Starting phenix.real_space_refine on Mon Mar 11 19:16:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3k_10092/03_2024/6s3k_10092.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3k_10092/03_2024/6s3k_10092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3k_10092/03_2024/6s3k_10092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3k_10092/03_2024/6s3k_10092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3k_10092/03_2024/6s3k_10092.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3k_10092/03_2024/6s3k_10092.pdb" } resolution = 3.7 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= 0.005 sd= 0.093 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: 5 Type Number sf(0) Gaussians K 6 8.98 5 S 34 5.16 5 C 5906 2.51 5 N 1436 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B GLU 511": "OE1" <-> "OE2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "B GLU 522": "OE1" <-> "OE2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B GLU 551": "OE1" <-> "OE2" Residue "B ARG 573": "NH1" <-> "NH2" Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 296": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A ARG 519": "NH1" <-> "NH2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A ARG 573": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8902 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4448 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 25, 'TRANS': 547} Chain breaks: 2 Chain: "A" Number of atoms: 4448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4448 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 25, 'TRANS': 547} Chain breaks: 2 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.43, per 1000 atoms: 0.61 Number of scatterers: 8902 At special positions: 0 Unit cell: (67.851, 119.547, 109.854, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 6 19.00 S 34 16.00 O 1520 8.00 N 1436 7.00 C 5906 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: 3.46 Conformation dependent library (CDL) restraints added in 1.8 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 1 sheets defined 67.6% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'B' and resid 30 through 38 removed outlier: 4.955A pdb=" N ASP B 36 " --> pdb=" O MET B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 62 through 88 Processing helix chain 'B' and resid 95 through 101 Processing helix chain 'B' and resid 107 through 132 removed outlier: 3.701A pdb=" N GLY B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 removed outlier: 4.321A pdb=" N ASP B 142 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 removed outlier: 3.645A pdb=" N ALA B 148 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE B 150 " --> pdb=" O PRO B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 193 removed outlier: 4.292A pdb=" N TYR B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 225 Processing helix chain 'B' and resid 226 through 229 Processing helix chain 'B' and resid 231 through 238 removed outlier: 3.962A pdb=" N ILE B 235 " --> pdb=" O GLY B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 275 Processing helix chain 'B' and resid 284 through 294 removed outlier: 3.890A pdb=" N GLN B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 331 removed outlier: 3.782A pdb=" N ILE B 303 " --> pdb=" O PHE B 299 " (cutoff:3.500A) Proline residue: B 323 - end of helix removed outlier: 3.564A pdb=" N ARG B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 removed outlier: 3.753A pdb=" N PHE B 339 " --> pdb=" O PRO B 336 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL B 341 " --> pdb=" O MET B 338 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG B 342 " --> pdb=" O PHE B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 367 Processing helix chain 'B' and resid 372 through 399 removed outlier: 4.243A pdb=" N LEU B 376 " --> pdb=" O HIS B 372 " (cutoff:3.500A) Proline residue: B 384 - end of helix removed outlier: 3.835A pdb=" N GLN B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 428 removed outlier: 3.559A pdb=" N LYS B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 461 removed outlier: 3.669A pdb=" N LEU B 437 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Proline residue: B 441 - end of helix Processing helix chain 'B' and resid 484 through 498 Processing helix chain 'B' and resid 511 through 524 removed outlier: 3.973A pdb=" N LYS B 515 " --> pdb=" O GLU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 553 Processing helix chain 'B' and resid 582 through 591 Processing helix chain 'A' and resid 30 through 38 removed outlier: 4.955A pdb=" N ASP A 36 " --> pdb=" O MET A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 62 through 88 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 107 through 132 removed outlier: 3.700A pdb=" N GLY A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 144 through 161 removed outlier: 3.646A pdb=" N ALA A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 193 removed outlier: 4.292A pdb=" N TYR A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 225 Processing helix chain 'A' and resid 226 through 229 Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.962A pdb=" N ILE A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 275 Processing helix chain 'A' and resid 284 through 294 removed outlier: 3.890A pdb=" N GLN A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 331 removed outlier: 3.783A pdb=" N ILE A 303 " --> pdb=" O PHE A 299 " (cutoff:3.500A) Proline residue: A 323 - end of helix removed outlier: 3.564A pdb=" N ARG A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 removed outlier: 3.753A pdb=" N PHE A 339 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL A 341 " --> pdb=" O MET A 338 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG A 342 " --> pdb=" O PHE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 367 Processing helix chain 'A' and resid 372 through 399 removed outlier: 4.244A pdb=" N LEU A 376 " --> pdb=" O HIS A 372 " (cutoff:3.500A) Proline residue: A 384 - end of helix removed outlier: 3.836A pdb=" N GLN A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 428 removed outlier: 3.559A pdb=" N LYS A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 461 removed outlier: 3.669A pdb=" N LEU A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 484 through 498 Processing helix chain 'A' and resid 511 through 524 removed outlier: 3.972A pdb=" N LYS A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 553 Processing helix chain 'A' and resid 582 through 591 Processing sheet with id=AA1, first strand: chain 'B' and resid 502 through 503 removed outlier: 8.423A pdb=" N ILE B 502 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 476 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL B 475 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU B 564 " --> pdb=" O VAL B 475 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE B 477 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET B 597 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 597 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL A 475 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU A 564 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE A 477 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ILE A 502 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 476 " --> pdb=" O ILE A 502 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1650 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2583 1.34 - 1.46: 1572 1.46 - 1.57: 4889 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 9106 Sorted by residual: bond pdb=" C ILE B 239 " pdb=" N PRO B 240 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.39e+00 bond pdb=" C ILE A 239 " pdb=" N PRO A 240 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.23e+00 bond pdb=" C VAL A 145 " pdb=" N PRO A 146 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.94e+00 bond pdb=" CG LEU B 120 " pdb=" CD1 LEU B 120 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 bond pdb=" C VAL B 145 " pdb=" N PRO B 146 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.91e+00 ... (remaining 9101 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.77: 287 106.77 - 113.58: 5163 113.58 - 120.40: 3803 120.40 - 127.21: 3017 127.21 - 134.03: 112 Bond angle restraints: 12382 Sorted by residual: angle pdb=" C PHE B 508 " pdb=" N ASP B 509 " pdb=" CA ASP B 509 " ideal model delta sigma weight residual 123.91 131.06 -7.15 1.66e+00 3.63e-01 1.85e+01 angle pdb=" C PHE A 508 " pdb=" N ASP A 509 " pdb=" CA ASP A 509 " ideal model delta sigma weight residual 123.91 131.06 -7.15 1.66e+00 3.63e-01 1.85e+01 angle pdb=" C MET B 193 " pdb=" N THR B 194 " pdb=" CA THR B 194 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C MET A 193 " pdb=" N THR A 194 " pdb=" CA THR A 194 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 angle pdb=" CA LEU A 461 " pdb=" CB LEU A 461 " pdb=" CG LEU A 461 " ideal model delta sigma weight residual 116.30 130.44 -14.14 3.50e+00 8.16e-02 1.63e+01 ... (remaining 12377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 4680 16.82 - 33.64: 528 33.64 - 50.46: 120 50.46 - 67.28: 14 67.28 - 84.10: 14 Dihedral angle restraints: 5356 sinusoidal: 2042 harmonic: 3314 Sorted by residual: dihedral pdb=" CA PHE B 382 " pdb=" C PHE B 382 " pdb=" N ILE B 383 " pdb=" CA ILE B 383 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA PHE A 382 " pdb=" C PHE A 382 " pdb=" N ILE A 383 " pdb=" CA ILE A 383 " ideal model delta harmonic sigma weight residual 180.00 153.83 26.17 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA LYS A 105 " pdb=" C LYS A 105 " pdb=" N PRO A 106 " pdb=" CA PRO A 106 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 5353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 944 0.050 - 0.101: 379 0.101 - 0.151: 130 0.151 - 0.201: 28 0.201 - 0.251: 11 Chirality restraints: 1492 Sorted by residual: chirality pdb=" CA ASP A 509 " pdb=" N ASP A 509 " pdb=" C ASP A 509 " pdb=" CB ASP A 509 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA ASP B 509 " pdb=" N ASP B 509 " pdb=" C ASP B 509 " pdb=" CB ASP B 509 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE B 239 " pdb=" CA ILE B 239 " pdb=" CG1 ILE B 239 " pdb=" CG2 ILE B 239 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1489 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 434 " 0.048 5.00e-02 4.00e+02 7.13e-02 8.12e+00 pdb=" N PRO A 435 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 435 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 435 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 434 " -0.048 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO B 435 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 435 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 435 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 335 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO B 336 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 336 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 336 " -0.038 5.00e-02 4.00e+02 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 3024 2.85 - 3.42: 9854 3.42 - 3.99: 15718 3.99 - 4.57: 21472 4.57 - 5.14: 31348 Nonbonded interactions: 81416 Sorted by model distance: nonbonded pdb=" OG SER B 507 " pdb=" O LEU B 532 " model vdw 2.276 2.440 nonbonded pdb=" OG SER A 507 " pdb=" O LEU A 532 " model vdw 2.277 2.440 nonbonded pdb=" OH TYR A 88 " pdb=" OE2 GLU A 100 " model vdw 2.284 2.440 nonbonded pdb=" OH TYR B 88 " pdb=" OE2 GLU B 100 " model vdw 2.284 2.440 nonbonded pdb=" OG SER B 80 " pdb=" OE1 GLN B 389 " model vdw 2.309 2.440 ... (remaining 81411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.740 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 28.150 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 : 0.008 0.079 9106 Z= 0.498 Angle : 1.124 14.143 12382 Z= 0.594 Chirality : 0.063 0.251 1492 Planarity : 0.009 0.071 1508 Dihedral : 15.380 84.105 3220 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 0.62 % Allowed : 12.29 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.19), residues: 1134 helix: -2.35 (0.14), residues: 748 sheet: -2.40 (0.57), residues: 66 loop : -4.38 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 520 HIS 0.004 0.002 HIS A 492 PHE 0.020 0.002 PHE A 299 TYR 0.030 0.003 TYR A 377 ARG 0.004 0.001 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 172 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5486 (mtt) cc_final: 0.5204 (ptp) REVERT: B 52 LEU cc_start: 0.8590 (tp) cc_final: 0.8333 (tp) REVERT: B 75 LEU cc_start: 0.8518 (tp) cc_final: 0.8316 (tp) REVERT: B 229 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8665 (pp) REVERT: B 294 PHE cc_start: 0.5568 (t80) cc_final: 0.5358 (t80) REVERT: B 573 ARG cc_start: 0.7709 (ptt180) cc_final: 0.7075 (mmm160) REVERT: A 32 MET cc_start: 0.5624 (mtt) cc_final: 0.5358 (ptp) REVERT: A 51 ILE cc_start: 0.7893 (mt) cc_final: 0.7616 (mt) REVERT: A 229 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8539 (pp) REVERT: A 393 CYS cc_start: 0.8647 (t) cc_final: 0.8423 (t) REVERT: A 404 TRP cc_start: 0.7490 (t60) cc_final: 0.7196 (t60) REVERT: A 551 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7920 (mt-10) REVERT: A 573 ARG cc_start: 0.7620 (ptt180) cc_final: 0.6988 (mmm160) outliers start: 6 outliers final: 2 residues processed: 177 average time/residue: 0.1977 time to fit residues: 49.0861 Evaluate side-chains 125 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 501 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN B 203 HIS B 316 ASN B 575 HIS A 47 GLN A 203 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9106 Z= 0.219 Angle : 0.703 9.485 12382 Z= 0.360 Chirality : 0.044 0.172 1492 Planarity : 0.006 0.054 1508 Dihedral : 5.683 32.231 1216 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.71 % Allowed : 18.12 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.24), residues: 1134 helix: -0.22 (0.19), residues: 750 sheet: -1.18 (0.71), residues: 48 loop : -3.87 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 520 HIS 0.002 0.001 HIS A 144 PHE 0.019 0.001 PHE A 448 TYR 0.020 0.002 TYR B 377 ARG 0.002 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5638 (mtt) cc_final: 0.5283 (ptp) REVERT: B 229 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8653 (pp) REVERT: B 440 MET cc_start: 0.8082 (tpp) cc_final: 0.7864 (tpt) REVERT: B 573 ARG cc_start: 0.7523 (ptt180) cc_final: 0.7051 (mmm160) REVERT: B 579 HIS cc_start: 0.7390 (OUTLIER) cc_final: 0.6228 (t-90) REVERT: A 32 MET cc_start: 0.5770 (mtt) cc_final: 0.5441 (ptp) REVERT: A 51 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7223 (mt) REVERT: A 229 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8584 (pp) REVERT: A 392 MET cc_start: 0.6960 (tpt) cc_final: 0.6701 (tpt) REVERT: A 440 MET cc_start: 0.7718 (tpp) cc_final: 0.7099 (mmt) REVERT: A 551 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7979 (mt-10) REVERT: A 573 ARG cc_start: 0.7433 (ptt180) cc_final: 0.7053 (mmm160) REVERT: A 579 HIS cc_start: 0.7424 (OUTLIER) cc_final: 0.7027 (m-70) outliers start: 26 outliers final: 12 residues processed: 162 average time/residue: 0.1663 time to fit residues: 39.8128 Evaluate side-chains 151 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 579 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9106 Z= 0.249 Angle : 0.703 11.922 12382 Z= 0.358 Chirality : 0.045 0.189 1492 Planarity : 0.005 0.049 1508 Dihedral : 5.309 22.591 1216 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.58 % Allowed : 19.90 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.25), residues: 1134 helix: 0.47 (0.19), residues: 758 sheet: -0.31 (0.80), residues: 46 loop : -3.64 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 520 HIS 0.002 0.001 HIS A 144 PHE 0.021 0.001 PHE A 448 TYR 0.020 0.002 TYR B 377 ARG 0.001 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 133 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5808 (mtt) cc_final: 0.5398 (ptp) REVERT: B 51 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.7083 (mt) REVERT: B 52 LEU cc_start: 0.8349 (tp) cc_final: 0.8030 (tp) REVERT: B 229 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8707 (pp) REVERT: B 259 ILE cc_start: 0.7902 (tt) cc_final: 0.7603 (tp) REVERT: B 335 MET cc_start: 0.8025 (mmm) cc_final: 0.6941 (mtp) REVERT: B 573 ARG cc_start: 0.7489 (ptt180) cc_final: 0.6981 (mmm160) REVERT: B 579 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.6413 (t-90) REVERT: A 51 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7195 (mt) REVERT: A 229 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8648 (pp) REVERT: A 294 PHE cc_start: 0.5607 (OUTLIER) cc_final: 0.5282 (t80) REVERT: A 440 MET cc_start: 0.7682 (tpp) cc_final: 0.7133 (mmt) REVERT: A 573 ARG cc_start: 0.7457 (ptt180) cc_final: 0.7024 (mmm160) REVERT: A 579 HIS cc_start: 0.7444 (OUTLIER) cc_final: 0.6279 (t-90) outliers start: 44 outliers final: 27 residues processed: 165 average time/residue: 0.1664 time to fit residues: 40.3983 Evaluate side-chains 163 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 598 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.0170 chunk 69 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9106 Z= 0.216 Angle : 0.676 10.394 12382 Z= 0.340 Chirality : 0.043 0.164 1492 Planarity : 0.005 0.048 1508 Dihedral : 5.056 22.841 1216 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.90 % Allowed : 22.08 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.26), residues: 1134 helix: 0.91 (0.19), residues: 762 sheet: 0.10 (0.84), residues: 46 loop : -3.51 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 520 HIS 0.004 0.001 HIS A 144 PHE 0.021 0.001 PHE A 448 TYR 0.018 0.001 TYR B 377 ARG 0.001 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 135 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5754 (mtt) cc_final: 0.5354 (ptp) REVERT: B 51 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6973 (mt) REVERT: B 52 LEU cc_start: 0.8380 (tp) cc_final: 0.8064 (tp) REVERT: B 133 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7826 (tp) REVERT: B 143 TYR cc_start: 0.7521 (p90) cc_final: 0.6970 (p90) REVERT: B 229 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8714 (pp) REVERT: B 573 ARG cc_start: 0.7468 (ptt180) cc_final: 0.7022 (mmm160) REVERT: B 579 HIS cc_start: 0.7360 (OUTLIER) cc_final: 0.6380 (t-90) REVERT: A 32 MET cc_start: 0.5904 (mtt) cc_final: 0.5493 (ptp) REVERT: A 133 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.7927 (tp) REVERT: A 229 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8646 (pp) REVERT: A 294 PHE cc_start: 0.5629 (OUTLIER) cc_final: 0.5172 (t80) REVERT: A 335 MET cc_start: 0.7978 (mmm) cc_final: 0.6835 (mtp) REVERT: A 440 MET cc_start: 0.7556 (tpp) cc_final: 0.7003 (mmt) REVERT: A 573 ARG cc_start: 0.7431 (ptt180) cc_final: 0.7017 (mmm160) REVERT: A 579 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.6300 (t-90) outliers start: 47 outliers final: 26 residues processed: 172 average time/residue: 0.1731 time to fit residues: 43.8707 Evaluate side-chains 163 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 489 LYS Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 598 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 94 optimal weight: 0.2980 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9106 Z= 0.236 Angle : 0.691 10.138 12382 Z= 0.347 Chirality : 0.044 0.164 1492 Planarity : 0.005 0.049 1508 Dihedral : 4.977 22.622 1214 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 5.10 % Allowed : 23.85 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1134 helix: 1.07 (0.19), residues: 754 sheet: 0.33 (0.85), residues: 46 loop : -3.35 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 520 HIS 0.003 0.001 HIS A 144 PHE 0.022 0.001 PHE B 448 TYR 0.019 0.001 TYR B 377 ARG 0.001 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 134 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5682 (mtt) cc_final: 0.5318 (ptp) REVERT: B 52 LEU cc_start: 0.8357 (tp) cc_final: 0.7993 (tp) REVERT: B 143 TYR cc_start: 0.7491 (p90) cc_final: 0.6977 (p90) REVERT: B 229 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8699 (pp) REVERT: B 259 ILE cc_start: 0.7883 (tt) cc_final: 0.7573 (tp) REVERT: B 335 MET cc_start: 0.7931 (mmm) cc_final: 0.6858 (mtp) REVERT: B 404 TRP cc_start: 0.6949 (t60) cc_final: 0.6727 (t60) REVERT: B 573 ARG cc_start: 0.7485 (ptt180) cc_final: 0.7026 (mmm160) REVERT: B 579 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.6424 (t-90) REVERT: A 133 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.7903 (tp) REVERT: A 229 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8674 (pp) REVERT: A 292 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.5891 (mp0) REVERT: A 294 PHE cc_start: 0.5892 (OUTLIER) cc_final: 0.5426 (t80) REVERT: A 335 MET cc_start: 0.7874 (mmm) cc_final: 0.6827 (mtp) REVERT: A 404 TRP cc_start: 0.7058 (t60) cc_final: 0.6857 (t60) REVERT: A 440 MET cc_start: 0.7534 (tpp) cc_final: 0.6964 (mmt) REVERT: A 445 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7441 (tt) REVERT: A 573 ARG cc_start: 0.7415 (ptt180) cc_final: 0.6997 (mmm160) REVERT: A 579 HIS cc_start: 0.7446 (OUTLIER) cc_final: 0.6471 (t-90) outliers start: 49 outliers final: 35 residues processed: 171 average time/residue: 0.1700 time to fit residues: 42.9822 Evaluate side-chains 174 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 131 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 598 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 0.0050 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN A 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9106 Z= 0.174 Angle : 0.650 13.453 12382 Z= 0.322 Chirality : 0.043 0.191 1492 Planarity : 0.005 0.047 1508 Dihedral : 4.777 22.637 1214 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.58 % Allowed : 25.10 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1134 helix: 1.24 (0.19), residues: 760 sheet: 0.33 (0.84), residues: 46 loop : -3.25 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 520 HIS 0.003 0.000 HIS A 144 PHE 0.022 0.001 PHE B 448 TYR 0.016 0.001 TYR B 377 ARG 0.002 0.000 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 138 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5669 (mtt) cc_final: 0.5311 (ptp) REVERT: B 133 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.7822 (tp) REVERT: B 229 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8624 (pp) REVERT: B 335 MET cc_start: 0.7764 (mmm) cc_final: 0.6722 (mtp) REVERT: B 573 ARG cc_start: 0.7444 (ptt180) cc_final: 0.7030 (mmm160) REVERT: B 579 HIS cc_start: 0.7311 (OUTLIER) cc_final: 0.6225 (t-90) REVERT: A 32 MET cc_start: 0.5874 (mtt) cc_final: 0.5515 (ptp) REVERT: A 51 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.7058 (mt) REVERT: A 133 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.7867 (tp) REVERT: A 143 TYR cc_start: 0.7447 (p90) cc_final: 0.7068 (p90) REVERT: A 229 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8612 (pp) REVERT: A 292 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.5663 (mp0) REVERT: A 294 PHE cc_start: 0.5648 (OUTLIER) cc_final: 0.5135 (t80) REVERT: A 335 MET cc_start: 0.7817 (mmm) cc_final: 0.6774 (mtp) REVERT: A 404 TRP cc_start: 0.7069 (t60) cc_final: 0.6856 (t60) REVERT: A 440 MET cc_start: 0.7494 (tpp) cc_final: 0.6928 (mmt) REVERT: A 573 ARG cc_start: 0.7391 (ptt180) cc_final: 0.7015 (mmm160) REVERT: A 579 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.6047 (t-90) outliers start: 44 outliers final: 30 residues processed: 170 average time/residue: 0.1640 time to fit residues: 41.3878 Evaluate side-chains 162 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 123 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 597 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 109 optimal weight: 8.9990 chunk 68 optimal weight: 0.0060 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9106 Z= 0.180 Angle : 0.650 12.051 12382 Z= 0.322 Chirality : 0.043 0.170 1492 Planarity : 0.005 0.047 1508 Dihedral : 4.664 22.162 1214 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 5.42 % Allowed : 25.52 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1134 helix: 1.35 (0.19), residues: 758 sheet: 0.44 (0.85), residues: 46 loop : -3.17 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 520 HIS 0.002 0.000 HIS A 144 PHE 0.023 0.001 PHE B 448 TYR 0.016 0.001 TYR A 377 ARG 0.002 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 137 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5638 (mtt) cc_final: 0.5312 (ptp) REVERT: B 133 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.7807 (tp) REVERT: B 229 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8599 (pp) REVERT: B 335 MET cc_start: 0.7748 (mmm) cc_final: 0.6693 (mtp) REVERT: B 520 TRP cc_start: 0.7177 (t60) cc_final: 0.6958 (t60) REVERT: B 573 ARG cc_start: 0.7414 (ptt180) cc_final: 0.7030 (mmm160) REVERT: B 579 HIS cc_start: 0.7323 (OUTLIER) cc_final: 0.6332 (t-90) REVERT: A 32 MET cc_start: 0.5710 (mtt) cc_final: 0.5444 (ptp) REVERT: A 51 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.6966 (mt) REVERT: A 133 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.7847 (tp) REVERT: A 143 TYR cc_start: 0.7405 (p90) cc_final: 0.7177 (p90) REVERT: A 229 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8540 (pp) REVERT: A 292 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.5620 (mp0) REVERT: A 294 PHE cc_start: 0.5797 (OUTLIER) cc_final: 0.5303 (t80) REVERT: A 335 MET cc_start: 0.7773 (mmm) cc_final: 0.6743 (mtp) REVERT: A 404 TRP cc_start: 0.6998 (t60) cc_final: 0.6777 (t60) REVERT: A 440 MET cc_start: 0.7495 (tpp) cc_final: 0.6919 (mmt) REVERT: A 520 TRP cc_start: 0.6976 (t60) cc_final: 0.6767 (t60) REVERT: A 573 ARG cc_start: 0.7388 (ptt180) cc_final: 0.7009 (mmm160) REVERT: A 579 HIS cc_start: 0.7308 (OUTLIER) cc_final: 0.6249 (t-90) outliers start: 52 outliers final: 36 residues processed: 178 average time/residue: 0.1676 time to fit residues: 44.2674 Evaluate side-chains 172 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 127 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 598 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.0270 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 0.0970 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9106 Z= 0.166 Angle : 0.644 11.494 12382 Z= 0.316 Chirality : 0.042 0.161 1492 Planarity : 0.005 0.047 1508 Dihedral : 4.534 21.898 1214 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 5.00 % Allowed : 26.15 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.27), residues: 1134 helix: 1.46 (0.19), residues: 762 sheet: 0.50 (0.85), residues: 46 loop : -3.27 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 520 HIS 0.002 0.000 HIS B 144 PHE 0.023 0.001 PHE B 448 TYR 0.013 0.001 TYR A 377 ARG 0.001 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 134 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5545 (mtt) cc_final: 0.5332 (ptp) REVERT: B 133 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7796 (tp) REVERT: B 229 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8554 (pp) REVERT: B 259 ILE cc_start: 0.7806 (tt) cc_final: 0.7472 (tp) REVERT: B 335 MET cc_start: 0.7885 (mmm) cc_final: 0.6864 (mtp) REVERT: B 573 ARG cc_start: 0.7393 (ptt180) cc_final: 0.7037 (mmm160) REVERT: B 579 HIS cc_start: 0.7305 (OUTLIER) cc_final: 0.6323 (t-90) REVERT: A 32 MET cc_start: 0.5583 (mtt) cc_final: 0.5372 (ptp) REVERT: A 133 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.7878 (tp) REVERT: A 229 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8469 (pp) REVERT: A 292 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.5566 (mp0) REVERT: A 294 PHE cc_start: 0.5687 (OUTLIER) cc_final: 0.5126 (t80) REVERT: A 335 MET cc_start: 0.7729 (mmm) cc_final: 0.6633 (mtp) REVERT: A 404 TRP cc_start: 0.6986 (t60) cc_final: 0.6764 (t60) REVERT: A 440 MET cc_start: 0.7409 (tpp) cc_final: 0.6850 (mmt) REVERT: A 573 ARG cc_start: 0.7360 (ptt180) cc_final: 0.6978 (mmm160) REVERT: A 579 HIS cc_start: 0.7295 (OUTLIER) cc_final: 0.6315 (t-90) REVERT: A 597 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7747 (ttm) outliers start: 48 outliers final: 31 residues processed: 173 average time/residue: 0.1694 time to fit residues: 42.9626 Evaluate side-chains 165 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 125 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 598 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 0.0040 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 92 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9106 Z= 0.163 Angle : 0.667 15.514 12382 Z= 0.319 Chirality : 0.042 0.195 1492 Planarity : 0.005 0.045 1508 Dihedral : 4.449 21.475 1214 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.48 % Allowed : 26.98 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.27), residues: 1134 helix: 1.54 (0.20), residues: 760 sheet: 0.61 (0.85), residues: 46 loop : -3.15 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 520 HIS 0.002 0.000 HIS B 144 PHE 0.023 0.001 PHE B 448 TYR 0.013 0.001 TYR A 95 ARG 0.003 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 130 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: B 133 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7768 (tp) REVERT: B 229 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8557 (pp) REVERT: B 335 MET cc_start: 0.7873 (mmm) cc_final: 0.6936 (ttp) REVERT: B 573 ARG cc_start: 0.7384 (ptt180) cc_final: 0.7021 (mmm160) REVERT: B 579 HIS cc_start: 0.7359 (OUTLIER) cc_final: 0.6528 (t-90) REVERT: A 32 MET cc_start: 0.5725 (mtt) cc_final: 0.5521 (ptp) REVERT: A 133 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7879 (tp) REVERT: A 229 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8453 (pp) REVERT: A 292 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.5653 (mp0) REVERT: A 294 PHE cc_start: 0.5905 (OUTLIER) cc_final: 0.5344 (t80) REVERT: A 335 MET cc_start: 0.7658 (mmm) cc_final: 0.6673 (ttp) REVERT: A 404 TRP cc_start: 0.7031 (t60) cc_final: 0.6795 (t60) REVERT: A 440 MET cc_start: 0.7495 (tpp) cc_final: 0.6910 (mmt) REVERT: A 445 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7488 (tt) REVERT: A 543 PHE cc_start: 0.7783 (t80) cc_final: 0.6988 (t80) REVERT: A 573 ARG cc_start: 0.7344 (ptt180) cc_final: 0.6977 (mmm160) REVERT: A 579 HIS cc_start: 0.7295 (OUTLIER) cc_final: 0.6355 (t-90) outliers start: 43 outliers final: 29 residues processed: 166 average time/residue: 0.1627 time to fit residues: 40.2804 Evaluate side-chains 163 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 125 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 104 optimal weight: 0.0970 chunk 90 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9106 Z= 0.178 Angle : 0.675 14.701 12382 Z= 0.325 Chirality : 0.043 0.191 1492 Planarity : 0.005 0.046 1508 Dihedral : 4.450 20.997 1214 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.38 % Allowed : 27.50 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.27), residues: 1134 helix: 1.49 (0.19), residues: 764 sheet: 0.63 (0.84), residues: 46 loop : -3.14 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 520 HIS 0.002 0.000 HIS B 144 PHE 0.023 0.001 PHE B 448 TYR 0.014 0.001 TYR A 377 ARG 0.002 0.000 ARG A 587 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 130 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 133 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7769 (tp) REVERT: B 229 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8528 (pp) REVERT: B 259 ILE cc_start: 0.7799 (tt) cc_final: 0.7463 (tp) REVERT: B 335 MET cc_start: 0.7821 (mmm) cc_final: 0.6902 (ttp) REVERT: B 402 LYS cc_start: 0.6607 (mttt) cc_final: 0.6348 (mmmt) REVERT: B 573 ARG cc_start: 0.7387 (ptt180) cc_final: 0.7022 (mmm160) REVERT: B 579 HIS cc_start: 0.7342 (OUTLIER) cc_final: 0.6429 (t-90) REVERT: A 32 MET cc_start: 0.5758 (mtt) cc_final: 0.5535 (ptp) REVERT: A 133 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.7873 (tp) REVERT: A 229 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8413 (pp) REVERT: A 292 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.5607 (mp0) REVERT: A 294 PHE cc_start: 0.5810 (OUTLIER) cc_final: 0.5245 (t80) REVERT: A 335 MET cc_start: 0.7661 (mmm) cc_final: 0.6681 (ttp) REVERT: A 404 TRP cc_start: 0.7077 (t60) cc_final: 0.6841 (t60) REVERT: A 440 MET cc_start: 0.7417 (tpp) cc_final: 0.6844 (mmt) REVERT: A 445 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7528 (tt) REVERT: A 573 ARG cc_start: 0.7348 (ptt180) cc_final: 0.6980 (mmm160) REVERT: A 579 HIS cc_start: 0.7264 (OUTLIER) cc_final: 0.6360 (t-90) outliers start: 42 outliers final: 29 residues processed: 165 average time/residue: 0.1764 time to fit residues: 42.3514 Evaluate side-chains 165 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 127 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 598 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 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 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.166981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.128346 restraints weight = 12902.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132674 restraints weight = 7405.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.135384 restraints weight = 5242.740| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9106 Z= 0.173 Angle : 0.673 14.421 12382 Z= 0.326 Chirality : 0.043 0.190 1492 Planarity : 0.005 0.046 1508 Dihedral : 4.429 21.003 1214 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.27 % Allowed : 27.50 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.27), residues: 1134 helix: 1.50 (0.19), residues: 764 sheet: 0.66 (0.85), residues: 46 loop : -3.04 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 520 HIS 0.002 0.000 HIS B 144 PHE 0.023 0.001 PHE B 448 TYR 0.013 0.001 TYR A 377 ARG 0.004 0.000 ARG A 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1738.21 seconds wall clock time: 32 minutes 46.78 seconds (1966.78 seconds total)