Starting phenix.real_space_refine on Sat Aug 3 20:11:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y94_39069/08_2024/8y94_39069.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y94_39069/08_2024/8y94_39069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y94_39069/08_2024/8y94_39069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y94_39069/08_2024/8y94_39069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y94_39069/08_2024/8y94_39069.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y94_39069/08_2024/8y94_39069.cif" } resolution = 3.29 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= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 6052 2.51 5 N 1412 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "C ARG 56": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 341": "NH1" <-> "NH2" Residue "C PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 440": "NH1" <-> "NH2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C ARG 518": "NH1" <-> "NH2" Residue "C TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 587": "NH1" <-> "NH2" Residue "C ARG 604": "NH1" <-> "NH2" Residue "C ARG 607": "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: 9032 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "C" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Time building chain proxies: 5.53, per 1000 atoms: 0.61 Number of scatterers: 9032 At special positions: 0 Unit cell: (85.41, 116.07, 91.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1528 8.00 N 1412 7.00 C 6052 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: 3.66 Conformation dependent library (CDL) restraints added in 1.5 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 0 sheets defined 77.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 61 through 72 removed outlier: 3.692A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 5.013A pdb=" N LEU A 76 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 94 through 121 Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 167 removed outlier: 3.900A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.570A pdb=" N GLU A 223 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.649A pdb=" N SER A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 284 removed outlier: 4.079A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.859A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.758A pdb=" N LEU A 302 " --> pdb=" O PHE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 320 removed outlier: 4.210A pdb=" N GLN A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.898A pdb=" N TYR A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 372 Processing helix chain 'A' and resid 385 through 398 removed outlier: 3.939A pdb=" N TYR A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.623A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 4.008A pdb=" N ARG A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 436 through 441' Processing helix chain 'A' and resid 441 through 457 Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.508A pdb=" N THR A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 494 removed outlier: 4.045A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 removed outlier: 3.501A pdb=" N PHE A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 removed outlier: 3.788A pdb=" N ALA A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.776A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 597 through 604 removed outlier: 3.767A pdb=" N VAL A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.014A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 72 removed outlier: 3.690A pdb=" N PHE C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 removed outlier: 5.018A pdb=" N LEU C 76 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA C 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 94 through 121 Proline residue: C 108 - end of helix Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 134 through 167 removed outlier: 3.894A pdb=" N GLY C 138 " --> pdb=" O PHE C 134 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 139 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE C 142 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR C 151 " --> pdb=" O TYR C 147 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N VAL C 154 " --> pdb=" O PHE C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 208 through 217 Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.570A pdb=" N GLU C 223 " --> pdb=" O HIS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 253 Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.652A pdb=" N SER C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 284 removed outlier: 4.086A pdb=" N PHE C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.860A pdb=" N GLY C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.758A pdb=" N LEU C 302 " --> pdb=" O PHE C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 320 removed outlier: 4.209A pdb=" N GLN C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C 320 " --> pdb=" O PHE C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 332 removed outlier: 3.908A pdb=" N TYR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 372 Processing helix chain 'C' and resid 385 through 398 removed outlier: 3.939A pdb=" N TYR C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) Proline residue: C 392 - end of helix Processing helix chain 'C' and resid 400 through 435 removed outlier: 3.623A pdb=" N TRP C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 441 removed outlier: 4.005A pdb=" N ARG C 440 " --> pdb=" O GLN C 436 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N HIS C 441 " --> pdb=" O VAL C 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 436 through 441' Processing helix chain 'C' and resid 441 through 457 Processing helix chain 'C' and resid 457 through 462 removed outlier: 3.507A pdb=" N THR C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 494 removed outlier: 4.045A pdb=" N VAL C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 509 removed outlier: 3.501A pdb=" N PHE C 501 " --> pdb=" O GLY C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 523 Processing helix chain 'C' and resid 523 through 539 removed outlier: 3.789A pdb=" N ALA C 527 " --> pdb=" O PHE C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 567 removed outlier: 3.775A pdb=" N ASN C 555 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER C 565 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET C 566 " --> pdb=" O ALA C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 579 Processing helix chain 'C' and resid 583 through 593 Processing helix chain 'C' and resid 597 through 604 removed outlier: 3.761A pdb=" N VAL C 601 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 602 " --> pdb=" O HIS C 598 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 603 " --> pdb=" O HIS C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 615 removed outlier: 4.013A pdb=" N TRP C 614 " --> pdb=" O GLN C 610 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1620 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: 2.80 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2658 1.34 - 1.46: 2276 1.46 - 1.58: 4330 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 9326 Sorted by residual: bond pdb=" C LEU C 269 " pdb=" N PRO C 270 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.28e-02 6.10e+03 1.10e+00 bond pdb=" C VAL A 379 " pdb=" O VAL A 379 " ideal model delta sigma weight residual 1.241 1.231 0.010 1.03e-02 9.43e+03 9.55e-01 bond pdb=" C ILE C 549 " pdb=" N PHE C 550 " ideal model delta sigma weight residual 1.331 1.359 -0.028 3.12e-02 1.03e+03 8.29e-01 bond pdb=" C ILE A 549 " pdb=" N PHE A 550 " ideal model delta sigma weight residual 1.331 1.359 -0.028 3.12e-02 1.03e+03 8.24e-01 bond pdb=" C LEU A 269 " pdb=" N PRO A 270 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.16e-01 ... (remaining 9321 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.26: 302 107.26 - 113.94: 5170 113.94 - 120.62: 3994 120.62 - 127.30: 3119 127.30 - 133.98: 141 Bond angle restraints: 12726 Sorted by residual: angle pdb=" N ILE C 265 " pdb=" CA ILE C 265 " pdb=" C ILE C 265 " ideal model delta sigma weight residual 111.90 109.56 2.34 8.10e-01 1.52e+00 8.34e+00 angle pdb=" N ILE A 265 " pdb=" CA ILE A 265 " pdb=" C ILE A 265 " ideal model delta sigma weight residual 111.90 109.57 2.33 8.10e-01 1.52e+00 8.25e+00 angle pdb=" C PHE A 388 " pdb=" N ILE A 389 " pdb=" CA ILE A 389 " ideal model delta sigma weight residual 123.08 120.24 2.84 1.01e+00 9.80e-01 7.90e+00 angle pdb=" C PHE C 388 " pdb=" N ILE C 389 " pdb=" CA ILE C 389 " ideal model delta sigma weight residual 123.08 120.29 2.79 1.01e+00 9.80e-01 7.63e+00 angle pdb=" N GLY A 231 " pdb=" CA GLY A 231 " pdb=" C GLY A 231 " ideal model delta sigma weight residual 111.21 113.74 -2.53 1.04e+00 9.25e-01 5.91e+00 ... (remaining 12721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.99: 4833 11.99 - 23.98: 255 23.98 - 35.97: 85 35.97 - 47.96: 32 47.96 - 59.95: 9 Dihedral angle restraints: 5214 sinusoidal: 1950 harmonic: 3264 Sorted by residual: dihedral pdb=" N PHE A 359 " pdb=" CA PHE A 359 " pdb=" CB PHE A 359 " pdb=" CG PHE A 359 " ideal model delta sinusoidal sigma weight residual -60.00 -119.95 59.95 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N PHE C 359 " pdb=" CA PHE C 359 " pdb=" CB PHE C 359 " pdb=" CG PHE C 359 " ideal model delta sinusoidal sigma weight residual -60.00 -119.94 59.94 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU A 190 " pdb=" CA LEU A 190 " pdb=" CB LEU A 190 " pdb=" CG LEU A 190 " ideal model delta sinusoidal sigma weight residual -60.00 -117.24 57.24 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 5211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 796 0.022 - 0.045: 360 0.045 - 0.067: 205 0.067 - 0.090: 36 0.090 - 0.112: 21 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CA PRO C 270 " pdb=" N PRO C 270 " pdb=" C PRO C 270 " pdb=" CB PRO C 270 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.15e-01 chirality pdb=" CA ILE A 606 " pdb=" N ILE A 606 " pdb=" C ILE A 606 " pdb=" CB ILE A 606 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.10e-01 chirality pdb=" CA ILE C 606 " pdb=" N ILE C 606 " pdb=" C ILE C 606 " pdb=" CB ILE C 606 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.02e-01 ... (remaining 1415 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 103 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C ILE C 103 " -0.019 2.00e-02 2.50e+03 pdb=" O ILE C 103 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE C 104 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " -0.006 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C ILE A 103 " 0.019 2.00e-02 2.50e+03 pdb=" O ILE A 103 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE A 104 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 477 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.20e+00 pdb=" C ALA C 477 " -0.019 2.00e-02 2.50e+03 pdb=" O ALA C 477 " 0.007 2.00e-02 2.50e+03 pdb=" N GLY C 478 " 0.006 2.00e-02 2.50e+03 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2669 2.82 - 3.34: 9057 3.34 - 3.86: 15119 3.86 - 4.38: 17356 4.38 - 4.90: 29697 Nonbonded interactions: 73898 Sorted by model distance: nonbonded pdb=" O LYS A 88 " pdb=" NH2 ARG A 301 " model vdw 2.295 3.120 nonbonded pdb=" O LYS C 88 " pdb=" NH2 ARG C 301 " model vdw 2.296 3.120 nonbonded pdb=" O SER C 251 " pdb=" OG1 THR C 258 " model vdw 2.309 3.040 nonbonded pdb=" O SER A 251 " pdb=" OG1 THR A 258 " model vdw 2.312 3.040 nonbonded pdb=" OG1 THR C 462 " pdb=" N LYS C 463 " model vdw 2.361 3.120 ... (remaining 73893 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 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.230 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.560 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 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 : 0.002 0.028 9326 Z= 0.110 Angle : 0.463 5.693 12726 Z= 0.278 Chirality : 0.033 0.112 1418 Planarity : 0.003 0.026 1552 Dihedral : 9.274 59.949 3138 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.15 % Allowed : 6.09 % Favored : 90.76 % 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: -1.50 (0.22), residues: 1126 helix: -0.56 (0.18), residues: 732 sheet: None (None), residues: 0 loop : -1.63 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP C 235 HIS 0.002 0.000 HIS A 296 PHE 0.005 0.001 PHE A 362 TYR 0.008 0.001 TYR A 151 ARG 0.002 0.000 ARG C 607 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 352 time to evaluate : 0.993 Fit side-chains REVERT: A 122 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7176 (mt-10) REVERT: A 126 THR cc_start: 0.8786 (p) cc_final: 0.8563 (p) REVERT: A 173 TRP cc_start: 0.7971 (OUTLIER) cc_final: 0.7658 (p90) REVERT: A 278 LEU cc_start: 0.6509 (mt) cc_final: 0.6248 (mt) REVERT: A 332 TYR cc_start: 0.8246 (m-80) cc_final: 0.8016 (m-10) REVERT: A 337 ASN cc_start: 0.6205 (m110) cc_final: 0.5223 (m110) REVERT: A 480 SER cc_start: 0.8365 (m) cc_final: 0.8164 (t) REVERT: A 559 TRP cc_start: 0.6645 (m100) cc_final: 0.5925 (t60) REVERT: C 126 THR cc_start: 0.8757 (p) cc_final: 0.8548 (p) REVERT: C 173 TRP cc_start: 0.7888 (OUTLIER) cc_final: 0.7582 (p90) REVERT: C 425 GLU cc_start: 0.7237 (tt0) cc_final: 0.6953 (tt0) REVERT: C 453 THR cc_start: 0.5477 (m) cc_final: 0.4734 (p) REVERT: C 480 SER cc_start: 0.8374 (m) cc_final: 0.8168 (t) REVERT: C 559 TRP cc_start: 0.6649 (m100) cc_final: 0.5894 (t60) outliers start: 30 outliers final: 9 residues processed: 372 average time/residue: 0.1905 time to fit residues: 99.1295 Evaluate side-chains 229 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 218 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 390 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 220 HIS A 236 GLN A 280 HIS A 314 GLN A 555 ASN C 153 ASN C 236 GLN C 280 HIS C 314 GLN ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 HIS C 555 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9326 Z= 0.289 Angle : 0.665 9.869 12726 Z= 0.339 Chirality : 0.043 0.183 1418 Planarity : 0.005 0.036 1552 Dihedral : 5.879 58.735 1238 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 5.36 % Allowed : 16.60 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.25), residues: 1126 helix: 0.71 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -1.10 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 128 HIS 0.013 0.002 HIS C 222 PHE 0.035 0.002 PHE C 82 TYR 0.019 0.002 TYR C 391 ARG 0.006 0.001 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 225 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.8149 (tpp80) REVERT: A 131 CYS cc_start: 0.8164 (t) cc_final: 0.7784 (m) REVERT: A 246 ILE cc_start: 0.6685 (OUTLIER) cc_final: 0.6343 (mp) REVERT: A 278 LEU cc_start: 0.6404 (mt) cc_final: 0.6004 (mt) REVERT: A 425 GLU cc_start: 0.7411 (tt0) cc_final: 0.7123 (tt0) REVERT: A 597 GLU cc_start: 0.8355 (mp0) cc_final: 0.7943 (mp0) REVERT: C 121 ARG cc_start: 0.8398 (mmm-85) cc_final: 0.8125 (tpp80) REVERT: C 131 CYS cc_start: 0.8162 (t) cc_final: 0.7719 (m) REVERT: C 246 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6362 (mp) REVERT: C 334 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8133 (ptmm) REVERT: C 425 GLU cc_start: 0.7390 (tt0) cc_final: 0.7100 (tt0) REVERT: C 515 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7524 (mt) REVERT: C 597 GLU cc_start: 0.8355 (mp0) cc_final: 0.7865 (mp0) outliers start: 51 outliers final: 28 residues processed: 258 average time/residue: 0.1895 time to fit residues: 69.3390 Evaluate side-chains 220 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 0.0010 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS C 280 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS C 436 GLN C 599 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9326 Z= 0.171 Angle : 0.544 9.086 12726 Z= 0.275 Chirality : 0.039 0.189 1418 Planarity : 0.004 0.037 1552 Dihedral : 5.640 56.547 1238 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.83 % Allowed : 17.12 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1126 helix: 1.04 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.80 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.010 0.001 HIS A 370 PHE 0.029 0.001 PHE A 82 TYR 0.014 0.001 TYR C 548 ARG 0.005 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 201 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8461 (mmtp) cc_final: 0.8230 (mmmt) REVERT: A 246 ILE cc_start: 0.6704 (OUTLIER) cc_final: 0.6191 (mp) REVERT: A 250 PHE cc_start: 0.8119 (m-80) cc_final: 0.7856 (m-10) REVERT: A 261 LYS cc_start: 0.8317 (mmmt) cc_final: 0.7827 (pptt) REVERT: A 274 LEU cc_start: 0.9053 (mp) cc_final: 0.8846 (mp) REVERT: A 315 ILE cc_start: 0.5170 (OUTLIER) cc_final: 0.4917 (mp) REVERT: A 425 GLU cc_start: 0.7337 (tt0) cc_final: 0.7049 (tt0) REVERT: A 597 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: C 246 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6233 (mp) REVERT: C 250 PHE cc_start: 0.8144 (m-80) cc_final: 0.7892 (m-10) REVERT: C 425 GLU cc_start: 0.7357 (tt0) cc_final: 0.7053 (tt0) REVERT: C 597 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7863 (mp0) outliers start: 46 outliers final: 30 residues processed: 236 average time/residue: 0.1851 time to fit residues: 62.3437 Evaluate side-chains 219 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 102 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS C 280 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN C 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9326 Z= 0.165 Angle : 0.552 9.047 12726 Z= 0.273 Chirality : 0.039 0.162 1418 Planarity : 0.004 0.038 1552 Dihedral : 5.282 57.148 1234 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.20 % Allowed : 18.91 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1126 helix: 1.15 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.55 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 494 HIS 0.010 0.001 HIS C 370 PHE 0.029 0.001 PHE C 82 TYR 0.014 0.001 TYR C 575 ARG 0.005 0.001 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 195 time to evaluate : 1.033 Fit side-chains REVERT: A 121 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.8196 (mmm-85) REVERT: A 246 ILE cc_start: 0.6743 (OUTLIER) cc_final: 0.6255 (mp) REVERT: A 261 LYS cc_start: 0.8285 (mmmt) cc_final: 0.7889 (pptt) REVERT: A 315 ILE cc_start: 0.5313 (OUTLIER) cc_final: 0.5099 (mp) REVERT: A 425 GLU cc_start: 0.7236 (tt0) cc_final: 0.6928 (tt0) REVERT: A 597 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: C 121 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.8193 (mmm-85) REVERT: C 246 ILE cc_start: 0.6746 (OUTLIER) cc_final: 0.6267 (mp) REVERT: C 315 ILE cc_start: 0.5350 (mp) cc_final: 0.5021 (mp) REVERT: C 425 GLU cc_start: 0.7218 (tt0) cc_final: 0.6924 (tt0) REVERT: C 597 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7893 (mp0) outliers start: 40 outliers final: 23 residues processed: 225 average time/residue: 0.1810 time to fit residues: 58.4097 Evaluate side-chains 206 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 0.0370 chunk 97 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 337 ASN A 370 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9326 Z= 0.159 Angle : 0.560 10.114 12726 Z= 0.273 Chirality : 0.039 0.160 1418 Planarity : 0.004 0.037 1552 Dihedral : 5.049 57.412 1230 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.10 % Allowed : 19.85 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1126 helix: 1.44 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -0.56 (0.35), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.010 0.001 HIS C 370 PHE 0.027 0.001 PHE C 82 TYR 0.018 0.002 TYR C 87 ARG 0.005 0.001 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 1.026 Fit side-chains REVERT: A 121 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.8092 (mmm-85) REVERT: A 246 ILE cc_start: 0.6675 (OUTLIER) cc_final: 0.6290 (mp) REVERT: A 261 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7874 (pptt) REVERT: A 315 ILE cc_start: 0.5497 (OUTLIER) cc_final: 0.5159 (mp) REVERT: A 597 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: C 121 ARG cc_start: 0.8344 (mmm-85) cc_final: 0.8052 (mmm-85) REVERT: C 246 ILE cc_start: 0.6727 (OUTLIER) cc_final: 0.6262 (mp) REVERT: C 597 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7953 (mp0) outliers start: 39 outliers final: 25 residues processed: 220 average time/residue: 0.1876 time to fit residues: 58.5075 Evaluate side-chains 205 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 152 TYR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 104 optimal weight: 0.3980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9326 Z= 0.205 Angle : 0.562 11.607 12726 Z= 0.281 Chirality : 0.040 0.163 1418 Planarity : 0.004 0.037 1552 Dihedral : 5.032 56.584 1230 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.52 % Allowed : 20.48 % Favored : 75.00 % 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: 1.03 (0.26), residues: 1126 helix: 1.31 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -0.60 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 494 HIS 0.011 0.001 HIS C 370 PHE 0.036 0.001 PHE C 82 TYR 0.032 0.002 TYR A 87 ARG 0.005 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 186 time to evaluate : 0.988 Fit side-chains REVERT: A 246 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6349 (mp) REVERT: A 315 ILE cc_start: 0.5848 (OUTLIER) cc_final: 0.5456 (mp) REVERT: A 597 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: C 597 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8014 (mp0) outliers start: 43 outliers final: 29 residues processed: 212 average time/residue: 0.1818 time to fit residues: 56.2703 Evaluate side-chains 207 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 0.0770 chunk 91 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.0970 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 370 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9326 Z= 0.153 Angle : 0.549 11.950 12726 Z= 0.272 Chirality : 0.039 0.172 1418 Planarity : 0.004 0.038 1552 Dihedral : 4.980 56.839 1230 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.68 % Allowed : 21.74 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.26), residues: 1126 helix: 1.36 (0.19), residues: 770 sheet: None (None), residues: 0 loop : -0.45 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 494 HIS 0.012 0.001 HIS C 370 PHE 0.028 0.001 PHE A 82 TYR 0.020 0.001 TYR A 87 ARG 0.007 0.001 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 186 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 126 THR cc_start: 0.8665 (p) cc_final: 0.8305 (p) REVERT: A 261 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7578 (pptt) REVERT: A 280 HIS cc_start: 0.7200 (OUTLIER) cc_final: 0.6957 (t-170) REVERT: A 597 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: C 89 ASN cc_start: 0.6258 (p0) cc_final: 0.6014 (p0) REVERT: C 126 THR cc_start: 0.8833 (p) cc_final: 0.8376 (p) REVERT: C 401 SER cc_start: 0.8738 (p) cc_final: 0.8296 (t) REVERT: C 425 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7457 (tp30) REVERT: C 597 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8008 (mp0) outliers start: 35 outliers final: 20 residues processed: 208 average time/residue: 0.1741 time to fit residues: 53.0870 Evaluate side-chains 199 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 73 optimal weight: 0.0000 chunk 53 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9326 Z= 0.196 Angle : 0.580 12.633 12726 Z= 0.289 Chirality : 0.040 0.158 1418 Planarity : 0.004 0.037 1552 Dihedral : 4.984 56.311 1230 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.26 % Allowed : 23.21 % Favored : 73.53 % 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: 1.14 (0.26), residues: 1126 helix: 1.35 (0.19), residues: 770 sheet: None (None), residues: 0 loop : -0.45 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 494 HIS 0.012 0.001 HIS C 370 PHE 0.028 0.001 PHE A 82 TYR 0.029 0.002 TYR C 87 ARG 0.007 0.001 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 186 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 126 THR cc_start: 0.8722 (p) cc_final: 0.8325 (p) REVERT: A 261 LYS cc_start: 0.8051 (mmmt) cc_final: 0.7548 (pptt) REVERT: A 425 GLU cc_start: 0.7785 (tp30) cc_final: 0.7539 (tp30) REVERT: A 597 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: C 89 ASN cc_start: 0.6375 (p0) cc_final: 0.6124 (p0) REVERT: C 126 THR cc_start: 0.8763 (p) cc_final: 0.8412 (p) REVERT: C 401 SER cc_start: 0.8745 (p) cc_final: 0.8291 (t) REVERT: C 425 GLU cc_start: 0.7755 (tp30) cc_final: 0.7505 (tp30) REVERT: C 597 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8037 (mp0) outliers start: 31 outliers final: 23 residues processed: 205 average time/residue: 0.1603 time to fit residues: 49.3932 Evaluate side-chains 200 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 175 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 0.0370 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 370 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9326 Z= 0.165 Angle : 0.587 14.199 12726 Z= 0.286 Chirality : 0.039 0.162 1418 Planarity : 0.004 0.038 1552 Dihedral : 4.853 56.068 1228 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.05 % Allowed : 23.63 % Favored : 73.32 % 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: 1.22 (0.26), residues: 1126 helix: 1.38 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -0.34 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 494 HIS 0.013 0.001 HIS C 370 PHE 0.025 0.001 PHE A 82 TYR 0.036 0.001 TYR C 391 ARG 0.006 0.001 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 126 THR cc_start: 0.8660 (p) cc_final: 0.8270 (p) REVERT: A 261 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7598 (pptt) REVERT: A 425 GLU cc_start: 0.7776 (tp30) cc_final: 0.7487 (tp30) REVERT: A 597 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: C 87 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.6320 (m-80) REVERT: C 89 ASN cc_start: 0.6128 (p0) cc_final: 0.5797 (p0) REVERT: C 126 THR cc_start: 0.8706 (p) cc_final: 0.8320 (p) REVERT: C 261 LYS cc_start: 0.8119 (mmmt) cc_final: 0.7628 (pptt) REVERT: C 425 GLU cc_start: 0.7694 (tp30) cc_final: 0.7451 (tp30) REVERT: C 597 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8038 (mp0) outliers start: 29 outliers final: 20 residues processed: 215 average time/residue: 0.1631 time to fit residues: 52.0745 Evaluate side-chains 208 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 597 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 70 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS A 289 ASN C 280 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9326 Z= 0.337 Angle : 0.691 14.229 12726 Z= 0.351 Chirality : 0.043 0.157 1418 Planarity : 0.004 0.035 1552 Dihedral : 5.137 54.015 1228 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.05 % Allowed : 24.37 % Favored : 72.58 % 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: 0.68 (0.25), residues: 1126 helix: 1.02 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -0.70 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 494 HIS 0.012 0.001 HIS C 370 PHE 0.037 0.002 PHE A 82 TYR 0.054 0.002 TYR A 391 ARG 0.007 0.001 ARG A 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 1.033 Fit side-chains REVERT: A 126 THR cc_start: 0.8815 (p) cc_final: 0.8463 (p) REVERT: A 261 LYS cc_start: 0.8048 (mmmt) cc_final: 0.7633 (pptt) REVERT: C 87 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.6537 (m-80) REVERT: C 89 ASN cc_start: 0.6369 (p0) cc_final: 0.6030 (p0) REVERT: C 126 THR cc_start: 0.8867 (p) cc_final: 0.8521 (p) REVERT: C 261 LYS cc_start: 0.8188 (mmmt) cc_final: 0.7673 (pptt) REVERT: C 425 GLU cc_start: 0.7853 (tp30) cc_final: 0.7613 (tp30) outliers start: 29 outliers final: 23 residues processed: 214 average time/residue: 0.1622 time to fit residues: 52.0123 Evaluate side-chains 206 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 182 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 0.0370 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.184116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.144596 restraints weight = 13006.538| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 3.04 r_work: 0.3803 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9326 Z= 0.189 Angle : 0.639 13.717 12726 Z= 0.316 Chirality : 0.041 0.189 1418 Planarity : 0.004 0.037 1552 Dihedral : 5.054 54.067 1228 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.42 % Allowed : 25.84 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1126 helix: 1.23 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -0.65 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP A 494 HIS 0.009 0.001 HIS C 370 PHE 0.034 0.001 PHE A 82 TYR 0.051 0.002 TYR C 391 ARG 0.006 0.001 ARG C 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2185.15 seconds wall clock time: 39 minutes 22.94 seconds (2362.94 seconds total)