Starting phenix.real_space_refine on Sat Aug 3 20:35:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3k_10092/08_2024/6s3k_10092.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3k_10092/08_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_10092/08_2024/6s3k_10092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3k_10092/08_2024/6s3k_10092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3k_10092/08_2024/6s3k_10092.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3k_10092/08_2024/6s3k_10092.cif" } 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-5409/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: 5.40, 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: 3.57 Conformation dependent library (CDL) restraints added in 1.6 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: 0.88 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: 2.57 Time building geometry restraints manager: 3.93 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 3.040 nonbonded pdb=" OG SER A 507 " pdb=" O LEU A 532 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR A 88 " pdb=" OE2 GLU A 100 " model vdw 2.284 3.040 nonbonded pdb=" OH TYR B 88 " pdb=" OE2 GLU B 100 " model vdw 2.284 3.040 nonbonded pdb=" OG SER B 80 " pdb=" OE1 GLN B 389 " model vdw 2.309 3.040 ... (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 Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 27.450 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.020 ------------------------------------------------------------------------------- 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 : 0.911 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: 0.1874 time to fit residues: 46.7092 Evaluate side-chains 125 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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: 0.4980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN B 203 HIS B 316 ASN B 558 GLN B 575 HIS A 47 GLN A 203 HIS A 316 ASN A 558 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9106 Z= 0.182 Angle : 0.687 9.210 12382 Z= 0.351 Chirality : 0.044 0.171 1492 Planarity : 0.006 0.053 1508 Dihedral : 5.604 31.090 1216 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.50 % Allowed : 18.33 % 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: -1.87 (0.24), residues: 1134 helix: -0.13 (0.18), residues: 754 sheet: -1.13 (0.71), residues: 48 loop : -3.86 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 520 HIS 0.003 0.001 HIS B 144 PHE 0.019 0.001 PHE A 448 TYR 0.017 0.002 TYR B 377 ARG 0.002 0.000 ARG B 337 *********************** 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: 24 poor density : 147 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5495 (mtt) cc_final: 0.5157 (ptp) REVERT: B 75 LEU cc_start: 0.8314 (tp) cc_final: 0.7840 (tt) REVERT: B 229 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8604 (pp) REVERT: B 573 ARG cc_start: 0.7501 (ptt180) cc_final: 0.7048 (mmm160) REVERT: B 579 HIS cc_start: 0.7426 (OUTLIER) cc_final: 0.6201 (t-90) REVERT: A 32 MET cc_start: 0.5762 (mtt) cc_final: 0.5453 (ptp) REVERT: A 229 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8565 (pp) REVERT: A 440 MET cc_start: 0.7693 (tpp) cc_final: 0.7076 (mmt) REVERT: A 573 ARG cc_start: 0.7457 (ptt180) cc_final: 0.7059 (mmm160) REVERT: A 579 HIS cc_start: 0.7334 (OUTLIER) cc_final: 0.7013 (m-70) outliers start: 24 outliers final: 12 residues processed: 164 average time/residue: 0.1609 time to fit residues: 39.4176 Evaluate side-chains 143 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7257 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9106 Z= 0.203 Angle : 0.679 11.449 12382 Z= 0.342 Chirality : 0.044 0.175 1492 Planarity : 0.005 0.048 1508 Dihedral : 5.187 22.699 1216 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.75 % Allowed : 20.31 % Favored : 75.94 % 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: -0.90 (0.25), residues: 1134 helix: 0.61 (0.19), residues: 752 sheet: -0.30 (0.79), residues: 46 loop : -3.52 (0.30), residues: 336 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 0.020 0.001 PHE A 448 TYR 0.017 0.002 TYR A 377 ARG 0.001 0.000 ARG B 587 *********************** 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 172 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5630 (mtt) cc_final: 0.5270 (ptp) REVERT: B 51 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6916 (mt) REVERT: B 229 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8601 (pp) REVERT: B 440 MET cc_start: 0.7794 (tpt) cc_final: 0.7547 (tpp) REVERT: B 573 ARG cc_start: 0.7480 (ptt180) cc_final: 0.7015 (mmm160) REVERT: B 579 HIS cc_start: 0.7392 (OUTLIER) cc_final: 0.6126 (t-90) REVERT: B 597 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7519 (ttm) REVERT: A 32 MET cc_start: 0.5639 (mtt) cc_final: 0.5282 (ptp) REVERT: A 51 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.7044 (mt) REVERT: A 229 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8568 (pp) REVERT: A 292 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.5898 (mp0) REVERT: A 440 MET cc_start: 0.7617 (tpp) cc_final: 0.7070 (mmt) REVERT: A 573 ARG cc_start: 0.7441 (ptt180) cc_final: 0.7029 (mmm160) REVERT: A 579 HIS cc_start: 0.7421 (OUTLIER) cc_final: 0.5900 (t-90) outliers start: 36 outliers final: 18 residues processed: 162 average time/residue: 0.1673 time to fit residues: 39.6959 Evaluate side-chains 157 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 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 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 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 292 GLU 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 501 VAL Chi-restraints excluded: chain A residue 527 VAL 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: 1.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9106 Z= 0.269 Angle : 0.720 9.943 12382 Z= 0.361 Chirality : 0.045 0.165 1492 Planarity : 0.005 0.049 1508 Dihedral : 5.090 23.148 1216 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 5.31 % Allowed : 22.29 % Favored : 72.40 % 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: -0.54 (0.26), residues: 1134 helix: 0.88 (0.19), residues: 762 sheet: 0.06 (0.83), residues: 46 loop : -3.51 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 520 HIS 0.002 0.001 HIS B 492 PHE 0.022 0.001 PHE A 448 TYR 0.019 0.002 TYR A 377 ARG 0.002 0.000 ARG A 161 *********************** 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 187 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 136 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5861 (mtt) cc_final: 0.5428 (ptp) REVERT: B 51 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7125 (mt) REVERT: B 52 LEU cc_start: 0.8329 (tp) cc_final: 0.8053 (tp) REVERT: B 133 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.7891 (tp) REVERT: B 229 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8679 (pp) REVERT: B 440 MET cc_start: 0.7881 (tpt) cc_final: 0.7523 (tpp) REVERT: B 573 ARG cc_start: 0.7491 (ptt180) cc_final: 0.7016 (mmm160) REVERT: B 579 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.6511 (t-90) REVERT: A 32 MET cc_start: 0.5733 (mtt) cc_final: 0.5330 (ptp) REVERT: A 51 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7141 (mt) REVERT: A 229 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8694 (pp) REVERT: A 282 ASP cc_start: 0.8380 (p0) cc_final: 0.8148 (p0) REVERT: A 335 MET cc_start: 0.7943 (mmm) cc_final: 0.6797 (mtp) REVERT: A 440 MET cc_start: 0.7584 (tpp) cc_final: 0.7003 (mmt) REVERT: A 573 ARG cc_start: 0.7486 (ptt180) cc_final: 0.7028 (mmm160) REVERT: A 579 HIS cc_start: 0.7390 (OUTLIER) cc_final: 0.6423 (t-90) outliers start: 51 outliers final: 30 residues processed: 174 average time/residue: 0.1596 time to fit residues: 40.9388 Evaluate side-chains 171 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 SER 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 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 374 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 489 LYS 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 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 298 VAL Chi-restraints excluded: chain A residue 300 TYR 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 487 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: 0.6980 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7235 moved from start: 0.2569 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= 0.177 Angle : 0.660 9.483 12382 Z= 0.329 Chirality : 0.043 0.160 1492 Planarity : 0.005 0.047 1508 Dihedral : 4.810 23.931 1214 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.85 % Allowed : 25.10 % 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: -0.06 (0.26), residues: 1134 helix: 1.19 (0.19), residues: 766 sheet: 0.30 (0.84), residues: 46 loop : -3.24 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 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 0.001 0.000 ARG B 587 *********************** 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 177 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5638 (mtt) cc_final: 0.5301 (ptp) REVERT: B 229 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8650 (pp) REVERT: B 335 MET cc_start: 0.7718 (mmm) cc_final: 0.6701 (mtp) REVERT: B 404 TRP cc_start: 0.6904 (t60) cc_final: 0.6652 (t60) REVERT: B 440 MET cc_start: 0.7804 (tpt) cc_final: 0.7429 (tpp) REVERT: B 573 ARG cc_start: 0.7459 (ptt180) cc_final: 0.6433 (tmt170) REVERT: B 579 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.6141 (t-90) REVERT: A 32 MET cc_start: 0.5705 (mtt) cc_final: 0.5349 (ptp) REVERT: A 51 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6907 (mt) REVERT: A 133 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.7971 (tp) REVERT: A 143 TYR cc_start: 0.7338 (p90) cc_final: 0.7109 (p90) REVERT: A 229 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8687 (pp) REVERT: A 292 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.5735 (mp0) REVERT: A 404 TRP cc_start: 0.7068 (t60) cc_final: 0.6862 (t60) REVERT: A 440 MET cc_start: 0.7547 (tpp) cc_final: 0.7015 (mmt) REVERT: A 573 ARG cc_start: 0.7397 (ptt180) cc_final: 0.6923 (mmm160) REVERT: A 579 HIS cc_start: 0.7448 (OUTLIER) cc_final: 0.5972 (t-90) outliers start: 37 outliers final: 22 residues processed: 165 average time/residue: 0.1615 time to fit residues: 39.5821 Evaluate side-chains 159 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 49 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 436 VAL 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 39 SER Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 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 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 478 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.6657 > 50: distance: 43 - 48: 6.340 distance: 48 - 49: 19.185 distance: 48 - 190: 4.695 distance: 49 - 50: 13.423 distance: 49 - 52: 34.437 distance: 50 - 51: 23.806 distance: 50 - 55: 12.643 distance: 51 - 197: 22.027 distance: 52 - 53: 13.124 distance: 52 - 54: 8.876 distance: 55 - 56: 16.485 distance: 56 - 57: 22.528 distance: 56 - 59: 13.231 distance: 57 - 58: 25.921 distance: 57 - 63: 21.817 distance: 59 - 60: 26.396 distance: 60 - 61: 18.199 distance: 60 - 62: 36.063 distance: 63 - 64: 20.928 distance: 63 - 200: 15.762 distance: 64 - 65: 37.102 distance: 64 - 67: 28.505 distance: 65 - 66: 17.950 distance: 65 - 74: 17.123 distance: 66 - 209: 31.522 distance: 67 - 68: 16.164 distance: 68 - 69: 25.471 distance: 68 - 70: 16.701 distance: 69 - 71: 19.978 distance: 70 - 72: 7.667 distance: 71 - 73: 26.450 distance: 72 - 73: 21.415 distance: 74 - 75: 18.926 distance: 74 - 80: 35.735 distance: 75 - 76: 34.078 distance: 75 - 78: 17.193 distance: 76 - 77: 7.354 distance: 76 - 81: 14.766 distance: 78 - 79: 20.149 distance: 79 - 80: 4.876 distance: 81 - 82: 18.281 distance: 81 - 212: 32.937 distance: 82 - 83: 25.972 distance: 82 - 85: 38.619 distance: 83 - 84: 20.987 distance: 83 - 90: 20.533 distance: 85 - 86: 17.186 distance: 86 - 87: 25.693 distance: 87 - 88: 22.288 distance: 87 - 89: 9.399 distance: 90 - 91: 21.699 distance: 91 - 92: 27.285 distance: 91 - 94: 10.828 distance: 92 - 93: 13.337 distance: 92 - 101: 21.775 distance: 95 - 96: 21.857 distance: 95 - 97: 7.583 distance: 96 - 98: 30.107 distance: 97 - 99: 28.644 distance: 98 - 100: 17.917 distance: 99 - 100: 34.536 distance: 101 - 102: 20.630 distance: 102 - 103: 33.352 distance: 102 - 105: 12.330 distance: 103 - 104: 11.523 distance: 103 - 109: 27.984 distance: 105 - 106: 15.637 distance: 105 - 107: 27.212 distance: 106 - 108: 47.125 distance: 109 - 110: 30.359 distance: 110 - 111: 28.205 distance: 110 - 113: 23.818 distance: 111 - 112: 18.663 distance: 111 - 116: 19.374 distance: 113 - 114: 13.311 distance: 113 - 115: 23.806 distance: 116 - 117: 22.357 distance: 117 - 118: 9.146 distance: 117 - 120: 9.626 distance: 118 - 119: 23.411 distance: 118 - 125: 10.374 distance: 120 - 121: 8.304 distance: 121 - 122: 3.749 distance: 122 - 123: 24.051 distance: 123 - 124: 10.899 distance: 125 - 126: 15.473 distance: 126 - 127: 18.738 distance: 126 - 129: 21.474 distance: 127 - 128: 16.436 distance: 127 - 134: 5.629 distance: 129 - 130: 22.081 distance: 130 - 131: 14.774 distance: 131 - 132: 6.910 distance: 132 - 133: 10.648