc_start: 0.8036 (mmm-85) cc_final: 0.7703 (mmm-85) REVERT: D 163 TRP cc_start: 0.5938 (t60) cc_final: 0.5677 (t60) REVERT: D 210 ASN cc_start: 0.7753 (m-40) cc_final: 0.7493 (m-40) REVERT: D 366 MET cc_start: 0.7279 (ppp) cc_final: 0.6955 (ppp) REVERT: D 401 HIS cc_start: 0.8544 (OUTLIER) cc_final: 0.7620 (t-90) outliers start: 19 outliers final: 16 residues processed: 126 average time/residue: 0.1988 time to fit residues: 32.7938 Evaluate side-chains 126 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 599 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6725 Z= 0.277 Angle : 0.657 10.399 9140 Z= 0.332 Chirality : 0.051 0.559 976 Planarity : 0.003 0.030 1177 Dihedral : 5.741 51.441 1011 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.86 % Allowed : 16.31 % Favored : 80.83 % 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: 0.85 (0.30), residues: 792 helix: 1.52 (0.26), residues: 382 sheet: -0.36 (0.61), residues: 62 loop : -0.28 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 477 HIS 0.005 0.001 HIS D 378 PHE 0.014 0.001 PHE A 374 TYR 0.016 0.001 TYR D 385 ARG 0.003 0.000 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 484 GLU cc_start: 0.6392 (tp30) cc_final: 0.5803 (mt-10) REVERT: A 498 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7884 (mt0) REVERT: D 210 ASN cc_start: 0.7745 (m-40) cc_final: 0.7492 (m-40) REVERT: D 401 HIS cc_start: 0.8613 (OUTLIER) cc_final: 0.7725 (t-90) outliers start: 20 outliers final: 16 residues processed: 119 average time/residue: 0.2081 time to fit residues: 32.6073 Evaluate side-chains 123 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 599 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6725 Z= 0.242 Angle : 0.639 9.063 9140 Z= 0.322 Chirality : 0.050 0.529 976 Planarity : 0.003 0.029 1177 Dihedral : 5.682 52.202 1011 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.72 % Allowed : 16.17 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.30), residues: 792 helix: 1.56 (0.26), residues: 382 sheet: 0.06 (0.68), residues: 52 loop : -0.37 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 163 HIS 0.006 0.001 HIS D 378 PHE 0.012 0.001 PHE A 374 TYR 0.016 0.001 TYR D 385 ARG 0.003 0.000 ARG D 582 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 498 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: D 56 GLU cc_start: 0.7903 (pm20) cc_final: 0.7575 (pm20) REVERT: D 115 ARG cc_start: 0.8084 (mmm-85) cc_final: 0.7855 (mmm160) REVERT: D 210 ASN cc_start: 0.7749 (m-40) cc_final: 0.7502 (m-40) REVERT: D 366 MET cc_start: 0.7381 (ppp) cc_final: 0.6720 (ppp) REVERT: D 401 HIS cc_start: 0.8517 (OUTLIER) cc_final: 0.7595 (t-90) outliers start: 19 outliers final: 16 residues processed: 121 average time/residue: 0.2134 time to fit residues: 33.8888 Evaluate side-chains 122 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 599 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 64 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.109120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.096764 restraints weight = 15362.330| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.73 r_work: 0.3364 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6725 Z= 0.240 Angle : 0.640 8.592 9140 Z= 0.324 Chirality : 0.050 0.534 976 Planarity : 0.003 0.030 1177 Dihedral : 5.706 51.973 1011 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.72 % Allowed : 16.74 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.30), residues: 792 helix: 1.56 (0.26), residues: 382 sheet: -0.04 (0.68), residues: 52 loop : -0.36 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 168 HIS 0.005 0.001 HIS D 378 PHE 0.012 0.001 PHE D 523 TYR 0.016 0.001 TYR A 365 ARG 0.002 0.000 ARG D 582 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1967.63 seconds wall clock time: 36 minutes 59.41 seconds (2219.41 seconds total)