Starting phenix.real_space_refine on Wed Jun 26 01:39:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y94_39069/06_2024/8y94_39069.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y94_39069/06_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_39069/06_2024/8y94_39069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y94_39069/06_2024/8y94_39069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y94_39069/06_2024/8y94_39069.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y94_39069/06_2024/8y94_39069.pdb" } 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-5370/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: 5.50, 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: 3.63 Conformation dependent library (CDL) restraints added in 1.8 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: 2.34 Time building geometry restraints manager: 4.03 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 2.520 nonbonded pdb=" O LYS C 88 " pdb=" NH2 ARG C 301 " model vdw 2.296 2.520 nonbonded pdb=" O SER C 251 " pdb=" OG1 THR C 258 " model vdw 2.309 2.440 nonbonded pdb=" O SER A 251 " pdb=" OG1 THR A 258 " model vdw 2.312 2.440 nonbonded pdb=" OG1 THR C 462 " pdb=" N LYS C 463 " model vdw 2.361 2.520 ... (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 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.720 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.140 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.960 ------------------------------------------------------------------------------- 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 : 0.881 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: 0.1822 time to fit residues: 95.0573 Evaluate side-chains 229 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 218 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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: 4.9990 chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 555 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9326 Z= 0.365 Angle : 0.687 9.649 12726 Z= 0.353 Chirality : 0.044 0.167 1418 Planarity : 0.005 0.033 1552 Dihedral : 5.933 58.918 1238 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 6.09 % Allowed : 16.91 % Favored : 77.00 % 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: -0.21 (0.24), residues: 1126 helix: 0.46 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.28 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 128 HIS 0.011 0.002 HIS C 222 PHE 0.027 0.002 PHE C 82 TYR 0.018 0.003 TYR C 151 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 273 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 215 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8305 (mmm-85) cc_final: 0.8036 (tpp80) REVERT: A 129 LYS cc_start: 0.8489 (mmtp) cc_final: 0.8273 (mmmt) REVERT: A 246 ILE cc_start: 0.6790 (OUTLIER) cc_final: 0.6419 (mp) REVERT: A 261 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7925 (mmmt) REVERT: A 278 LEU cc_start: 0.6445 (mt) cc_final: 0.6028 (mt) REVERT: A 332 TYR cc_start: 0.8561 (m-80) cc_final: 0.8339 (m-10) REVERT: C 121 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.8090 (tpp80) REVERT: C 261 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7950 (mmmt) REVERT: C 334 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8149 (ptmm) outliers start: 58 outliers final: 38 residues processed: 251 average time/residue: 0.1834 time to fit residues: 65.1611 Evaluate side-chains 231 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 191 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG 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 334 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 353 THR 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 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 81 ARG Chi-restraints excluded: chain C residue 137 VAL 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 174 THR 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 295 LEU Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 351 CYS Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 490 ILE 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: 1.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.0570 chunk 28 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 110 optimal weight: 0.0670 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9326 Z= 0.220 Angle : 0.579 10.771 12726 Z= 0.291 Chirality : 0.040 0.189 1418 Planarity : 0.004 0.037 1552 Dihedral : 5.722 55.427 1238 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.78 % Allowed : 17.23 % Favored : 77.00 % 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: 0.46 (0.25), residues: 1126 helix: 0.95 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -0.91 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 264 HIS 0.010 0.001 HIS C 370 PHE 0.030 0.001 PHE A 82 TYR 0.015 0.002 TYR C 87 ARG 0.007 0.001 ARG C 301 *********************** 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 258 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 203 time to evaluate : 0.754 Fit side-chains REVERT: A 76 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7412 (pp) REVERT: A 129 LYS cc_start: 0.8504 (mmtp) cc_final: 0.8294 (mmmt) REVERT: A 219 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6816 (mp) REVERT: A 246 ILE cc_start: 0.6719 (OUTLIER) cc_final: 0.6367 (mp) REVERT: A 250 PHE cc_start: 0.8207 (m-80) cc_final: 0.7997 (m-10) REVERT: A 315 ILE cc_start: 0.5685 (OUTLIER) cc_final: 0.5347 (mp) REVERT: A 332 TYR cc_start: 0.8530 (m-80) cc_final: 0.8328 (m-10) REVERT: A 395 ILE cc_start: 0.8382 (mm) cc_final: 0.7729 (mm) REVERT: A 494 TRP cc_start: 0.9015 (m100) cc_final: 0.8790 (m100) REVERT: C 129 LYS cc_start: 0.8503 (mmtp) cc_final: 0.8288 (mmmt) REVERT: C 315 ILE cc_start: 0.5515 (OUTLIER) cc_final: 0.5208 (mp) REVERT: C 494 TRP cc_start: 0.9028 (m100) cc_final: 0.8749 (m100) outliers start: 55 outliers final: 41 residues processed: 242 average time/residue: 0.1681 time to fit residues: 58.8545 Evaluate side-chains 226 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 180 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 163 LEU Chi-restraints excluded: chain A residue 168 THR 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 219 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 334 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 174 THR 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 295 LEU Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 351 CYS Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 505 ILE Chi-restraints excluded: chain C residue 507 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 0.0970 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9326 Z= 0.176 Angle : 0.574 15.096 12726 Z= 0.281 Chirality : 0.040 0.150 1418 Planarity : 0.004 0.038 1552 Dihedral : 5.854 56.513 1236 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.15 % Allowed : 20.59 % Favored : 74.26 % 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: 0.75 (0.25), residues: 1126 helix: 1.11 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.66 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.008 0.001 HIS C 370 PHE 0.030 0.001 PHE C 82 TYR 0.012 0.001 TYR C 548 ARG 0.004 0.001 ARG A 121 *********************** 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 246 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 197 time to evaluate : 1.000 Fit side-chains REVERT: A 121 ARG cc_start: 0.8344 (mmm-85) cc_final: 0.8096 (mmm-85) REVERT: A 131 CYS cc_start: 0.8278 (t) cc_final: 0.8073 (m) REVERT: A 219 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6524 (mp) REVERT: A 315 ILE cc_start: 0.5842 (OUTLIER) cc_final: 0.5494 (mp) REVERT: A 611 LEU cc_start: 0.7657 (mm) cc_final: 0.7438 (mm) REVERT: C 219 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6659 (mp) REVERT: C 494 TRP cc_start: 0.9063 (m100) cc_final: 0.8844 (m100) outliers start: 49 outliers final: 32 residues processed: 237 average time/residue: 0.1795 time to fit residues: 61.0992 Evaluate side-chains 214 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 179 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 182 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 219 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 334 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 593 THR 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 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 219 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 462 THR Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN C 370 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9326 Z= 0.176 Angle : 0.583 14.715 12726 Z= 0.283 Chirality : 0.040 0.149 1418 Planarity : 0.004 0.036 1552 Dihedral : 5.529 56.249 1234 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.31 % Allowed : 22.58 % Favored : 73.11 % 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: 0.94 (0.25), residues: 1126 helix: 1.20 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.47 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 494 HIS 0.009 0.001 HIS A 370 PHE 0.031 0.001 PHE A 82 TYR 0.022 0.002 TYR A 391 ARG 0.003 0.000 ARG C 121 *********************** 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 236 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 195 time to evaluate : 0.916 Fit side-chains REVERT: A 121 ARG cc_start: 0.8224 (mmm-85) cc_final: 0.7931 (mmm-85) REVERT: A 219 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6395 (mp) REVERT: A 315 ILE cc_start: 0.5866 (OUTLIER) cc_final: 0.5445 (mp) REVERT: A 425 GLU cc_start: 0.7680 (tp30) cc_final: 0.7370 (tp30) REVERT: A 611 LEU cc_start: 0.7635 (mm) cc_final: 0.7434 (mm) REVERT: C 219 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6605 (mp) REVERT: C 315 ILE cc_start: 0.5694 (OUTLIER) cc_final: 0.5263 (mp) REVERT: C 425 GLU cc_start: 0.7715 (tp30) cc_final: 0.7346 (tp30) REVERT: C 494 TRP cc_start: 0.9078 (m100) cc_final: 0.8860 (m100) outliers start: 41 outliers final: 31 residues processed: 224 average time/residue: 0.1814 time to fit residues: 57.9215 Evaluate side-chains 207 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 172 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 ARG 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 219 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 593 THR 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 196 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 315 ILE 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 507 GLN Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.8980 chunk 21 optimal weight: 0.0670 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9326 Z= 0.188 Angle : 0.600 14.877 12726 Z= 0.289 Chirality : 0.040 0.153 1418 Planarity : 0.004 0.035 1552 Dihedral : 5.254 55.157 1232 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.36 % Allowed : 23.00 % Favored : 71.64 % 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: 1.04 (0.25), residues: 1126 helix: 1.27 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.40 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 264 HIS 0.012 0.001 HIS C 370 PHE 0.026 0.001 PHE A 82 TYR 0.028 0.002 TYR C 87 ARG 0.004 0.000 ARG C 121 *********************** 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 238 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 187 time to evaluate : 0.938 Fit side-chains REVERT: A 126 THR cc_start: 0.8766 (p) cc_final: 0.8434 (p) REVERT: A 219 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6441 (mp) REVERT: A 278 LEU cc_start: 0.6570 (mt) cc_final: 0.6176 (mt) REVERT: A 315 ILE cc_start: 0.6027 (OUTLIER) cc_final: 0.5556 (mp) REVERT: A 425 GLU cc_start: 0.7771 (tp30) cc_final: 0.7438 (tp30) REVERT: A 611 LEU cc_start: 0.7678 (mm) cc_final: 0.7476 (mm) REVERT: C 126 THR cc_start: 0.8742 (p) cc_final: 0.8434 (p) REVERT: C 219 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6583 (mp) REVERT: C 315 ILE cc_start: 0.5853 (OUTLIER) cc_final: 0.5420 (mp) REVERT: C 425 GLU cc_start: 0.7746 (tp30) cc_final: 0.7392 (tp30) outliers start: 51 outliers final: 38 residues processed: 220 average time/residue: 0.1778 time to fit residues: 56.3742 Evaluate side-chains 217 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 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 81 ARG 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 219 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 580 THR 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 81 ARG Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 152 TYR Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 519 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.0570 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 C 599 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9326 Z= 0.159 Angle : 0.598 15.038 12726 Z= 0.284 Chirality : 0.039 0.144 1418 Planarity : 0.003 0.036 1552 Dihedral : 5.003 55.254 1230 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.41 % Allowed : 23.84 % 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: 1.17 (0.26), residues: 1126 helix: 1.37 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.36 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 494 HIS 0.012 0.001 HIS C 370 PHE 0.030 0.001 PHE C 82 TYR 0.029 0.001 TYR C 391 ARG 0.007 0.001 ARG A 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 238 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 196 time to evaluate : 0.843 Fit side-chains REVERT: A 126 THR cc_start: 0.8749 (p) cc_final: 0.8390 (p) REVERT: A 219 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6439 (mp) REVERT: A 261 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7551 (mmtt) REVERT: A 278 LEU cc_start: 0.6606 (mt) cc_final: 0.6237 (mt) REVERT: A 425 GLU cc_start: 0.7696 (tp30) cc_final: 0.7414 (tp30) REVERT: C 126 THR cc_start: 0.8756 (p) cc_final: 0.8380 (p) REVERT: C 315 ILE cc_start: 0.5795 (OUTLIER) cc_final: 0.5312 (mp) REVERT: C 425 GLU cc_start: 0.7730 (tp30) cc_final: 0.7430 (tp30) REVERT: C 494 TRP cc_start: 0.9090 (m100) cc_final: 0.8834 (m100) outliers start: 42 outliers final: 30 residues processed: 218 average time/residue: 0.1763 time to fit residues: 55.1954 Evaluate side-chains 215 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 580 THR 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 81 ARG Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 152 TYR Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 173 TRP Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 519 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.6878 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9326 Z= 0.236 Angle : 0.624 14.411 12726 Z= 0.306 Chirality : 0.041 0.149 1418 Planarity : 0.004 0.034 1552 Dihedral : 4.986 53.383 1230 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.83 % Allowed : 23.63 % Favored : 71.53 % 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: 0.94 (0.25), residues: 1126 helix: 1.13 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -0.33 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 494 HIS 0.011 0.001 HIS C 370 PHE 0.030 0.001 PHE A 82 TYR 0.039 0.002 TYR C 391 ARG 0.007 0.001 ARG A 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 237 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 191 time to evaluate : 0.871 Fit side-chains REVERT: A 126 THR cc_start: 0.8877 (p) cc_final: 0.8511 (p) REVERT: A 219 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6448 (mp) REVERT: A 261 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7561 (mttt) REVERT: A 278 LEU cc_start: 0.6662 (mt) cc_final: 0.6240 (mt) REVERT: A 425 GLU cc_start: 0.7874 (tp30) cc_final: 0.7538 (tp30) REVERT: C 126 THR cc_start: 0.8802 (p) cc_final: 0.8482 (p) REVERT: C 425 GLU cc_start: 0.7868 (tp30) cc_final: 0.7510 (tp30) outliers start: 46 outliers final: 35 residues processed: 222 average time/residue: 0.1662 time to fit residues: 53.6464 Evaluate side-chains 217 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 580 THR 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 81 ARG Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 152 TYR Chi-restraints excluded: chain C residue 174 THR 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 334 LYS Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 563 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN 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: 0.6877 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9326 Z= 0.222 Angle : 0.632 14.742 12726 Z= 0.306 Chirality : 0.041 0.153 1418 Planarity : 0.004 0.035 1552 Dihedral : 4.794 52.476 1226 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.20 % Allowed : 24.05 % 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: 1.08 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -0.27 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 494 HIS 0.013 0.001 HIS C 370 PHE 0.033 0.001 PHE C 82 TYR 0.039 0.002 TYR C 391 ARG 0.007 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 238 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 198 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 126 THR cc_start: 0.8821 (p) cc_final: 0.8463 (p) REVERT: A 261 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7569 (mttt) REVERT: A 425 GLU cc_start: 0.7800 (tp30) cc_final: 0.7460 (tp30) REVERT: C 126 THR cc_start: 0.8809 (p) cc_final: 0.8467 (p) REVERT: C 401 SER cc_start: 0.8734 (p) cc_final: 0.8500 (t) REVERT: C 425 GLU cc_start: 0.7799 (tp30) cc_final: 0.7423 (tp30) outliers start: 40 outliers final: 36 residues processed: 222 average time/residue: 0.1666 time to fit residues: 54.3254 Evaluate side-chains 224 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 580 THR 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 81 ARG Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 152 TYR 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 334 LYS Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 563 LEU 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 64 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 73 optimal weight: 0.0770 chunk 111 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 70 optimal weight: 0.1980 chunk 94 optimal weight: 7.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- 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 370 HIS A 599 HIS C 314 GLN ** 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: 0.6829 moved from start: 0.5766 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= 0.178 Angle : 0.633 15.050 12726 Z= 0.303 Chirality : 0.040 0.150 1418 Planarity : 0.004 0.036 1552 Dihedral : 4.754 52.522 1226 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.15 % Allowed : 25.00 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1126 helix: 1.14 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -0.23 (0.36), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 494 HIS 0.016 0.001 HIS A 370 PHE 0.035 0.001 PHE C 82 TYR 0.047 0.002 TYR C 391 ARG 0.006 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 226 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 126 THR cc_start: 0.8779 (p) cc_final: 0.8395 (p) REVERT: A 236 GLN cc_start: 0.5503 (mm-40) cc_final: 0.5113 (mm-40) REVERT: A 261 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7616 (mttt) REVERT: A 425 GLU cc_start: 0.7691 (tp30) cc_final: 0.7380 (tp30) REVERT: C 126 THR cc_start: 0.8789 (p) cc_final: 0.8425 (p) REVERT: C 401 SER cc_start: 0.8674 (p) cc_final: 0.8238 (t) REVERT: C 425 GLU cc_start: 0.7692 (tp30) cc_final: 0.7351 (tp30) outliers start: 30 outliers final: 29 residues processed: 213 average time/residue: 0.1582 time to fit residues: 49.8362 Evaluate side-chains 221 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 580 THR 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 81 ARG Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 152 TYR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 519 LEU 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: 0.7980 chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 370 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.180107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.141270 restraints weight = 13205.754| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 3.01 r_work: 0.3753 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9326 Z= 0.240 Angle : 0.646 14.466 12726 Z= 0.315 Chirality : 0.041 0.149 1418 Planarity : 0.004 0.035 1552 Dihedral : 4.796 51.448 1226 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.78 % Allowed : 24.58 % Favored : 71.64 % 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: 0.84 (0.26), residues: 1126 helix: 1.05 (0.19), residues: 782 sheet: None (None), residues: 0 loop : -0.42 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 494 HIS 0.019 0.001 HIS A 370 PHE 0.034 0.001 PHE C 82 TYR 0.046 0.002 TYR C 391 ARG 0.006 0.001 ARG A 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2136.18 seconds wall clock time: 38 minutes 40.26 seconds (2320.26 seconds total)