Starting phenix.real_space_refine on Mon Mar 11 07:53:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sep_25074/03_2024/7sep_25074.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sep_25074/03_2024/7sep_25074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sep_25074/03_2024/7sep_25074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sep_25074/03_2024/7sep_25074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sep_25074/03_2024/7sep_25074.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sep_25074/03_2024/7sep_25074.pdb" } resolution = 3.8 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= 0.017 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 15 5.16 5 C 4967 2.51 5 N 1261 2.21 5 O 1398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 7641 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4343 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 496} Chain breaks: 4 Chain: "B" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3298 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 368} Chain breaks: 3 Time building chain proxies: 4.78, per 1000 atoms: 0.63 Number of scatterers: 7641 At special positions: 0 Unit cell: (78.155, 98.455, 127.89, 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 15 16.00 O 1398 8.00 N 1261 7.00 C 4967 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: 3.14 Conformation dependent library (CDL) restraints added in 1.3 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 40.4% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 removed outlier: 3.928A pdb=" N ALA A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 124 through 127 Processing helix chain 'A' and resid 155 through 175 removed outlier: 3.731A pdb=" N ILE A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.907A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 271 removed outlier: 3.981A pdb=" N GLY A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 270 " --> pdb=" O TRP A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.520A pdb=" N THR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 311 Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 405 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.839A pdb=" N ILE A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 485 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.561A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.779A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 549 removed outlier: 3.515A pdb=" N GLN A 547 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.598A pdb=" N GLU B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.810A pdb=" N GLU B 89 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 90' Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.557A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 4.293A pdb=" N LYS B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 175 removed outlier: 4.052A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.504A pdb=" N TRP B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 removed outlier: 3.953A pdb=" N TRP B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 removed outlier: 4.219A pdb=" N LEU B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 311 Processing helix chain 'B' and resid 364 through 384 removed outlier: 3.540A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.679A pdb=" N THR B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.935A pdb=" N TRP B 406 " --> pdb=" O THR B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing helix chain 'B' and resid 422 through 428 removed outlier: 3.902A pdb=" N GLN B 428 " --> pdb=" O LYS B 424 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 326 through 328 removed outlier: 6.843A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 338 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.592A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 391 removed outlier: 6.571A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 455 through 459 removed outlier: 4.136A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 494 " --> pdb=" O GLU A 438 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 49 removed outlier: 4.020A pdb=" N ILE B 142 " --> pdb=" O ILE B 132 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AB3, first strand: chain 'B' and resid 106 through 110 Processing sheet with id=AB4, first strand: chain 'B' and resid 347 through 355 removed outlier: 7.964A pdb=" N LYS B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN B 343 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 341 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR B 351 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR B 339 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS B 353 " --> pdb=" O TRP B 337 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP B 337 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 284 hydrogen bonds defined for protein. 768 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: 1.97 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1784 1.33 - 1.45: 1570 1.45 - 1.57: 4465 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 7845 Sorted by residual: bond pdb=" N ASP A 237 " pdb=" CA ASP A 237 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.10e-02 8.26e+03 9.83e+00 bond pdb=" N HIS A 235 " pdb=" CA HIS A 235 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.18e-02 7.18e+03 9.42e+00 bond pdb=" N LEU A 234 " pdb=" CA LEU A 234 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.30e-02 5.92e+03 6.92e+00 bond pdb=" N TRP A 239 " pdb=" CA TRP A 239 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.26e-02 6.30e+03 5.84e+00 bond pdb=" N THR A 240 " pdb=" CA THR A 240 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.54e+00 ... (remaining 7840 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.76: 317 106.76 - 113.71: 4428 113.71 - 120.66: 3198 120.66 - 127.62: 2587 127.62 - 134.57: 122 Bond angle restraints: 10652 Sorted by residual: angle pdb=" C HIS A 235 " pdb=" CA HIS A 235 " pdb=" CB HIS A 235 " ideal model delta sigma weight residual 108.87 115.04 -6.17 1.55e+00 4.16e-01 1.59e+01 angle pdb=" N PRO A 236 " pdb=" CA PRO A 236 " pdb=" C PRO A 236 " ideal model delta sigma weight residual 112.47 119.69 -7.22 2.06e+00 2.36e-01 1.23e+01 angle pdb=" CA THR A 240 " pdb=" C THR A 240 " pdb=" O THR A 240 " ideal model delta sigma weight residual 121.45 117.82 3.63 1.07e+00 8.73e-01 1.15e+01 angle pdb=" CA LYS A 238 " pdb=" C LYS A 238 " pdb=" O LYS A 238 " ideal model delta sigma weight residual 121.51 118.20 3.31 1.12e+00 7.97e-01 8.71e+00 angle pdb=" C HIS A 235 " pdb=" N PRO A 236 " pdb=" CA PRO A 236 " ideal model delta sigma weight residual 119.84 123.26 -3.42 1.25e+00 6.40e-01 7.48e+00 ... (remaining 10647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 4317 16.64 - 33.27: 308 33.27 - 49.91: 78 49.91 - 66.54: 18 66.54 - 83.18: 4 Dihedral angle restraints: 4725 sinusoidal: 2009 harmonic: 2716 Sorted by residual: dihedral pdb=" CA LEU B 289 " pdb=" C LEU B 289 " pdb=" N THR B 290 " pdb=" CA THR B 290 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA PRO A 433 " pdb=" C PRO A 433 " pdb=" N ILE A 434 " pdb=" CA ILE A 434 " ideal model delta harmonic sigma weight residual -180.00 -159.97 -20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ASP B 185 " pdb=" C ASP B 185 " pdb=" N ASP B 186 " pdb=" CA ASP B 186 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 649 0.032 - 0.064: 326 0.064 - 0.096: 119 0.096 - 0.128: 54 0.128 - 0.160: 9 Chirality restraints: 1157 Sorted by residual: chirality pdb=" CB ILE A 434 " pdb=" CA ILE A 434 " pdb=" CG1 ILE A 434 " pdb=" CG2 ILE A 434 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA PRO A 236 " pdb=" N PRO A 236 " pdb=" C PRO A 236 " pdb=" CB PRO A 236 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA PRO B 140 " pdb=" N PRO B 140 " pdb=" C PRO B 140 " pdb=" CB PRO B 140 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 1154 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 420 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 421 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 239 " 0.024 2.00e-02 2.50e+03 1.25e-02 3.88e+00 pdb=" CG TRP A 239 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 239 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 239 " -0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP A 239 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 239 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 239 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 239 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 239 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 239 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 411 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO B 412 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 412 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 412 " 0.025 5.00e-02 4.00e+02 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 270 2.70 - 3.25: 7642 3.25 - 3.80: 11915 3.80 - 4.35: 13907 4.35 - 4.90: 23690 Nonbonded interactions: 57424 Sorted by model distance: nonbonded pdb=" N ASN A 545 " pdb=" OD1 ASN A 545 " model vdw 2.155 2.520 nonbonded pdb=" O SER A 162 " pdb=" OG1 THR A 165 " model vdw 2.219 2.440 nonbonded pdb=" OH TYR B 354 " pdb=" OE1 GLU B 370 " model vdw 2.228 2.440 nonbonded pdb=" OG1 THR A 419 " pdb=" O PRO A 421 " model vdw 2.234 2.440 nonbonded pdb=" OG1 THR B 253 " pdb=" O GLU B 291 " model vdw 2.240 2.440 ... (remaining 57419 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 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.810 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 24.060 Find NCS groups from input model: 0.350 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 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 : 0.006 0.048 7845 Z= 0.383 Angle : 0.659 8.506 10652 Z= 0.378 Chirality : 0.046 0.160 1157 Planarity : 0.006 0.050 1335 Dihedral : 12.759 83.180 2969 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 8.22 % Allowed : 8.94 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.19 (0.29), residues: 912 helix: 1.24 (0.31), residues: 297 sheet: -0.86 (0.42), residues: 150 loop : -0.73 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 239 HIS 0.006 0.001 HIS A 235 PHE 0.011 0.002 PHE A 124 TYR 0.019 0.002 TYR A 441 ARG 0.004 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 386 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7338 (pp20) REVERT: A 47 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6672 (tt) REVERT: A 48 SER cc_start: 0.8279 (t) cc_final: 0.7776 (p) REVERT: A 56 TYR cc_start: 0.7694 (m-80) cc_final: 0.7060 (m-80) REVERT: A 75 VAL cc_start: 0.7654 (t) cc_final: 0.7278 (m) REVERT: A 79 GLU cc_start: 0.6254 (pt0) cc_final: 0.5980 (pt0) REVERT: A 83 ARG cc_start: 0.7854 (mtt-85) cc_final: 0.5570 (mtp85) REVERT: A 86 ASP cc_start: 0.7125 (t70) cc_final: 0.6825 (t0) REVERT: A 87 PHE cc_start: 0.7684 (m-80) cc_final: 0.7420 (m-10) REVERT: A 101 LYS cc_start: 0.8415 (mttm) cc_final: 0.7687 (mtpp) REVERT: A 104 LYS cc_start: 0.8590 (tmtt) cc_final: 0.8273 (mtpp) REVERT: A 106 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7924 (t) REVERT: A 108 VAL cc_start: 0.8596 (t) cc_final: 0.8347 (p) REVERT: A 110 ASP cc_start: 0.6783 (p0) cc_final: 0.6557 (p0) REVERT: A 123 ASP cc_start: 0.8520 (p0) cc_final: 0.6693 (t0) REVERT: A 124 PHE cc_start: 0.8296 (t80) cc_final: 0.7982 (t80) REVERT: A 126 LYS cc_start: 0.8644 (mttm) cc_final: 0.8239 (mtmm) REVERT: A 142 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7104 (pt) REVERT: A 144 TYR cc_start: 0.6505 (m-80) cc_final: 0.6182 (m-80) REVERT: A 161 GLN cc_start: 0.8406 (tt0) cc_final: 0.7944 (tt0) REVERT: A 162 SER cc_start: 0.8719 (m) cc_final: 0.8488 (p) REVERT: A 169 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7488 (mm-30) REVERT: A 172 LYS cc_start: 0.8858 (tttp) cc_final: 0.8497 (ttpt) REVERT: A 173 LYS cc_start: 0.8781 (tttt) cc_final: 0.8571 (tttt) REVERT: A 180 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8371 (mt) REVERT: A 181 TYR cc_start: 0.7498 (m-80) cc_final: 0.7161 (m-80) REVERT: A 182 GLN cc_start: 0.7160 (tm-30) cc_final: 0.6890 (tm-30) REVERT: A 203 GLU cc_start: 0.7549 (tt0) cc_final: 0.7318 (tt0) REVERT: A 204 GLU cc_start: 0.7485 (tp30) cc_final: 0.7124 (tm-30) REVERT: A 206 ARG cc_start: 0.8125 (mtp-110) cc_final: 0.7441 (ttm-80) REVERT: A 208 HIS cc_start: 0.8153 (t-90) cc_final: 0.7823 (t-170) REVERT: A 217 PRO cc_start: 0.8027 (Cg_exo) cc_final: 0.7779 (Cg_endo) REVERT: A 232 TYR cc_start: 0.7930 (m-80) cc_final: 0.7689 (m-80) REVERT: A 233 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6798 (mt-10) REVERT: A 264 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8440 (mp) REVERT: A 303 LEU cc_start: 0.8693 (mt) cc_final: 0.8293 (mt) REVERT: A 328 GLU cc_start: 0.7705 (tt0) cc_final: 0.7049 (tt0) REVERT: A 329 ILE cc_start: 0.8502 (mt) cc_final: 0.8224 (mt) REVERT: A 347 LYS cc_start: 0.8550 (mttt) cc_final: 0.8213 (mttm) REVERT: A 350 LYS cc_start: 0.8071 (tttt) cc_final: 0.7831 (ttpp) REVERT: A 354 TYR cc_start: 0.6330 (t80) cc_final: 0.6074 (t80) REVERT: A 357 MET cc_start: 0.5552 (tpt) cc_final: 0.5278 (tpt) REVERT: A 363 ASN cc_start: 0.7853 (t0) cc_final: 0.7543 (t0) REVERT: A 366 LYS cc_start: 0.8337 (tptm) cc_final: 0.7777 (ttmm) REVERT: A 370 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7322 (mt-10) REVERT: A 374 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8004 (ttpp) REVERT: A 378 GLU cc_start: 0.7802 (tp30) cc_final: 0.7563 (tp30) REVERT: A 406 TRP cc_start: 0.7835 (p90) cc_final: 0.7296 (p90) REVERT: A 407 GLN cc_start: 0.7886 (mt0) cc_final: 0.7318 (mt0) REVERT: A 417 VAL cc_start: 0.8358 (t) cc_final: 0.8157 (m) REVERT: A 419 THR cc_start: 0.7623 (OUTLIER) cc_final: 0.7210 (p) REVERT: A 422 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7767 (mp) REVERT: A 424 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.6899 (ttpp) REVERT: A 429 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8415 (mt) REVERT: A 454 LYS cc_start: 0.4669 (OUTLIER) cc_final: 0.4302 (mttp) REVERT: A 478 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7215 (mm-30) REVERT: A 479 LEU cc_start: 0.8439 (tp) cc_final: 0.8133 (mm) REVERT: A 483 TYR cc_start: 0.7797 (t80) cc_final: 0.7421 (t80) REVERT: A 492 GLU cc_start: 0.6951 (mp0) cc_final: 0.6728 (mp0) REVERT: A 494 ASN cc_start: 0.7522 (m110) cc_final: 0.6997 (m110) REVERT: A 496 VAL cc_start: 0.8296 (t) cc_final: 0.7991 (m) REVERT: A 500 GLN cc_start: 0.7667 (pt0) cc_final: 0.7352 (pt0) REVERT: A 503 LEU cc_start: 0.8249 (tp) cc_final: 0.7822 (tp) REVERT: A 507 GLN cc_start: 0.8697 (pt0) cc_final: 0.8435 (pt0) REVERT: A 523 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7692 (mt-10) REVERT: A 524 GLN cc_start: 0.7842 (tp40) cc_final: 0.7488 (mm-40) REVERT: A 529 GLU cc_start: 0.6989 (tp30) cc_final: 0.6757 (tp30) REVERT: A 540 LYS cc_start: 0.8292 (mmtt) cc_final: 0.8002 (mmtt) REVERT: A 545 ASN cc_start: 0.4369 (OUTLIER) cc_final: 0.3365 (p0) REVERT: A 548 VAL cc_start: 0.2320 (t) cc_final: 0.1515 (m) REVERT: B 21 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.7964 (m) REVERT: B 22 LYS cc_start: 0.8263 (tttp) cc_final: 0.7859 (tttp) REVERT: B 27 THR cc_start: 0.8006 (p) cc_final: 0.7620 (p) REVERT: B 34 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8119 (tp) REVERT: B 37 ILE cc_start: 0.8439 (mp) cc_final: 0.8164 (tt) REVERT: B 41 MET cc_start: 0.7683 (mtt) cc_final: 0.7457 (mtt) REVERT: B 42 GLU cc_start: 0.7023 (tt0) cc_final: 0.6649 (tt0) REVERT: B 57 ASN cc_start: 0.8083 (t0) cc_final: 0.7752 (t0) REVERT: B 77 PHE cc_start: 0.7999 (m-80) cc_final: 0.7720 (m-10) REVERT: B 82 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8148 (ttmt) REVERT: B 104 LYS cc_start: 0.7879 (ttmt) cc_final: 0.7321 (ttmt) REVERT: B 131 THR cc_start: 0.7592 (m) cc_final: 0.7186 (p) REVERT: B 135 ILE cc_start: 0.8441 (mm) cc_final: 0.8108 (mm) REVERT: B 144 TYR cc_start: 0.8691 (m-80) cc_final: 0.8457 (m-80) REVERT: B 175 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.6753 (p0) REVERT: B 192 ASP cc_start: 0.8093 (t70) cc_final: 0.7671 (t70) REVERT: B 201 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7643 (mmtm) REVERT: B 204 GLU cc_start: 0.7985 (tp30) cc_final: 0.7568 (tp30) REVERT: B 256 ASP cc_start: 0.7366 (t70) cc_final: 0.6515 (t0) REVERT: B 257 ILE cc_start: 0.7823 (mt) cc_final: 0.7612 (mm) REVERT: B 260 LEU cc_start: 0.7595 (tp) cc_final: 0.7244 (mt) REVERT: B 263 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7704 (ttmp) REVERT: B 264 LEU cc_start: 0.8870 (tp) cc_final: 0.8615 (mm) REVERT: B 266 TRP cc_start: 0.7727 (t60) cc_final: 0.7383 (t60) REVERT: B 293 ILE cc_start: 0.6631 (mm) cc_final: 0.6382 (mm) REVERT: B 298 GLU cc_start: 0.8340 (pt0) cc_final: 0.7896 (tt0) REVERT: B 309 ILE cc_start: 0.8556 (mt) cc_final: 0.7979 (mt) REVERT: B 322 SER cc_start: 0.8746 (m) cc_final: 0.8239 (t) REVERT: B 328 GLU cc_start: 0.7067 (tt0) cc_final: 0.6850 (tt0) REVERT: B 347 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7930 (mttm) REVERT: B 350 LYS cc_start: 0.8203 (tptp) cc_final: 0.7920 (tppp) REVERT: B 356 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.6509 (mmm160) REVERT: B 357 MET cc_start: 0.6218 (ptp) cc_final: 0.5984 (ptp) REVERT: B 391 LEU cc_start: 0.8518 (mt) cc_final: 0.8040 (mt) REVERT: B 396 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6903 (mt-10) REVERT: B 398 TRP cc_start: 0.8883 (t-100) cc_final: 0.8323 (t-100) outliers start: 69 outliers final: 28 residues processed: 426 average time/residue: 0.2284 time to fit residues: 125.6735 Evaluate side-chains 404 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 357 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 367 GLN A 480 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7845 Z= 0.238 Angle : 0.610 9.270 10652 Z= 0.316 Chirality : 0.045 0.146 1157 Planarity : 0.006 0.075 1335 Dihedral : 9.895 83.848 1090 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 8.34 % Allowed : 18.36 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.08 (0.28), residues: 912 helix: 1.27 (0.30), residues: 310 sheet: -0.71 (0.41), residues: 140 loop : -0.72 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 239 HIS 0.003 0.001 HIS B 198 PHE 0.022 0.002 PHE A 227 TYR 0.025 0.002 TYR A 319 ARG 0.006 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 344 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.6033 (mmt) cc_final: 0.5381 (mmt) REVERT: A 29 GLU cc_start: 0.7749 (tm-30) cc_final: 0.6956 (tm-30) REVERT: A 47 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6651 (tt) REVERT: A 50 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6374 (mm) REVERT: A 56 TYR cc_start: 0.7632 (m-80) cc_final: 0.7017 (m-80) REVERT: A 83 ARG cc_start: 0.7761 (mtt-85) cc_final: 0.6274 (mtt90) REVERT: A 86 ASP cc_start: 0.7055 (t70) cc_final: 0.6817 (t0) REVERT: A 87 PHE cc_start: 0.7638 (m-80) cc_final: 0.7394 (m-10) REVERT: A 101 LYS cc_start: 0.8348 (mttm) cc_final: 0.7837 (mtpt) REVERT: A 104 LYS cc_start: 0.8568 (tmtt) cc_final: 0.8272 (mmmm) REVERT: A 126 LYS cc_start: 0.8629 (mttm) cc_final: 0.8163 (mtmm) REVERT: A 142 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7180 (pt) REVERT: A 144 TYR cc_start: 0.6454 (m-80) cc_final: 0.6185 (m-80) REVERT: A 161 GLN cc_start: 0.8308 (tt0) cc_final: 0.7842 (tt0) REVERT: A 162 SER cc_start: 0.8589 (m) cc_final: 0.8378 (p) REVERT: A 169 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7477 (mm-30) REVERT: A 173 LYS cc_start: 0.8765 (tttt) cc_final: 0.8453 (tppt) REVERT: A 180 ILE cc_start: 0.8594 (tp) cc_final: 0.8256 (mt) REVERT: A 181 TYR cc_start: 0.7470 (m-80) cc_final: 0.7169 (m-80) REVERT: A 182 GLN cc_start: 0.7101 (tm-30) cc_final: 0.6798 (tm-30) REVERT: A 203 GLU cc_start: 0.7427 (tt0) cc_final: 0.7201 (tt0) REVERT: A 204 GLU cc_start: 0.7437 (tp30) cc_final: 0.7189 (tp30) REVERT: A 206 ARG cc_start: 0.8141 (mtp-110) cc_final: 0.7472 (ttm-80) REVERT: A 208 HIS cc_start: 0.7962 (t-90) cc_final: 0.7762 (t-170) REVERT: A 227 PHE cc_start: 0.7773 (m-80) cc_final: 0.6613 (m-80) REVERT: A 232 TYR cc_start: 0.8065 (m-80) cc_final: 0.7622 (m-80) REVERT: A 295 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7268 (pp) REVERT: A 328 GLU cc_start: 0.7393 (tt0) cc_final: 0.7096 (tt0) REVERT: A 329 ILE cc_start: 0.8413 (mt) cc_final: 0.8136 (mt) REVERT: A 330 GLN cc_start: 0.7556 (mp10) cc_final: 0.7180 (mp10) REVERT: A 349 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8594 (mt) REVERT: A 350 LYS cc_start: 0.8396 (tttt) cc_final: 0.8094 (ttpp) REVERT: A 357 MET cc_start: 0.5634 (tpt) cc_final: 0.5291 (tpt) REVERT: A 366 LYS cc_start: 0.8283 (tptm) cc_final: 0.7763 (mtpp) REVERT: A 369 THR cc_start: 0.8118 (m) cc_final: 0.7901 (p) REVERT: A 370 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7315 (mt-10) REVERT: A 374 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8010 (ttpp) REVERT: A 406 TRP cc_start: 0.7813 (p90) cc_final: 0.7249 (p90) REVERT: A 407 GLN cc_start: 0.7662 (mt0) cc_final: 0.7237 (mt0) REVERT: A 417 VAL cc_start: 0.8322 (t) cc_final: 0.8119 (m) REVERT: A 422 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7720 (mp) REVERT: A 424 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7994 (ptmm) REVERT: A 431 LYS cc_start: 0.8639 (mttt) cc_final: 0.8345 (mmmm) REVERT: A 454 LYS cc_start: 0.4570 (OUTLIER) cc_final: 0.4054 (mttt) REVERT: A 476 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8076 (mtpp) REVERT: A 478 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7362 (mm-30) REVERT: A 479 LEU cc_start: 0.8427 (tp) cc_final: 0.8085 (mm) REVERT: A 494 ASN cc_start: 0.7478 (m110) cc_final: 0.7172 (m110) REVERT: A 500 GLN cc_start: 0.7608 (pt0) cc_final: 0.7362 (pt0) REVERT: A 503 LEU cc_start: 0.8094 (tp) cc_final: 0.7564 (tp) REVERT: A 507 GLN cc_start: 0.8740 (pt0) cc_final: 0.8417 (pt0) REVERT: A 518 VAL cc_start: 0.8988 (t) cc_final: 0.8787 (p) REVERT: A 520 GLN cc_start: 0.7563 (tp40) cc_final: 0.7018 (tp-100) REVERT: A 523 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7651 (mt-10) REVERT: A 524 GLN cc_start: 0.7786 (tp40) cc_final: 0.7579 (mm-40) REVERT: A 540 LYS cc_start: 0.8272 (mmtt) cc_final: 0.8017 (mmmm) REVERT: A 545 ASN cc_start: 0.4269 (OUTLIER) cc_final: 0.3897 (p0) REVERT: A 548 VAL cc_start: 0.2327 (OUTLIER) cc_final: 0.1484 (m) REVERT: B 21 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8061 (m) REVERT: B 22 LYS cc_start: 0.8106 (tttp) cc_final: 0.7656 (tttp) REVERT: B 34 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8178 (tt) REVERT: B 36 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7027 (mt-10) REVERT: B 43 LYS cc_start: 0.8029 (tttp) cc_final: 0.7566 (tttp) REVERT: B 57 ASN cc_start: 0.8097 (t0) cc_final: 0.7821 (t0) REVERT: B 77 PHE cc_start: 0.7963 (m-80) cc_final: 0.7547 (m-10) REVERT: B 82 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8056 (ttmm) REVERT: B 86 ASP cc_start: 0.6975 (p0) cc_final: 0.6664 (p0) REVERT: B 105 SER cc_start: 0.8024 (t) cc_final: 0.7773 (p) REVERT: B 128 THR cc_start: 0.7833 (p) cc_final: 0.7303 (t) REVERT: B 131 THR cc_start: 0.7689 (m) cc_final: 0.7390 (p) REVERT: B 167 ILE cc_start: 0.5223 (OUTLIER) cc_final: 0.4848 (tt) REVERT: B 178 ILE cc_start: 0.8418 (mt) cc_final: 0.7996 (tp) REVERT: B 192 ASP cc_start: 0.8031 (t70) cc_final: 0.7758 (t70) REVERT: B 204 GLU cc_start: 0.7873 (tp30) cc_final: 0.7670 (tp30) REVERT: B 256 ASP cc_start: 0.7092 (t70) cc_final: 0.6609 (t70) REVERT: B 260 LEU cc_start: 0.7447 (tp) cc_final: 0.7219 (mt) REVERT: B 263 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7748 (ttmp) REVERT: B 264 LEU cc_start: 0.8760 (tp) cc_final: 0.8486 (mm) REVERT: B 266 TRP cc_start: 0.7730 (t60) cc_final: 0.7152 (t60) REVERT: B 275 LYS cc_start: 0.8486 (mttm) cc_final: 0.8212 (mmtt) REVERT: B 298 GLU cc_start: 0.8455 (pt0) cc_final: 0.7905 (tt0) REVERT: B 309 ILE cc_start: 0.8367 (mt) cc_final: 0.8033 (mm) REVERT: B 322 SER cc_start: 0.8738 (m) cc_final: 0.8298 (p) REVERT: B 328 GLU cc_start: 0.7170 (tt0) cc_final: 0.6928 (tt0) REVERT: B 347 LYS cc_start: 0.8104 (mmtm) cc_final: 0.7761 (mtpp) REVERT: B 374 LYS cc_start: 0.8128 (tttt) cc_final: 0.7822 (tptm) REVERT: B 391 LEU cc_start: 0.8470 (mt) cc_final: 0.8097 (mt) REVERT: B 396 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6713 (mt-10) REVERT: B 398 TRP cc_start: 0.8862 (t-100) cc_final: 0.8362 (t-100) REVERT: B 409 THR cc_start: 0.8269 (p) cc_final: 0.8068 (m) outliers start: 70 outliers final: 28 residues processed: 381 average time/residue: 0.2223 time to fit residues: 109.1496 Evaluate side-chains 387 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 343 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 171 PHE Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 0.0470 chunk 74 optimal weight: 0.0010 chunk 82 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 343 GLN A 348 ASN A 367 GLN A 480 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 197 GLN B 258 GLN B 373 GLN B 394 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7845 Z= 0.175 Angle : 0.572 8.954 10652 Z= 0.293 Chirality : 0.044 0.144 1157 Planarity : 0.005 0.056 1335 Dihedral : 8.200 86.739 1043 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 7.99 % Allowed : 21.57 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.28), residues: 912 helix: 1.38 (0.31), residues: 311 sheet: -0.80 (0.40), residues: 145 loop : -0.69 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 337 HIS 0.006 0.001 HIS B 235 PHE 0.024 0.002 PHE A 124 TYR 0.022 0.002 TYR A 319 ARG 0.005 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 345 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.5887 (mmt) cc_final: 0.5646 (mmt) REVERT: A 29 GLU cc_start: 0.7609 (tm-30) cc_final: 0.6910 (tm-30) REVERT: A 47 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6450 (tt) REVERT: A 50 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6112 (mt) REVERT: A 56 TYR cc_start: 0.7615 (m-80) cc_final: 0.6947 (m-80) REVERT: A 83 ARG cc_start: 0.7718 (mtt-85) cc_final: 0.6548 (mtp85) REVERT: A 101 LYS cc_start: 0.8302 (mttm) cc_final: 0.8066 (tttm) REVERT: A 104 LYS cc_start: 0.8538 (tmtt) cc_final: 0.8258 (mmmm) REVERT: A 110 ASP cc_start: 0.6526 (p0) cc_final: 0.6324 (p0) REVERT: A 126 LYS cc_start: 0.8500 (mttm) cc_final: 0.8181 (mtmm) REVERT: A 142 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7245 (pt) REVERT: A 161 GLN cc_start: 0.8250 (tt0) cc_final: 0.7740 (tt0) REVERT: A 166 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8313 (tmtt) REVERT: A 169 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7423 (mm-30) REVERT: A 172 LYS cc_start: 0.8821 (tttp) cc_final: 0.8610 (tttp) REVERT: A 173 LYS cc_start: 0.8716 (tttt) cc_final: 0.8336 (tppt) REVERT: A 180 ILE cc_start: 0.8484 (tp) cc_final: 0.8214 (mt) REVERT: A 181 TYR cc_start: 0.7560 (m-80) cc_final: 0.7258 (m-80) REVERT: A 182 GLN cc_start: 0.7089 (tm-30) cc_final: 0.6738 (tm-30) REVERT: A 203 GLU cc_start: 0.7337 (tt0) cc_final: 0.6939 (tt0) REVERT: A 204 GLU cc_start: 0.7385 (tp30) cc_final: 0.6994 (tm-30) REVERT: A 206 ARG cc_start: 0.8110 (mtp-110) cc_final: 0.7505 (ttm-80) REVERT: A 233 GLU cc_start: 0.7396 (tp30) cc_final: 0.7033 (tp30) REVERT: A 311 LYS cc_start: 0.7363 (ttpp) cc_final: 0.7149 (ttpp) REVERT: A 329 ILE cc_start: 0.8383 (mt) cc_final: 0.8094 (mt) REVERT: A 330 GLN cc_start: 0.7598 (mp10) cc_final: 0.7185 (mp10) REVERT: A 342 TYR cc_start: 0.8234 (p90) cc_final: 0.7991 (p90) REVERT: A 349 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8582 (mt) REVERT: A 350 LYS cc_start: 0.8414 (tttt) cc_final: 0.8139 (ttpp) REVERT: A 357 MET cc_start: 0.5660 (tpt) cc_final: 0.5282 (tpt) REVERT: A 366 LYS cc_start: 0.8245 (tptm) cc_final: 0.7763 (mtpp) REVERT: A 369 THR cc_start: 0.8135 (m) cc_final: 0.7902 (p) REVERT: A 370 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7313 (mt-10) REVERT: A 374 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8031 (ttpp) REVERT: A 401 TRP cc_start: 0.8279 (t60) cc_final: 0.8039 (t-100) REVERT: A 406 TRP cc_start: 0.7828 (p90) cc_final: 0.7176 (p90) REVERT: A 407 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7359 (mt0) REVERT: A 422 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7703 (mp) REVERT: A 424 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8051 (ptmm) REVERT: A 431 LYS cc_start: 0.8595 (mttt) cc_final: 0.8308 (mmmm) REVERT: A 454 LYS cc_start: 0.4530 (OUTLIER) cc_final: 0.3929 (mttt) REVERT: A 476 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8012 (mmmm) REVERT: A 478 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7259 (mm-30) REVERT: A 479 LEU cc_start: 0.8423 (tp) cc_final: 0.8195 (mm) REVERT: A 483 TYR cc_start: 0.7947 (t80) cc_final: 0.6933 (t80) REVERT: A 494 ASN cc_start: 0.7418 (m110) cc_final: 0.7103 (m110) REVERT: A 500 GLN cc_start: 0.7573 (pt0) cc_final: 0.7240 (pt0) REVERT: A 503 LEU cc_start: 0.8046 (tp) cc_final: 0.7142 (tp) REVERT: A 507 GLN cc_start: 0.8699 (pt0) cc_final: 0.8063 (pt0) REVERT: A 518 VAL cc_start: 0.8989 (t) cc_final: 0.8763 (p) REVERT: A 520 GLN cc_start: 0.7556 (tp40) cc_final: 0.6320 (tp-100) REVERT: A 523 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7621 (mt-10) REVERT: A 535 TRP cc_start: 0.8590 (t60) cc_final: 0.8314 (t60) REVERT: A 540 LYS cc_start: 0.8365 (mmtt) cc_final: 0.8011 (mmmm) REVERT: A 545 ASN cc_start: 0.4665 (OUTLIER) cc_final: 0.4109 (p0) REVERT: A 548 VAL cc_start: 0.2181 (OUTLIER) cc_final: 0.1346 (m) REVERT: B 21 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8119 (m) REVERT: B 22 LYS cc_start: 0.8085 (tttp) cc_final: 0.7669 (tttp) REVERT: B 36 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6953 (mt-10) REVERT: B 43 LYS cc_start: 0.7992 (tttp) cc_final: 0.7540 (tttp) REVERT: B 57 ASN cc_start: 0.8075 (t0) cc_final: 0.7768 (t0) REVERT: B 76 ASP cc_start: 0.8253 (t0) cc_final: 0.8052 (t0) REVERT: B 77 PHE cc_start: 0.7839 (m-80) cc_final: 0.7488 (m-10) REVERT: B 82 LYS cc_start: 0.8485 (mtpt) cc_final: 0.8208 (ttmm) REVERT: B 86 ASP cc_start: 0.6968 (p0) cc_final: 0.6418 (p0) REVERT: B 102 LYS cc_start: 0.8630 (mptt) cc_final: 0.8321 (mppt) REVERT: B 128 THR cc_start: 0.7880 (p) cc_final: 0.7427 (t) REVERT: B 131 THR cc_start: 0.7682 (m) cc_final: 0.7404 (p) REVERT: B 167 ILE cc_start: 0.5026 (OUTLIER) cc_final: 0.4710 (tt) REVERT: B 178 ILE cc_start: 0.8397 (mt) cc_final: 0.7999 (tp) REVERT: B 204 GLU cc_start: 0.7892 (tp30) cc_final: 0.7678 (tp30) REVERT: B 256 ASP cc_start: 0.6959 (t70) cc_final: 0.6113 (t70) REVERT: B 260 LEU cc_start: 0.7458 (tp) cc_final: 0.7232 (mt) REVERT: B 263 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7648 (ttmp) REVERT: B 266 TRP cc_start: 0.7796 (t60) cc_final: 0.7183 (t60) REVERT: B 298 GLU cc_start: 0.8298 (pt0) cc_final: 0.7653 (tt0) REVERT: B 309 ILE cc_start: 0.8441 (mt) cc_final: 0.8042 (mm) REVERT: B 322 SER cc_start: 0.8743 (m) cc_final: 0.8315 (p) REVERT: B 328 GLU cc_start: 0.7253 (tt0) cc_final: 0.7040 (tt0) REVERT: B 347 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7866 (mttm) REVERT: B 368 LEU cc_start: 0.8282 (tp) cc_final: 0.8068 (tp) REVERT: B 374 LYS cc_start: 0.8159 (tttt) cc_final: 0.7793 (tptp) REVERT: B 391 LEU cc_start: 0.8502 (mt) cc_final: 0.8125 (mt) REVERT: B 396 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6616 (mt-10) REVERT: B 398 TRP cc_start: 0.8831 (t-100) cc_final: 0.8240 (t-100) outliers start: 67 outliers final: 30 residues processed: 374 average time/residue: 0.2111 time to fit residues: 102.3930 Evaluate side-chains 377 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 332 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 88 optimal weight: 0.1980 chunk 79 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS A 332 GLN A 348 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 182 GLN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7845 Z= 0.182 Angle : 0.567 9.069 10652 Z= 0.290 Chirality : 0.044 0.146 1157 Planarity : 0.005 0.049 1335 Dihedral : 7.909 86.368 1037 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 7.51 % Allowed : 21.93 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.03 (0.29), residues: 912 helix: 1.49 (0.31), residues: 311 sheet: -0.80 (0.40), residues: 145 loop : -0.70 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 383 HIS 0.007 0.001 HIS A 208 PHE 0.028 0.002 PHE A 87 TYR 0.024 0.002 TYR A 319 ARG 0.005 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 335 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7614 (tm-30) cc_final: 0.6934 (tm-30) REVERT: A 47 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.6174 (tt) REVERT: A 56 TYR cc_start: 0.7615 (m-80) cc_final: 0.6995 (m-80) REVERT: A 101 LYS cc_start: 0.8298 (mttm) cc_final: 0.7707 (mtpp) REVERT: A 104 LYS cc_start: 0.8548 (tmtt) cc_final: 0.8228 (mmmm) REVERT: A 126 LYS cc_start: 0.8336 (mttm) cc_final: 0.7963 (mtmm) REVERT: A 144 TYR cc_start: 0.6627 (m-80) cc_final: 0.6376 (m-80) REVERT: A 166 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8324 (tmtt) REVERT: A 169 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7442 (mm-30) REVERT: A 172 LYS cc_start: 0.8779 (tttp) cc_final: 0.8566 (tttp) REVERT: A 173 LYS cc_start: 0.8684 (tttt) cc_final: 0.8316 (tppt) REVERT: A 180 ILE cc_start: 0.8467 (tp) cc_final: 0.8220 (mt) REVERT: A 181 TYR cc_start: 0.7578 (m-80) cc_final: 0.7254 (m-80) REVERT: A 182 GLN cc_start: 0.7082 (tm-30) cc_final: 0.6725 (tm-30) REVERT: A 203 GLU cc_start: 0.7340 (tt0) cc_final: 0.6940 (tt0) REVERT: A 204 GLU cc_start: 0.7399 (tp30) cc_final: 0.7014 (tm-30) REVERT: A 206 ARG cc_start: 0.8100 (mtp-110) cc_final: 0.7513 (ttm-80) REVERT: A 233 GLU cc_start: 0.7286 (tp30) cc_final: 0.6982 (tp30) REVERT: A 263 LYS cc_start: 0.8871 (ttmm) cc_final: 0.8584 (tttm) REVERT: A 329 ILE cc_start: 0.8415 (mt) cc_final: 0.8084 (mt) REVERT: A 330 GLN cc_start: 0.7675 (mp10) cc_final: 0.7234 (mp10) REVERT: A 349 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8613 (mt) REVERT: A 350 LYS cc_start: 0.8374 (tttt) cc_final: 0.8109 (ttpp) REVERT: A 357 MET cc_start: 0.5650 (tpt) cc_final: 0.5246 (tpt) REVERT: A 366 LYS cc_start: 0.8214 (tptm) cc_final: 0.7757 (mtpp) REVERT: A 369 THR cc_start: 0.8201 (m) cc_final: 0.7971 (p) REVERT: A 370 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7244 (mt-10) REVERT: A 374 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8012 (ttpp) REVERT: A 406 TRP cc_start: 0.7770 (p90) cc_final: 0.7396 (p90) REVERT: A 407 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7426 (mt0) REVERT: A 410 TRP cc_start: 0.8146 (t60) cc_final: 0.7899 (t60) REVERT: A 422 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7767 (mp) REVERT: A 424 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8156 (ptmm) REVERT: A 431 LYS cc_start: 0.8631 (mttt) cc_final: 0.8301 (mmmm) REVERT: A 454 LYS cc_start: 0.4523 (OUTLIER) cc_final: 0.4044 (mttt) REVERT: A 476 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7933 (mtpp) REVERT: A 478 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7179 (mm-30) REVERT: A 494 ASN cc_start: 0.7468 (m110) cc_final: 0.7152 (m110) REVERT: A 500 GLN cc_start: 0.7583 (pt0) cc_final: 0.7361 (pt0) REVERT: A 503 LEU cc_start: 0.8044 (tp) cc_final: 0.7100 (tp) REVERT: A 505 ILE cc_start: 0.8532 (mt) cc_final: 0.8297 (mm) REVERT: A 507 GLN cc_start: 0.8705 (pt0) cc_final: 0.8039 (pt0) REVERT: A 523 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7609 (mt-10) REVERT: A 540 LYS cc_start: 0.8349 (mmtt) cc_final: 0.7989 (mmmm) REVERT: A 545 ASN cc_start: 0.4640 (OUTLIER) cc_final: 0.4149 (p0) REVERT: A 548 VAL cc_start: 0.2252 (OUTLIER) cc_final: 0.1374 (m) REVERT: B 21 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8086 (m) REVERT: B 22 LYS cc_start: 0.8087 (tttp) cc_final: 0.7664 (tttp) REVERT: B 34 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8119 (tt) REVERT: B 36 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6960 (mt-10) REVERT: B 57 ASN cc_start: 0.8021 (t0) cc_final: 0.7749 (t0) REVERT: B 76 ASP cc_start: 0.8303 (t0) cc_final: 0.8023 (t0) REVERT: B 77 PHE cc_start: 0.7857 (m-80) cc_final: 0.7453 (m-10) REVERT: B 82 LYS cc_start: 0.8579 (mtpt) cc_final: 0.8203 (ttmm) REVERT: B 86 ASP cc_start: 0.7030 (p0) cc_final: 0.6591 (p0) REVERT: B 102 LYS cc_start: 0.8721 (mptt) cc_final: 0.8486 (mppt) REVERT: B 128 THR cc_start: 0.7875 (p) cc_final: 0.7449 (t) REVERT: B 143 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.6162 (ptt180) REVERT: B 167 ILE cc_start: 0.4987 (OUTLIER) cc_final: 0.4694 (tt) REVERT: B 178 ILE cc_start: 0.8403 (mt) cc_final: 0.7985 (tp) REVERT: B 256 ASP cc_start: 0.6943 (t70) cc_final: 0.5972 (t70) REVERT: B 263 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7715 (ttmp) REVERT: B 266 TRP cc_start: 0.7795 (t60) cc_final: 0.7149 (t60) REVERT: B 298 GLU cc_start: 0.8233 (pt0) cc_final: 0.7377 (tt0) REVERT: B 300 GLU cc_start: 0.7913 (tt0) cc_final: 0.7709 (tt0) REVERT: B 308 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7285 (tm-30) REVERT: B 309 ILE cc_start: 0.8434 (mt) cc_final: 0.8006 (mm) REVERT: B 322 SER cc_start: 0.8760 (m) cc_final: 0.8341 (p) REVERT: B 328 GLU cc_start: 0.7270 (tt0) cc_final: 0.6999 (tt0) REVERT: B 347 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7852 (mttm) REVERT: B 391 LEU cc_start: 0.8478 (mt) cc_final: 0.8049 (mt) REVERT: B 396 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6573 (mt-10) REVERT: B 397 THR cc_start: 0.8065 (p) cc_final: 0.7755 (t) REVERT: B 398 TRP cc_start: 0.8837 (t-100) cc_final: 0.8299 (t-100) outliers start: 63 outliers final: 34 residues processed: 366 average time/residue: 0.2239 time to fit residues: 105.6887 Evaluate side-chains 379 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 330 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 chunk 79 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS A 332 GLN A 348 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 96 HIS B 258 GLN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7845 Z= 0.203 Angle : 0.575 8.987 10652 Z= 0.293 Chirality : 0.044 0.164 1157 Planarity : 0.005 0.046 1335 Dihedral : 7.801 83.784 1035 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 8.10 % Allowed : 22.88 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.08 (0.29), residues: 912 helix: 1.52 (0.31), residues: 310 sheet: -0.66 (0.41), residues: 140 loop : -0.71 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 337 HIS 0.007 0.001 HIS A 208 PHE 0.022 0.002 PHE A 171 TYR 0.026 0.002 TYR A 319 ARG 0.005 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 333 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7620 (tm-30) cc_final: 0.6958 (tm-30) REVERT: A 47 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6227 (tt) REVERT: A 56 TYR cc_start: 0.7615 (m-80) cc_final: 0.7191 (m-80) REVERT: A 83 ARG cc_start: 0.7407 (mtt-85) cc_final: 0.6998 (mtt180) REVERT: A 101 LYS cc_start: 0.8288 (mttm) cc_final: 0.7679 (mtpp) REVERT: A 104 LYS cc_start: 0.8568 (tmtt) cc_final: 0.8283 (mmmm) REVERT: A 125 ARG cc_start: 0.7355 (ptt180) cc_final: 0.6933 (ptt180) REVERT: A 126 LYS cc_start: 0.8338 (mttm) cc_final: 0.7700 (tptt) REVERT: A 142 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7310 (pt) REVERT: A 144 TYR cc_start: 0.6646 (m-80) cc_final: 0.6411 (m-80) REVERT: A 166 LYS cc_start: 0.8700 (mtpt) cc_final: 0.8329 (tmtt) REVERT: A 169 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7455 (mm-30) REVERT: A 172 LYS cc_start: 0.8792 (tttp) cc_final: 0.8563 (tttp) REVERT: A 173 LYS cc_start: 0.8682 (tttt) cc_final: 0.8302 (tppt) REVERT: A 180 ILE cc_start: 0.8460 (tp) cc_final: 0.8217 (mt) REVERT: A 181 TYR cc_start: 0.7594 (m-80) cc_final: 0.7295 (m-80) REVERT: A 182 GLN cc_start: 0.7095 (tm-30) cc_final: 0.6752 (tm-30) REVERT: A 203 GLU cc_start: 0.7342 (tt0) cc_final: 0.6957 (tt0) REVERT: A 204 GLU cc_start: 0.7413 (tp30) cc_final: 0.7018 (tm-30) REVERT: A 206 ARG cc_start: 0.8131 (mtp-110) cc_final: 0.7549 (ttm-80) REVERT: A 233 GLU cc_start: 0.7296 (tp30) cc_final: 0.6972 (tp30) REVERT: A 263 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8608 (tttm) REVERT: A 329 ILE cc_start: 0.8400 (mt) cc_final: 0.8068 (mt) REVERT: A 330 GLN cc_start: 0.7720 (mp10) cc_final: 0.7174 (mp10) REVERT: A 349 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8617 (mt) REVERT: A 350 LYS cc_start: 0.8369 (tttt) cc_final: 0.8099 (ttpp) REVERT: A 357 MET cc_start: 0.5516 (tpt) cc_final: 0.5199 (tpt) REVERT: A 366 LYS cc_start: 0.8274 (tptm) cc_final: 0.7741 (mtpp) REVERT: A 369 THR cc_start: 0.8176 (m) cc_final: 0.7932 (p) REVERT: A 370 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7259 (mt-10) REVERT: A 374 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8051 (ttpp) REVERT: A 406 TRP cc_start: 0.7808 (p90) cc_final: 0.7450 (p90) REVERT: A 407 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7403 (mt0) REVERT: A 422 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7778 (mp) REVERT: A 454 LYS cc_start: 0.4621 (OUTLIER) cc_final: 0.4206 (mttt) REVERT: A 476 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8005 (mtpp) REVERT: A 478 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7228 (mm-30) REVERT: A 494 ASN cc_start: 0.7490 (m110) cc_final: 0.7160 (m110) REVERT: A 500 GLN cc_start: 0.7603 (pt0) cc_final: 0.7395 (pt0) REVERT: A 503 LEU cc_start: 0.8084 (tp) cc_final: 0.7126 (tp) REVERT: A 505 ILE cc_start: 0.8515 (mt) cc_final: 0.8293 (mm) REVERT: A 507 GLN cc_start: 0.8699 (pt0) cc_final: 0.8059 (pt0) REVERT: A 520 GLN cc_start: 0.7115 (tp40) cc_final: 0.6747 (tm-30) REVERT: A 523 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7657 (mt-10) REVERT: A 540 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7997 (mmmm) REVERT: A 545 ASN cc_start: 0.4731 (OUTLIER) cc_final: 0.3726 (p0) REVERT: A 548 VAL cc_start: 0.2152 (OUTLIER) cc_final: 0.1273 (m) REVERT: B 13 LYS cc_start: 0.7553 (mmtp) cc_final: 0.7296 (mmtp) REVERT: B 21 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8049 (m) REVERT: B 22 LYS cc_start: 0.8101 (tttp) cc_final: 0.7667 (tttp) REVERT: B 34 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8113 (tt) REVERT: B 36 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6958 (mt-10) REVERT: B 57 ASN cc_start: 0.8007 (t0) cc_final: 0.7751 (t0) REVERT: B 76 ASP cc_start: 0.8319 (t0) cc_final: 0.8084 (t0) REVERT: B 77 PHE cc_start: 0.7860 (m-80) cc_final: 0.7518 (m-10) REVERT: B 82 LYS cc_start: 0.8607 (mtpt) cc_final: 0.8217 (ttmm) REVERT: B 86 ASP cc_start: 0.7021 (p0) cc_final: 0.6534 (p0) REVERT: B 102 LYS cc_start: 0.8712 (mptt) cc_final: 0.8461 (mppt) REVERT: B 128 THR cc_start: 0.7859 (p) cc_final: 0.7422 (t) REVERT: B 143 ARG cc_start: 0.6481 (OUTLIER) cc_final: 0.6192 (ptt180) REVERT: B 167 ILE cc_start: 0.4953 (OUTLIER) cc_final: 0.4653 (tt) REVERT: B 178 ILE cc_start: 0.8393 (mt) cc_final: 0.7945 (tp) REVERT: B 192 ASP cc_start: 0.8117 (t0) cc_final: 0.7818 (m-30) REVERT: B 256 ASP cc_start: 0.7186 (t70) cc_final: 0.6870 (t70) REVERT: B 260 LEU cc_start: 0.7623 (mt) cc_final: 0.7413 (mt) REVERT: B 263 LYS cc_start: 0.7957 (ttmp) cc_final: 0.7722 (ttmp) REVERT: B 266 TRP cc_start: 0.7812 (t60) cc_final: 0.7205 (t60) REVERT: B 297 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7297 (tp30) REVERT: B 298 GLU cc_start: 0.8280 (pt0) cc_final: 0.6963 (tt0) REVERT: B 300 GLU cc_start: 0.7877 (tt0) cc_final: 0.7453 (tt0) REVERT: B 309 ILE cc_start: 0.8465 (mt) cc_final: 0.7952 (mm) REVERT: B 312 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6904 (mt-10) REVERT: B 322 SER cc_start: 0.8771 (m) cc_final: 0.8379 (p) REVERT: B 328 GLU cc_start: 0.7287 (tt0) cc_final: 0.7008 (tt0) REVERT: B 347 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7846 (mttm) REVERT: B 353 LYS cc_start: 0.8303 (ptpp) cc_final: 0.7763 (ptpp) REVERT: B 391 LEU cc_start: 0.8515 (mt) cc_final: 0.8113 (mt) REVERT: B 396 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6616 (mt-10) REVERT: B 397 THR cc_start: 0.8156 (p) cc_final: 0.7860 (t) REVERT: B 398 TRP cc_start: 0.8868 (t-100) cc_final: 0.8290 (t-100) outliers start: 68 outliers final: 39 residues processed: 368 average time/residue: 0.2205 time to fit residues: 104.8734 Evaluate side-chains 395 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 341 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 348 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN B 81 ASN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN B 373 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7845 Z= 0.309 Angle : 0.614 9.461 10652 Z= 0.320 Chirality : 0.046 0.159 1157 Planarity : 0.005 0.046 1335 Dihedral : 8.018 84.544 1027 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 8.82 % Allowed : 23.12 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.15 (0.29), residues: 912 helix: 1.40 (0.31), residues: 305 sheet: -1.02 (0.41), residues: 145 loop : -0.78 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 337 HIS 0.005 0.001 HIS A 208 PHE 0.026 0.002 PHE A 171 TYR 0.027 0.002 TYR A 319 ARG 0.005 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 330 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: A 47 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6261 (tt) REVERT: A 56 TYR cc_start: 0.7733 (m-80) cc_final: 0.7064 (m-80) REVERT: A 83 ARG cc_start: 0.7486 (mtt-85) cc_final: 0.7048 (mtt180) REVERT: A 101 LYS cc_start: 0.8314 (mttm) cc_final: 0.7728 (mttm) REVERT: A 104 LYS cc_start: 0.8575 (tmtt) cc_final: 0.8327 (mtpp) REVERT: A 125 ARG cc_start: 0.7386 (ptt180) cc_final: 0.6949 (ptt180) REVERT: A 126 LYS cc_start: 0.8401 (mttm) cc_final: 0.7986 (mtmm) REVERT: A 142 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7291 (pt) REVERT: A 144 TYR cc_start: 0.6626 (m-80) cc_final: 0.6414 (m-80) REVERT: A 161 GLN cc_start: 0.8381 (tt0) cc_final: 0.7883 (tt0) REVERT: A 166 LYS cc_start: 0.8745 (mtpt) cc_final: 0.8357 (tmtt) REVERT: A 169 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7479 (mm-30) REVERT: A 172 LYS cc_start: 0.8853 (tttp) cc_final: 0.8635 (tttp) REVERT: A 173 LYS cc_start: 0.8731 (tttt) cc_final: 0.8520 (tttt) REVERT: A 180 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8321 (mt) REVERT: A 181 TYR cc_start: 0.7618 (m-80) cc_final: 0.7298 (m-80) REVERT: A 182 GLN cc_start: 0.7177 (tm-30) cc_final: 0.6810 (tm-30) REVERT: A 203 GLU cc_start: 0.7418 (tt0) cc_final: 0.7149 (tt0) REVERT: A 204 GLU cc_start: 0.7513 (tp30) cc_final: 0.7298 (tp30) REVERT: A 206 ARG cc_start: 0.8104 (mtp-110) cc_final: 0.7490 (ttm-80) REVERT: A 233 GLU cc_start: 0.7277 (tp30) cc_final: 0.6961 (tp30) REVERT: A 234 LEU cc_start: 0.8020 (mt) cc_final: 0.7655 (mm) REVERT: A 329 ILE cc_start: 0.8410 (mt) cc_final: 0.8086 (mt) REVERT: A 330 GLN cc_start: 0.7756 (mp10) cc_final: 0.7252 (mp10) REVERT: A 347 LYS cc_start: 0.8428 (mttt) cc_final: 0.8093 (mttp) REVERT: A 350 LYS cc_start: 0.8354 (tttt) cc_final: 0.8109 (ttpp) REVERT: A 357 MET cc_start: 0.5513 (tpt) cc_final: 0.5208 (tpt) REVERT: A 366 LYS cc_start: 0.8299 (tptm) cc_final: 0.7783 (mtpp) REVERT: A 369 THR cc_start: 0.8137 (m) cc_final: 0.7885 (p) REVERT: A 370 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7331 (mt-10) REVERT: A 374 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8040 (ttpp) REVERT: A 406 TRP cc_start: 0.7823 (p90) cc_final: 0.7455 (p90) REVERT: A 407 GLN cc_start: 0.7808 (mt0) cc_final: 0.7447 (mt0) REVERT: A 422 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7707 (mp) REVERT: A 478 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7286 (mm-30) REVERT: A 494 ASN cc_start: 0.7552 (m110) cc_final: 0.7241 (m110) REVERT: A 500 GLN cc_start: 0.7658 (pt0) cc_final: 0.7352 (pt0) REVERT: A 503 LEU cc_start: 0.8116 (tp) cc_final: 0.7240 (tp) REVERT: A 507 GLN cc_start: 0.8699 (pt0) cc_final: 0.7993 (pt0) REVERT: A 520 GLN cc_start: 0.7051 (tp40) cc_final: 0.6812 (tm-30) REVERT: A 523 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7651 (mt-10) REVERT: A 540 LYS cc_start: 0.8339 (mmtt) cc_final: 0.8072 (mmtt) REVERT: A 545 ASN cc_start: 0.4702 (OUTLIER) cc_final: 0.4308 (p0) REVERT: A 548 VAL cc_start: 0.1939 (OUTLIER) cc_final: 0.1055 (m) REVERT: B 21 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8118 (m) REVERT: B 22 LYS cc_start: 0.8093 (tttp) cc_final: 0.7638 (tttp) REVERT: B 34 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8143 (tt) REVERT: B 36 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7026 (mt-10) REVERT: B 44 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7151 (mm-30) REVERT: B 77 PHE cc_start: 0.7887 (m-80) cc_final: 0.7504 (m-10) REVERT: B 82 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8171 (mttm) REVERT: B 102 LYS cc_start: 0.8736 (mptt) cc_final: 0.8460 (mppt) REVERT: B 128 THR cc_start: 0.7817 (p) cc_final: 0.7340 (t) REVERT: B 143 ARG cc_start: 0.6509 (OUTLIER) cc_final: 0.6210 (ptt180) REVERT: B 167 ILE cc_start: 0.4956 (OUTLIER) cc_final: 0.4612 (tt) REVERT: B 178 ILE cc_start: 0.8382 (mt) cc_final: 0.7931 (tp) REVERT: B 256 ASP cc_start: 0.7215 (t70) cc_final: 0.6778 (t70) REVERT: B 260 LEU cc_start: 0.7573 (mt) cc_final: 0.7284 (mt) REVERT: B 263 LYS cc_start: 0.8009 (ttmp) cc_final: 0.7755 (ttmp) REVERT: B 266 TRP cc_start: 0.7821 (t60) cc_final: 0.7259 (t60) REVERT: B 298 GLU cc_start: 0.8438 (pt0) cc_final: 0.7751 (pt0) REVERT: B 300 GLU cc_start: 0.7887 (tt0) cc_final: 0.7619 (tt0) REVERT: B 308 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7057 (tm-30) REVERT: B 309 ILE cc_start: 0.8461 (mt) cc_final: 0.8059 (mm) REVERT: B 312 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7150 (mt-10) REVERT: B 322 SER cc_start: 0.8790 (m) cc_final: 0.8406 (p) REVERT: B 328 GLU cc_start: 0.7290 (tt0) cc_final: 0.7040 (tt0) REVERT: B 347 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7756 (mtpp) REVERT: B 353 LYS cc_start: 0.8306 (ptpp) cc_final: 0.7757 (ptpp) REVERT: B 391 LEU cc_start: 0.8573 (mt) cc_final: 0.8211 (mt) REVERT: B 396 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6722 (mt-10) REVERT: B 398 TRP cc_start: 0.8892 (t-100) cc_final: 0.8318 (t-100) outliers start: 74 outliers final: 44 residues processed: 368 average time/residue: 0.2297 time to fit residues: 108.3480 Evaluate side-chains 381 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 324 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 419 THR 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: 3.9990 chunk 65 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A 348 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 81 ASN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7845 Z= 0.240 Angle : 0.616 10.210 10652 Z= 0.316 Chirality : 0.045 0.214 1157 Planarity : 0.005 0.045 1335 Dihedral : 7.620 83.934 1021 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 7.75 % Allowed : 25.51 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.13 (0.29), residues: 912 helix: 1.41 (0.31), residues: 306 sheet: -0.93 (0.41), residues: 140 loop : -0.81 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 401 HIS 0.005 0.001 HIS A 208 PHE 0.026 0.002 PHE A 171 TYR 0.030 0.002 TYR A 319 ARG 0.007 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 333 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: A 47 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.6206 (tt) REVERT: A 56 TYR cc_start: 0.7678 (m-80) cc_final: 0.7051 (m-80) REVERT: A 83 ARG cc_start: 0.7422 (mtt-85) cc_final: 0.7042 (mtt180) REVERT: A 101 LYS cc_start: 0.8310 (mttm) cc_final: 0.7760 (mttm) REVERT: A 104 LYS cc_start: 0.8592 (tmtt) cc_final: 0.8339 (mtpp) REVERT: A 126 LYS cc_start: 0.8393 (mttm) cc_final: 0.7976 (mtmm) REVERT: A 142 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7321 (pt) REVERT: A 144 TYR cc_start: 0.6666 (m-80) cc_final: 0.6447 (m-80) REVERT: A 161 GLN cc_start: 0.8325 (tt0) cc_final: 0.7836 (tt0) REVERT: A 166 LYS cc_start: 0.8747 (mtpt) cc_final: 0.8343 (tmtt) REVERT: A 169 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 172 LYS cc_start: 0.8825 (tttp) cc_final: 0.8606 (tttp) REVERT: A 173 LYS cc_start: 0.8697 (tttt) cc_final: 0.8486 (tttt) REVERT: A 180 ILE cc_start: 0.8520 (tp) cc_final: 0.8277 (mt) REVERT: A 181 TYR cc_start: 0.7596 (m-80) cc_final: 0.7238 (m-80) REVERT: A 182 GLN cc_start: 0.7153 (tm-30) cc_final: 0.6772 (tm-30) REVERT: A 203 GLU cc_start: 0.7390 (tt0) cc_final: 0.7122 (tt0) REVERT: A 204 GLU cc_start: 0.7490 (tp30) cc_final: 0.7284 (tp30) REVERT: A 206 ARG cc_start: 0.8113 (mtp-110) cc_final: 0.7520 (ttm-80) REVERT: A 233 GLU cc_start: 0.7284 (tp30) cc_final: 0.6943 (tp30) REVERT: A 234 LEU cc_start: 0.8017 (mt) cc_final: 0.7667 (mm) REVERT: A 329 ILE cc_start: 0.8409 (mt) cc_final: 0.8075 (mt) REVERT: A 330 GLN cc_start: 0.7770 (mp10) cc_final: 0.7253 (mp10) REVERT: A 347 LYS cc_start: 0.8321 (mttt) cc_final: 0.8094 (mttp) REVERT: A 350 LYS cc_start: 0.8360 (tttt) cc_final: 0.8118 (ttpp) REVERT: A 357 MET cc_start: 0.5526 (tpt) cc_final: 0.5212 (tpt) REVERT: A 366 LYS cc_start: 0.8268 (tptm) cc_final: 0.7757 (mtpp) REVERT: A 369 THR cc_start: 0.8116 (m) cc_final: 0.7863 (p) REVERT: A 370 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7252 (mt-10) REVERT: A 374 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8033 (ttpp) REVERT: A 406 TRP cc_start: 0.7823 (p90) cc_final: 0.7405 (p90) REVERT: A 407 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7402 (mt0) REVERT: A 414 TRP cc_start: 0.8725 (p-90) cc_final: 0.8070 (p-90) REVERT: A 422 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7683 (mp) REVERT: A 478 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7297 (mm-30) REVERT: A 494 ASN cc_start: 0.7547 (m110) cc_final: 0.7245 (m110) REVERT: A 500 GLN cc_start: 0.7629 (pt0) cc_final: 0.7280 (pt0) REVERT: A 503 LEU cc_start: 0.8110 (tp) cc_final: 0.7200 (tp) REVERT: A 507 GLN cc_start: 0.8688 (pt0) cc_final: 0.7976 (pt0) REVERT: A 520 GLN cc_start: 0.7062 (tp40) cc_final: 0.6802 (tm-30) REVERT: A 523 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7629 (mt-10) REVERT: A 535 TRP cc_start: 0.8590 (t60) cc_final: 0.8349 (t60) REVERT: A 540 LYS cc_start: 0.8322 (mmtt) cc_final: 0.8045 (mmtt) REVERT: A 545 ASN cc_start: 0.4650 (OUTLIER) cc_final: 0.4158 (p0) REVERT: A 548 VAL cc_start: 0.2063 (OUTLIER) cc_final: 0.1165 (m) REVERT: B 21 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8166 (m) REVERT: B 22 LYS cc_start: 0.8094 (tttp) cc_final: 0.7632 (tttp) REVERT: B 34 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8117 (tt) REVERT: B 36 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6978 (mt-10) REVERT: B 44 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7141 (mm-30) REVERT: B 77 PHE cc_start: 0.7881 (m-80) cc_final: 0.7541 (m-10) REVERT: B 82 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8148 (mttm) REVERT: B 102 LYS cc_start: 0.8746 (mptt) cc_final: 0.8211 (mptt) REVERT: B 128 THR cc_start: 0.7814 (p) cc_final: 0.7335 (t) REVERT: B 143 ARG cc_start: 0.6476 (OUTLIER) cc_final: 0.6194 (ptt180) REVERT: B 167 ILE cc_start: 0.5043 (OUTLIER) cc_final: 0.4714 (tt) REVERT: B 178 ILE cc_start: 0.8368 (mt) cc_final: 0.7920 (tp) REVERT: B 192 ASP cc_start: 0.8088 (t0) cc_final: 0.7712 (m-30) REVERT: B 256 ASP cc_start: 0.7168 (t70) cc_final: 0.6667 (t70) REVERT: B 260 LEU cc_start: 0.7546 (mt) cc_final: 0.7190 (mt) REVERT: B 263 LYS cc_start: 0.7985 (ttmp) cc_final: 0.7737 (ttmp) REVERT: B 264 LEU cc_start: 0.8545 (mm) cc_final: 0.8317 (mm) REVERT: B 266 TRP cc_start: 0.7783 (t60) cc_final: 0.7256 (t60) REVERT: B 298 GLU cc_start: 0.8397 (pt0) cc_final: 0.7704 (pt0) REVERT: B 300 GLU cc_start: 0.7871 (tt0) cc_final: 0.7626 (tt0) REVERT: B 308 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7036 (tm-30) REVERT: B 309 ILE cc_start: 0.8460 (mt) cc_final: 0.8022 (mm) REVERT: B 312 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: B 322 SER cc_start: 0.8804 (m) cc_final: 0.8414 (p) REVERT: B 328 GLU cc_start: 0.7299 (tt0) cc_final: 0.7061 (tt0) REVERT: B 347 LYS cc_start: 0.8074 (mmtm) cc_final: 0.7763 (mtpp) REVERT: B 353 LYS cc_start: 0.8253 (ptpp) cc_final: 0.7697 (ptpp) REVERT: B 365 VAL cc_start: 0.8361 (m) cc_final: 0.8106 (p) REVERT: B 391 LEU cc_start: 0.8527 (mt) cc_final: 0.8186 (mt) REVERT: B 396 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6641 (mt-10) REVERT: B 398 TRP cc_start: 0.8865 (t-100) cc_final: 0.8295 (t-100) outliers start: 65 outliers final: 44 residues processed: 365 average time/residue: 0.2415 time to fit residues: 113.9272 Evaluate side-chains 387 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 330 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 81 ASN B 332 GLN B 373 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7845 Z= 0.267 Angle : 0.627 10.621 10652 Z= 0.322 Chirality : 0.046 0.191 1157 Planarity : 0.005 0.044 1335 Dihedral : 7.686 83.443 1021 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 7.51 % Allowed : 26.22 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.23 (0.29), residues: 912 helix: 1.34 (0.31), residues: 306 sheet: -1.12 (0.40), residues: 145 loop : -0.82 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 337 HIS 0.004 0.001 HIS A 208 PHE 0.027 0.002 PHE A 171 TYR 0.032 0.002 TYR A 319 ARG 0.007 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 326 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: A 56 TYR cc_start: 0.7691 (m-80) cc_final: 0.7080 (m-80) REVERT: A 83 ARG cc_start: 0.7425 (mtt-85) cc_final: 0.7168 (mtt180) REVERT: A 101 LYS cc_start: 0.8329 (mttm) cc_final: 0.7791 (mttm) REVERT: A 104 LYS cc_start: 0.8596 (tmtt) cc_final: 0.8264 (mmmm) REVERT: A 126 LYS cc_start: 0.8419 (mttm) cc_final: 0.7991 (mtmm) REVERT: A 161 GLN cc_start: 0.8340 (tt0) cc_final: 0.7802 (tt0) REVERT: A 169 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7490 (mm-30) REVERT: A 172 LYS cc_start: 0.8833 (tttp) cc_final: 0.8621 (tttp) REVERT: A 173 LYS cc_start: 0.8708 (tttt) cc_final: 0.8341 (tppt) REVERT: A 180 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8228 (mt) REVERT: A 181 TYR cc_start: 0.7602 (m-80) cc_final: 0.7250 (m-80) REVERT: A 182 GLN cc_start: 0.7179 (tm-30) cc_final: 0.6836 (tm-30) REVERT: A 203 GLU cc_start: 0.7409 (tt0) cc_final: 0.7140 (tt0) REVERT: A 206 ARG cc_start: 0.8113 (mtp-110) cc_final: 0.7506 (ttm-80) REVERT: A 233 GLU cc_start: 0.7239 (tp30) cc_final: 0.6935 (tp30) REVERT: A 234 LEU cc_start: 0.8024 (mt) cc_final: 0.7682 (mm) REVERT: A 330 GLN cc_start: 0.7812 (mp10) cc_final: 0.7313 (mp10) REVERT: A 347 LYS cc_start: 0.8358 (mttt) cc_final: 0.8079 (mttp) REVERT: A 350 LYS cc_start: 0.8366 (tttt) cc_final: 0.8131 (ttpp) REVERT: A 357 MET cc_start: 0.5314 (tpt) cc_final: 0.5071 (tpt) REVERT: A 366 LYS cc_start: 0.8312 (tptm) cc_final: 0.8022 (mtpp) REVERT: A 369 THR cc_start: 0.8148 (m) cc_final: 0.7884 (p) REVERT: A 374 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8031 (ttpp) REVERT: A 406 TRP cc_start: 0.7828 (p90) cc_final: 0.7409 (p90) REVERT: A 407 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7415 (mt0) REVERT: A 414 TRP cc_start: 0.8765 (p-90) cc_final: 0.8001 (p-90) REVERT: A 422 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7683 (mp) REVERT: A 476 LYS cc_start: 0.8276 (mttm) cc_final: 0.7913 (mtpp) REVERT: A 478 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7348 (mm-30) REVERT: A 494 ASN cc_start: 0.7566 (m110) cc_final: 0.7281 (m110) REVERT: A 500 GLN cc_start: 0.7671 (pt0) cc_final: 0.7317 (pt0) REVERT: A 503 LEU cc_start: 0.8122 (tp) cc_final: 0.7206 (tp) REVERT: A 507 GLN cc_start: 0.8690 (pt0) cc_final: 0.8008 (pt0) REVERT: A 520 GLN cc_start: 0.7016 (tp40) cc_final: 0.6745 (tm-30) REVERT: A 523 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 535 TRP cc_start: 0.8572 (t60) cc_final: 0.8370 (t60) REVERT: A 545 ASN cc_start: 0.4722 (OUTLIER) cc_final: 0.4237 (p0) REVERT: A 548 VAL cc_start: 0.1917 (OUTLIER) cc_final: 0.1031 (m) REVERT: B 21 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8159 (m) REVERT: B 22 LYS cc_start: 0.8084 (tttp) cc_final: 0.7624 (tttp) REVERT: B 34 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8146 (tt) REVERT: B 36 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7002 (mt-10) REVERT: B 44 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7143 (mm-30) REVERT: B 77 PHE cc_start: 0.7889 (m-80) cc_final: 0.7580 (m-10) REVERT: B 82 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8158 (mttm) REVERT: B 102 LYS cc_start: 0.8739 (mptt) cc_final: 0.8448 (mppt) REVERT: B 128 THR cc_start: 0.7803 (p) cc_final: 0.7315 (t) REVERT: B 167 ILE cc_start: 0.5015 (OUTLIER) cc_final: 0.4678 (tt) REVERT: B 178 ILE cc_start: 0.8373 (mt) cc_final: 0.7912 (tp) REVERT: B 192 ASP cc_start: 0.8084 (t0) cc_final: 0.7699 (m-30) REVERT: B 256 ASP cc_start: 0.7192 (t70) cc_final: 0.6655 (t70) REVERT: B 260 LEU cc_start: 0.7567 (mt) cc_final: 0.7166 (mt) REVERT: B 263 LYS cc_start: 0.8020 (ttmp) cc_final: 0.7770 (ttmp) REVERT: B 266 TRP cc_start: 0.7780 (t60) cc_final: 0.7373 (t60) REVERT: B 298 GLU cc_start: 0.8417 (pt0) cc_final: 0.7827 (pt0) REVERT: B 300 GLU cc_start: 0.7887 (tt0) cc_final: 0.7654 (tt0) REVERT: B 308 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7369 (tm-30) REVERT: B 309 ILE cc_start: 0.8471 (mt) cc_final: 0.8037 (mm) REVERT: B 322 SER cc_start: 0.8789 (m) cc_final: 0.8407 (p) REVERT: B 328 GLU cc_start: 0.7309 (tt0) cc_final: 0.7048 (tt0) REVERT: B 330 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7526 (pm20) REVERT: B 347 LYS cc_start: 0.8085 (mmtm) cc_final: 0.7761 (mtpp) REVERT: B 353 LYS cc_start: 0.8254 (ptpp) cc_final: 0.7725 (ptpp) REVERT: B 365 VAL cc_start: 0.8355 (m) cc_final: 0.8118 (p) REVERT: B 391 LEU cc_start: 0.8526 (mt) cc_final: 0.8187 (mt) REVERT: B 396 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6687 (mt-10) REVERT: B 397 THR cc_start: 0.8205 (p) cc_final: 0.7941 (t) REVERT: B 398 TRP cc_start: 0.8878 (t-100) cc_final: 0.8327 (t-100) outliers start: 63 outliers final: 42 residues processed: 357 average time/residue: 0.2171 time to fit residues: 100.6062 Evaluate side-chains 376 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 323 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 239 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 0.3980 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 81 ASN B 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7845 Z= 0.210 Angle : 0.615 10.890 10652 Z= 0.312 Chirality : 0.045 0.188 1157 Planarity : 0.005 0.049 1335 Dihedral : 7.360 82.067 1019 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.91 % Allowed : 26.82 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.08 (0.29), residues: 912 helix: 1.40 (0.31), residues: 305 sheet: -0.94 (0.41), residues: 140 loop : -0.72 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 401 HIS 0.009 0.001 HIS A 208 PHE 0.027 0.002 PHE A 171 TYR 0.032 0.002 TYR A 319 ARG 0.006 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 335 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7086 (tm-30) REVERT: A 56 TYR cc_start: 0.7620 (m-80) cc_final: 0.7097 (m-80) REVERT: A 101 LYS cc_start: 0.8312 (mttm) cc_final: 0.7780 (mttm) REVERT: A 104 LYS cc_start: 0.8576 (tmtt) cc_final: 0.8314 (mtpp) REVERT: A 126 LYS cc_start: 0.8397 (mttm) cc_final: 0.7797 (tptt) REVERT: A 161 GLN cc_start: 0.8310 (tt0) cc_final: 0.7793 (tt0) REVERT: A 166 LYS cc_start: 0.8753 (mtpt) cc_final: 0.8354 (tmtt) REVERT: A 169 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7451 (mm-30) REVERT: A 172 LYS cc_start: 0.8806 (tttp) cc_final: 0.8577 (tttp) REVERT: A 173 LYS cc_start: 0.8684 (tttt) cc_final: 0.8456 (tttt) REVERT: A 180 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8216 (mt) REVERT: A 181 TYR cc_start: 0.7607 (m-80) cc_final: 0.7305 (m-80) REVERT: A 182 GLN cc_start: 0.7124 (tm-30) cc_final: 0.6764 (tm-30) REVERT: A 203 GLU cc_start: 0.7375 (tt0) cc_final: 0.6980 (tt0) REVERT: A 206 ARG cc_start: 0.8088 (mtp-110) cc_final: 0.7501 (ttm-80) REVERT: A 233 GLU cc_start: 0.7231 (tp30) cc_final: 0.6825 (tp30) REVERT: A 234 LEU cc_start: 0.8018 (mt) cc_final: 0.7662 (mm) REVERT: A 329 ILE cc_start: 0.8369 (mt) cc_final: 0.8035 (mt) REVERT: A 330 GLN cc_start: 0.7798 (mp10) cc_final: 0.7275 (mp10) REVERT: A 347 LYS cc_start: 0.8327 (mttt) cc_final: 0.8044 (mtpp) REVERT: A 350 LYS cc_start: 0.8345 (tttt) cc_final: 0.8102 (ttpp) REVERT: A 357 MET cc_start: 0.5299 (tpt) cc_final: 0.5053 (tpt) REVERT: A 366 LYS cc_start: 0.8285 (tptm) cc_final: 0.8010 (mtpp) REVERT: A 369 THR cc_start: 0.8168 (m) cc_final: 0.7902 (p) REVERT: A 374 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8021 (ttpp) REVERT: A 406 TRP cc_start: 0.7780 (p90) cc_final: 0.7077 (p90) REVERT: A 407 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7177 (mt0) REVERT: A 414 TRP cc_start: 0.8751 (p-90) cc_final: 0.7927 (p-90) REVERT: A 422 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7750 (mp) REVERT: A 478 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7338 (mm-30) REVERT: A 494 ASN cc_start: 0.7544 (m110) cc_final: 0.7261 (m110) REVERT: A 500 GLN cc_start: 0.7655 (pt0) cc_final: 0.7327 (pt0) REVERT: A 503 LEU cc_start: 0.8103 (tp) cc_final: 0.7185 (tp) REVERT: A 505 ILE cc_start: 0.8532 (mt) cc_final: 0.8290 (mm) REVERT: A 507 GLN cc_start: 0.8682 (pt0) cc_final: 0.7974 (pt0) REVERT: A 520 GLN cc_start: 0.7005 (tp40) cc_final: 0.6684 (tm-30) REVERT: A 523 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7618 (mt-10) REVERT: A 545 ASN cc_start: 0.4672 (OUTLIER) cc_final: 0.4189 (p0) REVERT: A 548 VAL cc_start: 0.1919 (OUTLIER) cc_final: 0.1054 (m) REVERT: B 21 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8139 (m) REVERT: B 22 LYS cc_start: 0.8104 (tttp) cc_final: 0.7638 (tttp) REVERT: B 34 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8118 (tt) REVERT: B 36 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6969 (mt-10) REVERT: B 44 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7132 (mm-30) REVERT: B 77 PHE cc_start: 0.7865 (m-80) cc_final: 0.7560 (m-10) REVERT: B 82 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8166 (mttp) REVERT: B 102 LYS cc_start: 0.8739 (mptt) cc_final: 0.8450 (mppt) REVERT: B 128 THR cc_start: 0.7823 (p) cc_final: 0.7346 (t) REVERT: B 167 ILE cc_start: 0.4961 (OUTLIER) cc_final: 0.4644 (tt) REVERT: B 178 ILE cc_start: 0.8370 (mt) cc_final: 0.7923 (tp) REVERT: B 192 ASP cc_start: 0.8045 (t0) cc_final: 0.7670 (m-30) REVERT: B 256 ASP cc_start: 0.7177 (t70) cc_final: 0.6398 (t70) REVERT: B 260 LEU cc_start: 0.7694 (mt) cc_final: 0.7399 (mt) REVERT: B 263 LYS cc_start: 0.8104 (ttmp) cc_final: 0.7901 (ttmp) REVERT: B 266 TRP cc_start: 0.7724 (t60) cc_final: 0.7379 (t60) REVERT: B 298 GLU cc_start: 0.8363 (pt0) cc_final: 0.7684 (pt0) REVERT: B 300 GLU cc_start: 0.7880 (tt0) cc_final: 0.7674 (tt0) REVERT: B 309 ILE cc_start: 0.8461 (mt) cc_final: 0.8208 (tt) REVERT: B 322 SER cc_start: 0.8818 (m) cc_final: 0.8454 (p) REVERT: B 328 GLU cc_start: 0.7303 (tt0) cc_final: 0.7060 (tt0) REVERT: B 346 PHE cc_start: 0.7671 (m-80) cc_final: 0.7202 (m-10) REVERT: B 347 LYS cc_start: 0.8100 (mmtm) cc_final: 0.7783 (mtpp) REVERT: B 353 LYS cc_start: 0.8222 (ptpp) cc_final: 0.7666 (ptpp) REVERT: B 365 VAL cc_start: 0.8366 (m) cc_final: 0.8115 (p) REVERT: B 391 LEU cc_start: 0.8504 (mt) cc_final: 0.8102 (mt) REVERT: B 396 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6563 (mt-10) REVERT: B 397 THR cc_start: 0.8140 (p) cc_final: 0.7899 (t) REVERT: B 398 TRP cc_start: 0.8872 (t-100) cc_final: 0.8267 (t-100) outliers start: 58 outliers final: 40 residues processed: 361 average time/residue: 0.2579 time to fit residues: 122.1649 Evaluate side-chains 372 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 323 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 239 TRP Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 84 optimal weight: 0.0030 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 0.0980 chunk 77 optimal weight: 6.9990 chunk 22 optimal weight: 0.0570 overall best weight: 0.3108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN B 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7845 Z= 0.175 Angle : 0.615 11.224 10652 Z= 0.310 Chirality : 0.045 0.219 1157 Planarity : 0.005 0.047 1335 Dihedral : 7.019 80.819 1019 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.96 % Allowed : 27.77 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.11 (0.29), residues: 912 helix: 1.43 (0.31), residues: 310 sheet: -0.68 (0.42), residues: 140 loop : -0.58 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 401 HIS 0.009 0.001 HIS A 208 PHE 0.028 0.002 PHE A 171 TYR 0.030 0.002 TYR A 319 ARG 0.009 0.000 ARG A 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 325 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7040 (tm-30) REVERT: A 56 TYR cc_start: 0.7528 (m-80) cc_final: 0.7050 (m-80) REVERT: A 101 LYS cc_start: 0.8281 (mttm) cc_final: 0.7771 (mttm) REVERT: A 104 LYS cc_start: 0.8564 (tmtt) cc_final: 0.8188 (mmmm) REVERT: A 122 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.5453 (tp30) REVERT: A 126 LYS cc_start: 0.8360 (mttm) cc_final: 0.7725 (tptt) REVERT: A 144 TYR cc_start: 0.6594 (m-80) cc_final: 0.6171 (m-80) REVERT: A 166 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8341 (tmtt) REVERT: A 169 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7437 (mm-30) REVERT: A 172 LYS cc_start: 0.8751 (tttp) cc_final: 0.8535 (tttp) REVERT: A 173 LYS cc_start: 0.8604 (tttt) cc_final: 0.8201 (tppt) REVERT: A 180 ILE cc_start: 0.8440 (tp) cc_final: 0.8218 (mt) REVERT: A 181 TYR cc_start: 0.7597 (m-80) cc_final: 0.7257 (m-80) REVERT: A 182 GLN cc_start: 0.7015 (tm-30) cc_final: 0.6725 (tm-30) REVERT: A 203 GLU cc_start: 0.7286 (tt0) cc_final: 0.6893 (tt0) REVERT: A 206 ARG cc_start: 0.8036 (mtp-110) cc_final: 0.7457 (ttm-80) REVERT: A 233 GLU cc_start: 0.7162 (tp30) cc_final: 0.6881 (tp30) REVERT: A 234 LEU cc_start: 0.7971 (mt) cc_final: 0.7689 (mm) REVERT: A 271 TYR cc_start: 0.8098 (m-80) cc_final: 0.7833 (m-80) REVERT: A 336 GLN cc_start: 0.7613 (mt0) cc_final: 0.7406 (mt0) REVERT: A 342 TYR cc_start: 0.8151 (p90) cc_final: 0.7944 (p90) REVERT: A 350 LYS cc_start: 0.8341 (tttt) cc_final: 0.8110 (ttpp) REVERT: A 357 MET cc_start: 0.5250 (tpt) cc_final: 0.5029 (tpt) REVERT: A 366 LYS cc_start: 0.8268 (tptm) cc_final: 0.8059 (mtpp) REVERT: A 369 THR cc_start: 0.8152 (m) cc_final: 0.7893 (p) REVERT: A 374 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7993 (ttpp) REVERT: A 406 TRP cc_start: 0.7760 (p90) cc_final: 0.7059 (p90) REVERT: A 407 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7170 (mt0) REVERT: A 414 TRP cc_start: 0.8742 (p-90) cc_final: 0.7950 (p-90) REVERT: A 422 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7734 (mp) REVERT: A 476 LYS cc_start: 0.8267 (mttm) cc_final: 0.7906 (mtpp) REVERT: A 478 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7362 (mm-30) REVERT: A 494 ASN cc_start: 0.7469 (m110) cc_final: 0.7188 (m110) REVERT: A 500 GLN cc_start: 0.7613 (pt0) cc_final: 0.7297 (pt0) REVERT: A 503 LEU cc_start: 0.8097 (tp) cc_final: 0.7159 (tp) REVERT: A 505 ILE cc_start: 0.8459 (mt) cc_final: 0.8240 (mm) REVERT: A 507 GLN cc_start: 0.8657 (pt0) cc_final: 0.8015 (pt0) REVERT: A 520 GLN cc_start: 0.6992 (tp40) cc_final: 0.6461 (tm-30) REVERT: A 523 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7617 (mt-10) REVERT: A 548 VAL cc_start: 0.1961 (OUTLIER) cc_final: 0.1119 (m) REVERT: B 21 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8149 (m) REVERT: B 22 LYS cc_start: 0.8127 (tttp) cc_final: 0.7659 (tttp) REVERT: B 34 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7853 (tt) REVERT: B 36 GLU cc_start: 0.7344 (mt-10) cc_final: 0.7045 (mt-10) REVERT: B 44 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7126 (mm-30) REVERT: B 77 PHE cc_start: 0.7808 (m-80) cc_final: 0.7528 (m-10) REVERT: B 82 LYS cc_start: 0.8682 (mtpt) cc_final: 0.8133 (mttm) REVERT: B 102 LYS cc_start: 0.8730 (mptt) cc_final: 0.8138 (mptt) REVERT: B 128 THR cc_start: 0.7867 (p) cc_final: 0.7311 (t) REVERT: B 132 ILE cc_start: 0.8431 (pt) cc_final: 0.8071 (mt) REVERT: B 167 ILE cc_start: 0.4862 (OUTLIER) cc_final: 0.4601 (tt) REVERT: B 178 ILE cc_start: 0.8354 (mt) cc_final: 0.7952 (tp) REVERT: B 256 ASP cc_start: 0.7101 (t70) cc_final: 0.6372 (t70) REVERT: B 260 LEU cc_start: 0.7693 (mt) cc_final: 0.7384 (mt) REVERT: B 263 LYS cc_start: 0.8147 (ttmp) cc_final: 0.7932 (ttmp) REVERT: B 266 TRP cc_start: 0.7644 (t60) cc_final: 0.7277 (t60) REVERT: B 298 GLU cc_start: 0.8270 (pt0) cc_final: 0.7540 (pt0) REVERT: B 309 ILE cc_start: 0.8436 (mt) cc_final: 0.8111 (mm) REVERT: B 322 SER cc_start: 0.8744 (m) cc_final: 0.8372 (p) REVERT: B 328 GLU cc_start: 0.7270 (tt0) cc_final: 0.6873 (tt0) REVERT: B 330 GLN cc_start: 0.7735 (pm20) cc_final: 0.7132 (pm20) REVERT: B 346 PHE cc_start: 0.7618 (m-80) cc_final: 0.7187 (m-10) REVERT: B 347 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7828 (mtpp) REVERT: B 353 LYS cc_start: 0.8202 (ptpp) cc_final: 0.7676 (ptpp) REVERT: B 365 VAL cc_start: 0.8385 (m) cc_final: 0.8141 (p) REVERT: B 396 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6580 (mt-10) REVERT: B 397 THR cc_start: 0.8013 (p) cc_final: 0.7747 (t) outliers start: 50 outliers final: 35 residues processed: 346 average time/residue: 0.2259 time to fit residues: 101.1749 Evaluate side-chains 364 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 321 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 239 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 332 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.130184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.113768 restraints weight = 14274.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117659 restraints weight = 7129.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.120113 restraints weight = 4248.651| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7845 Z= 0.245 Angle : 0.644 10.997 10652 Z= 0.328 Chirality : 0.046 0.230 1157 Planarity : 0.005 0.041 1335 Dihedral : 6.705 80.956 1011 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.60 % Allowed : 28.37 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.04 (0.29), residues: 912 helix: 1.35 (0.31), residues: 306 sheet: -0.81 (0.42), residues: 140 loop : -0.55 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 535 HIS 0.008 0.001 HIS A 208 PHE 0.029 0.002 PHE A 171 TYR 0.030 0.002 TYR A 319 ARG 0.008 0.000 ARG A 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2551.14 seconds wall clock time: 46 minutes 25.71 seconds (2785.71 seconds total)