Starting phenix.real_space_refine on Thu Jul 2 17:04:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o24_12698/07_2026/7o24_12698.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o24_12698/07_2026/7o24_12698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7o24_12698/07_2026/7o24_12698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o24_12698/07_2026/7o24_12698.map" model { file = "/net/cci-nas-00/data/ceres_data/7o24_12698/07_2026/7o24_12698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o24_12698/07_2026/7o24_12698.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 44 5.49 5 S 10 5.16 5 C 5850 2.51 5 N 1597 2.21 5 O 1817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9318 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3754 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 28, 'TRANS': 447} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3494 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 29, 'TRANS': 429} Chain breaks: 3 Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 122 Chain: "C" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1132 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 3 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 488 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "F" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 450 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Time building chain proxies: 1.78, per 1000 atoms: 0.19 Number of scatterers: 9318 At special positions: 0 Unit cell: (85.14, 113.52, 129, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 44 15.00 O 1817 8.00 N 1597 7.00 C 5850 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 - 3.00 Amino acid : True - 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: 0.64 Conformation dependent library (CDL) restraints added in 222.7 milliseconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 11 sheets defined 45.7% alpha, 12.7% beta 22 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 119 through 133 Processing helix chain 'A' and resid 134 through 137 removed outlier: 3.606A pdb=" N TRP A 137 " --> pdb=" O ASP A 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 134 through 137' Processing helix chain 'A' and resid 173 through 187 Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 254 through 259 removed outlier: 4.206A pdb=" N HIS A 259 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.819A pdb=" N GLN A 266 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TRP A 267 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 268 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 270 " --> pdb=" O TRP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 321 through 340 Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 385 through 399 removed outlier: 4.239A pdb=" N ALA A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 420 removed outlier: 4.817A pdb=" N ILE A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) Proline residue: A 412 - end of helix removed outlier: 3.728A pdb=" N ILE A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 444 removed outlier: 3.511A pdb=" N THR A 432 " --> pdb=" O THR A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 494 removed outlier: 3.956A pdb=" N LYS A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 517 removed outlier: 4.734A pdb=" N LYS A 511 " --> pdb=" O LYS A 507 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP A 514 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 536 Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 554 through 557 removed outlier: 3.531A pdb=" N ASP A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 554 through 557' Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 119 through 132 Processing helix chain 'B' and resid 133 through 137 removed outlier: 4.013A pdb=" N TRP B 137 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 187 removed outlier: 3.505A pdb=" N ILE B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 223 removed outlier: 4.043A pdb=" N THR B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 removed outlier: 3.841A pdb=" N HIS B 259 " --> pdb=" O PHE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 270 removed outlier: 5.011A pdb=" N TRP B 267 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 268 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 270 " --> pdb=" O TRP B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 302 removed outlier: 3.721A pdb=" N ASP B 300 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 340 Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.548A pdb=" N LYS B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 397 Processing helix chain 'B' and resid 398 through 402 Processing helix chain 'B' and resid 403 through 404 No H-bonds generated for 'chain 'B' and resid 403 through 404' Processing helix chain 'B' and resid 405 through 420 Proline residue: B 412 - end of helix Processing helix chain 'B' and resid 428 through 444 removed outlier: 3.581A pdb=" N THR B 432 " --> pdb=" O THR B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 494 removed outlier: 3.570A pdb=" N LYS B 494 " --> pdb=" O ASN B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 516 Processing helix chain 'B' and resid 528 through 535 Processing helix chain 'B' and resid 537 through 541 removed outlier: 3.639A pdb=" N GLU B 540 " --> pdb=" O PRO B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 556 removed outlier: 3.691A pdb=" N ILE B 549 " --> pdb=" O SER B 545 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR B 550 " --> pdb=" O THR B 546 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 659 Processing helix chain 'C' and resid 669 through 684 removed outlier: 4.039A pdb=" N ALA C 673 " --> pdb=" O SER C 669 " (cutoff:3.500A) Proline residue: C 681 - end of helix Processing helix chain 'C' and resid 698 through 712 Processing helix chain 'C' and resid 730 through 747 removed outlier: 4.508A pdb=" N GLY C 734 " --> pdb=" O ILE C 730 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 205 removed outlier: 3.673A pdb=" N VAL A 214 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 309 through 311 removed outlier: 6.672A pdb=" N THR A 249 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU A 350 " --> pdb=" O THR A 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 355 through 357 Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 487 removed outlier: 6.544A pdb=" N LEU A 457 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR A 524 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 459 " --> pdb=" O TYR A 524 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 201 through 205 Processing sheet with id=AA7, first strand: chain 'B' and resid 309 through 311 Processing sheet with id=AA8, first strand: chain 'B' and resid 271 through 273 Processing sheet with id=AA9, first strand: chain 'B' and resid 355 through 357 removed outlier: 3.509A pdb=" N VAL B 355 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 483 through 487 removed outlier: 3.584A pdb=" N ALA B 484 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE B 470 " --> pdb=" O ALA B 484 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS B 486 " --> pdb=" O GLY B 468 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY B 468 " --> pdb=" O HIS B 486 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 628 through 637 removed outlier: 6.680A pdb=" N SER C 613 " --> pdb=" O LEU C 636 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL C 663 " --> pdb=" O ILE C 716 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2585 1.33 - 1.45: 1821 1.45 - 1.57: 5124 1.57 - 1.69: 88 1.69 - 1.81: 19 Bond restraints: 9637 Sorted by residual: bond pdb=" C3' DG F 3 " pdb=" C2' DG F 3 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.59e+00 bond pdb=" N ASP C 598 " pdb=" CA ASP C 598 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.18e-02 7.18e+03 7.56e+00 bond pdb=" C3' DG E 9 " pdb=" C2' DG E 9 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.12e+00 bond pdb=" C3' DG E 18 " pdb=" C2' DG E 18 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.53e+00 bond pdb=" C3' DC F 20 " pdb=" C2' DC F 20 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.42e+00 ... (remaining 9632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 12846 1.53 - 3.07: 426 3.07 - 4.60: 46 4.60 - 6.14: 24 6.14 - 7.67: 4 Bond angle restraints: 13346 Sorted by residual: angle pdb=" N3 DT E 20 " pdb=" C4 DT E 20 " pdb=" O4 DT E 20 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" O4' DT E 8 " pdb=" C4' DT E 8 " pdb=" C3' DT E 8 " ideal model delta sigma weight residual 106.00 103.41 2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT F 1 " pdb=" C4 DT F 1 " pdb=" O4 DT F 1 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT E 21 " pdb=" C4 DT E 21 " pdb=" O4 DT E 21 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT F 19 " pdb=" C4 DT F 19 " pdb=" O4 DT F 19 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 ... (remaining 13341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 4851 16.98 - 33.97: 510 33.97 - 50.95: 187 50.95 - 67.93: 66 67.93 - 84.92: 14 Dihedral angle restraints: 5628 sinusoidal: 2414 harmonic: 3214 Sorted by residual: dihedral pdb=" CA PHE A 406 " pdb=" C PHE A 406 " pdb=" N SER A 407 " pdb=" CA SER A 407 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA LYS A 132 " pdb=" C LYS A 132 " pdb=" N TYR A 133 " pdb=" CA TYR A 133 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA HIS C 630 " pdb=" C HIS C 630 " pdb=" N GLN C 631 " pdb=" CA GLN C 631 " ideal model delta harmonic sigma weight residual 180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1029 0.037 - 0.073: 347 0.073 - 0.110: 134 0.110 - 0.147: 31 0.147 - 0.183: 4 Chirality restraints: 1545 Sorted by residual: chirality pdb=" CB VAL C 649 " pdb=" CA VAL C 649 " pdb=" CG1 VAL C 649 " pdb=" CG2 VAL C 649 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CG LEU A 345 " pdb=" CB LEU A 345 " pdb=" CD1 LEU A 345 " pdb=" CD2 LEU A 345 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA GLN A 478 " pdb=" N GLN A 478 " pdb=" C GLN A 478 " pdb=" CB GLN A 478 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 1542 not shown) Planarity restraints: 1534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 411 " -0.032 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO B 412 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 412 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 412 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 477 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C GLY A 477 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY A 477 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 478 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 525 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO B 526 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 526 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 526 " -0.017 5.00e-02 4.00e+02 ... (remaining 1531 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 158 2.65 - 3.21: 8851 3.21 - 3.77: 14719 3.77 - 4.34: 18664 4.34 - 4.90: 28959 Nonbonded interactions: 71351 Sorted by model distance: nonbonded pdb=" N GLN A 478 " pdb=" OE1 GLN A 478 " model vdw 2.084 3.120 nonbonded pdb=" O VAL C 621 " pdb=" OG1 THR C 627 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR A 199 " pdb=" O ALA A 270 " model vdw 2.244 3.040 nonbonded pdb=" O LEU A 533 " pdb=" OG1 THR A 536 " model vdw 2.249 3.040 nonbonded pdb=" O THR A 550 " pdb=" OG SER A 553 " model vdw 2.253 3.040 ... (remaining 71346 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' and ((resid 97 through 99 and (name N or name CA or name C or name O \ or name CB )) or resid 100 through 101 or (resid 102 through 103 and (name N or \ name CA or name C or name O or name CB )) or resid 104 through 114 or (resid 115 \ through 116 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 17 through 121 or (resid 122 through 123 and (name N or name CA or name C or nam \ e O or name CB )) or resid 124 through 125 or (resid 126 through 127 and (name N \ or name CA or name C or name O or name CB )) or resid 128 or (resid 129 and (na \ me N or name CA or name C or name O or name CB )) or resid 130 through 139 or (r \ esid 140 and (name N or name CA or name C or name O or name CB )) or resid 141 t \ hrough 148 or (resid 149 and (name N or name CA or name C or name O or name CB ) \ ) or resid 150 through 173 or (resid 174 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE )) or resid 175 through 181 or ( \ resid 182 and (name N or name CA or name C or name O or name CB )) or resid 183 \ through 226 or (resid 227 and (name N or name CA or name C or name O or name CB \ )) or resid 243 or (resid 244 and (name N or name CA or name C or name O or name \ CB )) or resid 245 through 282 or (resid 283 and (name N or name CA or name C o \ r name O or name CB )) or resid 284 through 316 or (resid 317 and (name N or nam \ e CA or name C or name O or name CB )) or resid 318 through 323 or (resid 324 an \ d (name N or name CA or name C or name O or name CB )) or resid 325 through 330 \ or (resid 331 and (name N or name CA or name C or name O or name CB )) or resid \ 332 through 351 or (resid 352 and (name N or name CA or name C or name O or name \ CB )) or resid 353 or (resid 354 and (name N or name CA or name C or name O or \ name CB )) or resid 355 through 365 or resid 371 through 372 or (resid 373 throu \ gh 374 and (name N or name CA or name C or name O or name CB )) or resid 375 or \ (resid 376 and (name N or name CA or name C or name O or name CB )) or resid 378 \ through 386 or (resid 387 through 388 and (name N or name CA or name C or name \ O or name CB )) or resid 389 through 396 or (resid 397 and (name N or name CA or \ name C or name O or name CB )) or resid 398 through 399 or (resid 400 through 4 \ 01 and (name N or name CA or name C or name O or name CB )) or resid 402 through \ 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) or r \ esid 409 or (resid 410 through 411 and (name N or name CA or name C or name O or \ name CB )) or resid 412 or (resid 413 and (name N or name CA or name C or name \ O or name CB )) or resid 414 through 415 or (resid 416 and (name N or name CA or \ name C or name O or name CB )) or resid 417 through 426 or (resid 427 and (name \ N or name CA or name C or name O or name CB )) or resid 428 through 434 or (res \ id 435 through 436 and (name N or name CA or name C or name O or name CB )) or r \ esid 437 through 441 or (resid 442 and (name N or name CA or name C or name O or \ name CB )) or resid 443 or (resid 444 through 445 and (name N or name CA or nam \ e C or name O or name CB )) or resid 446 through 456 or (resid 457 and (name N o \ r name CA or name C or name O or name CB )) or resid 458 through 469 or (resid 4 \ 70 and (name N or name CA or name C or name O or name CB )) or resid 471 through \ 478 or (resid 479 and (name N or name CA or name C or name O or name CB )) or r \ esid 480 through 492 or (resid 493 through 494 and (name N or name CA or name C \ or name O or name CB )) or resid 495 through 501 or (resid 502 and (name N or na \ me CA or name C or name O or name CB )) or resid 503 through 508 or (resid 509 a \ nd (name N or name CA or name C or name O or name CB )) or resid 510 through 513 \ or (resid 514 and (name N or name CA or name C or name O or name CB )) or resid \ 515 through 516 or (resid 519 and (name N or name CA or name C or name O or nam \ e CB )) or resid 520 through 555 or (resid 556 and (name N or name CA or name C \ or name O or name CB )) or resid 557 through 571)) selection = (chain 'B' and (resid 97 through 108 or (resid 109 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE )) or resid 110 throug \ h 171 or (resid 172 through 173 and (name N or name CA or name C or name O or na \ me CB )) or resid 174 through 196 or (resid 197 and (name N or name CA or name C \ or name O or name CB )) or resid 198 through 205 or (resid 206 and (name N or n \ ame CA or name C or name O or name CB )) or resid 207 through 213 or (resid 214 \ and (name N or name CA or name C or name O or name CB )) or resid 215 through 27 \ 5 or (resid 276 and (name N or name CA or name C or name O or name CB )) or resi \ d 277 through 325 or (resid 326 and (name N or name CA or name C or name O or na \ me CB )) or resid 327 through 336 or (resid 337 through 339 and (name N or name \ CA or name C or name O or name CB )) or resid 340 through 346 or (resid 347 and \ (name N or name CA or name C or name O or name CB )) or resid 348 through 389 or \ (resid 390 and (name N or name CA or name C or name O or name CB )) or resid 39 \ 1 through 429 or (resid 430 and (name N or name CA or name C or name O or name C \ B )) or resid 431 through 489 or (resid 490 and (name N or name CA or name C or \ name O or name CB )) or resid 491 through 521 or (resid 522 and (name N or name \ CA or name C or name O or name CB )) or resid 523 through 531 or (resid 532 thro \ ugh 533 and (name N or name CA or name C or name O or name CB )) or resid 534 th \ rough 570 or (resid 571 and (name N or name CA or name C or name O or name CB )) \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.090 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.710 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.004 0.035 9637 Z= 0.267 Angle : 0.656 7.670 13346 Z= 0.430 Chirality : 0.044 0.183 1545 Planarity : 0.004 0.049 1534 Dihedral : 17.348 84.917 3538 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.17 % Favored : 96.64 % Rotamer: Outliers : 1.38 % Allowed : 0.80 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.26), residues: 1072 helix: 1.46 (0.26), residues: 420 sheet: 0.09 (0.38), residues: 177 loop : -1.41 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 684 TYR 0.015 0.001 TYR A 133 PHE 0.016 0.001 PHE A 294 TRP 0.020 0.001 TRP A 137 HIS 0.010 0.001 HIS C 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.27 ( 9637) covalent geometry : angle 0.65591 / 0.43 (13346) hydrogen bonds : bond 0.13935 / 9.31 ( 445) hydrogen bonds : angle 8.13727 / 5.70 ( 1186) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8860 (m-30) cc_final: 0.8490 (t70) REVERT: A 212 ARG cc_start: 0.5299 (OUTLIER) cc_final: 0.4798 (ttm170) REVERT: A 252 LEU cc_start: 0.8969 (mm) cc_final: 0.8730 (mm) REVERT: A 287 PHE cc_start: 0.8795 (t80) cc_final: 0.7576 (t80) REVERT: A 289 ASN cc_start: 0.9348 (m-40) cc_final: 0.8706 (m110) REVERT: A 505 MET cc_start: 0.9149 (tpt) cc_final: 0.8701 (tpt) REVERT: A 509 LEU cc_start: 0.9546 (mp) cc_final: 0.9191 (mp) REVERT: B 330 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8780 (tm-30) REVERT: B 443 ASN cc_start: 0.9136 (t160) cc_final: 0.8908 (p0) REVERT: B 462 ASN cc_start: 0.8291 (t0) cc_final: 0.7902 (t0) REVERT: B 541 ARG cc_start: 0.8933 (mtt-85) cc_final: 0.8543 (mtt-85) REVERT: C 630 HIS cc_start: 0.7842 (t70) cc_final: 0.7564 (p-80) REVERT: C 634 ILE cc_start: 0.8552 (mp) cc_final: 0.8108 (mp) outliers start: 12 outliers final: 7 residues processed: 165 average time/residue: 0.0676 time to fit residues: 15.9589 Evaluate side-chains 122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.0070 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS ** C 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 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 = 0.3035 r_free = 0.3035 target = 0.062457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.050969 restraints weight = 49060.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.052624 restraints weight = 27743.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.053780 restraints weight = 17985.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.054609 restraints weight = 12748.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.055218 restraints weight = 9616.990| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9637 Z= 0.149 Angle : 0.600 6.678 13346 Z= 0.326 Chirality : 0.044 0.165 1545 Planarity : 0.004 0.046 1534 Dihedral : 16.401 59.783 1652 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.17 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.26), residues: 1072 helix: 1.36 (0.25), residues: 426 sheet: 0.11 (0.38), residues: 178 loop : -1.49 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 282 TYR 0.010 0.001 TYR A 316 PHE 0.007 0.001 PHE C 651 TRP 0.013 0.001 TRP A 548 HIS 0.011 0.001 HIS C 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 ( 9637) covalent geometry : angle 0.60013 / 0.33 (13346) hydrogen bonds : bond 0.05322 / 3.59 ( 445) hydrogen bonds : angle 4.49403 / 3.19 ( 1186) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8860 (m-30) cc_final: 0.8533 (t70) REVERT: A 252 LEU cc_start: 0.8907 (mm) cc_final: 0.8672 (mm) REVERT: A 287 PHE cc_start: 0.8826 (t80) cc_final: 0.7697 (t80) REVERT: A 289 ASN cc_start: 0.9366 (m-40) cc_final: 0.8723 (m110) REVERT: A 301 LEU cc_start: 0.9046 (mp) cc_final: 0.8669 (mp) REVERT: A 375 ASP cc_start: 0.9451 (m-30) cc_final: 0.9225 (m-30) REVERT: A 505 MET cc_start: 0.9297 (tpt) cc_final: 0.8477 (tpt) REVERT: A 509 LEU cc_start: 0.9653 (mp) cc_final: 0.9070 (mp) REVERT: B 443 ASN cc_start: 0.8986 (t0) cc_final: 0.8703 (p0) REVERT: B 462 ASN cc_start: 0.8637 (t0) cc_final: 0.8235 (t0) REVERT: B 541 ARG cc_start: 0.8994 (mtt-85) cc_final: 0.8602 (mtt-85) REVERT: B 551 TRP cc_start: 0.8684 (m100) cc_final: 0.8206 (m-90) REVERT: C 634 ILE cc_start: 0.8651 (mp) cc_final: 0.8192 (mp) REVERT: C 694 LYS cc_start: 0.8954 (tppt) cc_final: 0.8641 (ptpt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.0698 time to fit residues: 15.9546 Evaluate side-chains 113 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 99 optimal weight: 0.0470 chunk 16 optimal weight: 10.0000 overall best weight: 2.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN B 378 GLN ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.061790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.050441 restraints weight = 49727.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.052074 restraints weight = 28271.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.053196 restraints weight = 18265.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.054001 restraints weight = 12959.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.054527 restraints weight = 9834.611| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9637 Z= 0.169 Angle : 0.617 7.174 13346 Z= 0.333 Chirality : 0.043 0.198 1545 Planarity : 0.004 0.044 1534 Dihedral : 16.402 59.989 1652 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.36 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1072 helix: 1.31 (0.25), residues: 425 sheet: -0.10 (0.38), residues: 179 loop : -1.53 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 451 TYR 0.019 0.001 TYR A 316 PHE 0.011 0.001 PHE A 488 TRP 0.012 0.001 TRP A 548 HIS 0.005 0.001 HIS C 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 ( 9637) covalent geometry : angle 0.61745 / 0.33 (13346) hydrogen bonds : bond 0.04803 / 3.20 ( 445) hydrogen bonds : angle 4.42182 / 3.14 ( 1186) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8879 (m-30) cc_final: 0.8561 (t70) REVERT: A 213 MET cc_start: 0.7232 (mmt) cc_final: 0.6915 (mmm) REVERT: A 252 LEU cc_start: 0.8947 (mm) cc_final: 0.8669 (mm) REVERT: A 287 PHE cc_start: 0.8834 (t80) cc_final: 0.7576 (t80) REVERT: A 289 ASN cc_start: 0.9263 (m-40) cc_final: 0.8595 (m110) REVERT: A 301 LEU cc_start: 0.9047 (mp) cc_final: 0.8648 (mp) REVERT: A 505 MET cc_start: 0.9221 (tpt) cc_final: 0.8412 (tpt) REVERT: A 509 LEU cc_start: 0.9668 (mp) cc_final: 0.9033 (mp) REVERT: B 271 PHE cc_start: 0.9255 (p90) cc_final: 0.9049 (p90) REVERT: B 462 ASN cc_start: 0.8802 (t0) cc_final: 0.8304 (t0) REVERT: B 541 ARG cc_start: 0.8969 (mtt-85) cc_final: 0.8563 (mtt-85) REVERT: C 634 ILE cc_start: 0.8682 (mp) cc_final: 0.8181 (mp) REVERT: C 651 PHE cc_start: 0.8956 (t80) cc_final: 0.8612 (t80) REVERT: C 654 LYS cc_start: 0.8751 (pptt) cc_final: 0.8545 (pptt) REVERT: C 694 LYS cc_start: 0.8999 (tppt) cc_final: 0.8656 (ptpt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.0634 time to fit residues: 13.9022 Evaluate side-chains 111 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 75 optimal weight: 0.4980 chunk 7 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.062897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.051408 restraints weight = 49245.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.053078 restraints weight = 27932.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.054246 restraints weight = 18041.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.055018 restraints weight = 12698.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.055642 restraints weight = 9657.098| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9637 Z= 0.127 Angle : 0.578 6.766 13346 Z= 0.311 Chirality : 0.043 0.181 1545 Planarity : 0.004 0.040 1534 Dihedral : 16.251 59.542 1652 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.64 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.25), residues: 1072 helix: 1.36 (0.25), residues: 427 sheet: -0.00 (0.38), residues: 179 loop : -1.60 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 684 TYR 0.012 0.001 TYR A 316 PHE 0.009 0.001 PHE A 488 TRP 0.011 0.001 TRP C 683 HIS 0.003 0.001 HIS C 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 ( 9637) covalent geometry : angle 0.57811 / 0.31 (13346) hydrogen bonds : bond 0.04263 / 2.86 ( 445) hydrogen bonds : angle 4.21110 / 3.00 ( 1186) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8856 (m-30) cc_final: 0.8531 (t70) REVERT: A 131 ASP cc_start: 0.9436 (t0) cc_final: 0.9182 (t70) REVERT: A 213 MET cc_start: 0.7134 (mmt) cc_final: 0.6859 (mmm) REVERT: A 252 LEU cc_start: 0.8929 (mm) cc_final: 0.8511 (mm) REVERT: A 287 PHE cc_start: 0.8784 (t80) cc_final: 0.7521 (t80) REVERT: A 289 ASN cc_start: 0.9283 (m-40) cc_final: 0.8569 (m110) REVERT: A 301 LEU cc_start: 0.9012 (mp) cc_final: 0.8726 (mp) REVERT: A 375 ASP cc_start: 0.9345 (m-30) cc_final: 0.9098 (m-30) REVERT: A 505 MET cc_start: 0.9223 (tpt) cc_final: 0.8385 (tpt) REVERT: A 509 LEU cc_start: 0.9678 (mp) cc_final: 0.9103 (mp) REVERT: B 271 PHE cc_start: 0.9241 (p90) cc_final: 0.9012 (p90) REVERT: B 462 ASN cc_start: 0.8823 (t0) cc_final: 0.8337 (t0) REVERT: B 541 ARG cc_start: 0.8961 (mtt-85) cc_final: 0.8517 (mtt-85) REVERT: B 551 TRP cc_start: 0.8684 (m100) cc_final: 0.8209 (m-90) REVERT: C 634 ILE cc_start: 0.8702 (mp) cc_final: 0.8184 (mp) REVERT: C 654 LYS cc_start: 0.8738 (pptt) cc_final: 0.8451 (pptt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.0587 time to fit residues: 13.3521 Evaluate side-chains 112 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 0.3980 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.061505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.050379 restraints weight = 50601.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.051981 restraints weight = 28856.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.053124 restraints weight = 18688.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.053865 restraints weight = 13214.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.054433 restraints weight = 10120.543| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9637 Z= 0.180 Angle : 0.617 8.371 13346 Z= 0.331 Chirality : 0.043 0.193 1545 Planarity : 0.004 0.044 1534 Dihedral : 16.271 59.850 1652 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.48 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.25), residues: 1072 helix: 1.24 (0.25), residues: 427 sheet: -0.22 (0.37), residues: 179 loop : -1.63 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 684 TYR 0.013 0.001 TYR A 316 PHE 0.012 0.001 PHE C 595 TRP 0.009 0.001 TRP A 548 HIS 0.003 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 ( 9637) covalent geometry : angle 0.61675 / 0.33 (13346) hydrogen bonds : bond 0.04556 / 3.05 ( 445) hydrogen bonds : angle 4.26090 / 3.03 ( 1186) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8902 (m-30) cc_final: 0.8570 (t70) REVERT: A 131 ASP cc_start: 0.9453 (t0) cc_final: 0.9213 (t70) REVERT: A 213 MET cc_start: 0.7123 (mmt) cc_final: 0.6896 (mmm) REVERT: A 252 LEU cc_start: 0.8913 (mm) cc_final: 0.8710 (mm) REVERT: A 287 PHE cc_start: 0.8798 (t80) cc_final: 0.7568 (t80) REVERT: A 289 ASN cc_start: 0.9226 (m-40) cc_final: 0.8556 (m110) REVERT: A 375 ASP cc_start: 0.9334 (m-30) cc_final: 0.9101 (m-30) REVERT: A 505 MET cc_start: 0.9189 (tpt) cc_final: 0.8288 (tpt) REVERT: A 509 LEU cc_start: 0.9681 (mp) cc_final: 0.9109 (mp) REVERT: B 271 PHE cc_start: 0.9289 (p90) cc_final: 0.9006 (p90) REVERT: B 462 ASN cc_start: 0.8898 (t0) cc_final: 0.8345 (t0) REVERT: B 541 ARG cc_start: 0.8963 (mtt-85) cc_final: 0.8542 (mtt-85) REVERT: B 551 TRP cc_start: 0.8759 (m100) cc_final: 0.8273 (m-90) REVERT: C 595 PHE cc_start: 0.8887 (m-10) cc_final: 0.8607 (m-10) REVERT: C 634 ILE cc_start: 0.8662 (mp) cc_final: 0.8178 (mp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0649 time to fit residues: 13.5050 Evaluate side-chains 111 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.060202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.049085 restraints weight = 50752.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.050706 restraints weight = 28660.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.051822 restraints weight = 18507.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.052617 restraints weight = 13041.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.053163 restraints weight = 9878.478| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 9637 Z= 0.226 Angle : 0.661 8.350 13346 Z= 0.358 Chirality : 0.044 0.193 1545 Planarity : 0.004 0.043 1534 Dihedral : 16.339 59.720 1652 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.66 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.25), residues: 1072 helix: 1.12 (0.25), residues: 425 sheet: -0.33 (0.38), residues: 179 loop : -1.67 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 282 TYR 0.015 0.002 TYR A 316 PHE 0.013 0.002 PHE C 595 TRP 0.012 0.002 TRP C 683 HIS 0.005 0.002 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.23 ( 9637) covalent geometry : angle 0.66053 / 0.36 (13346) hydrogen bonds : bond 0.04990 / 3.32 ( 445) hydrogen bonds : angle 4.48945 / 3.19 ( 1186) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8968 (m-30) cc_final: 0.8599 (t70) REVERT: A 131 ASP cc_start: 0.9488 (t0) cc_final: 0.9216 (t70) REVERT: A 287 PHE cc_start: 0.8853 (t80) cc_final: 0.7632 (t80) REVERT: A 289 ASN cc_start: 0.9254 (m-40) cc_final: 0.8621 (m110) REVERT: A 301 LEU cc_start: 0.8994 (mp) cc_final: 0.8612 (mp) REVERT: A 375 ASP cc_start: 0.9327 (m-30) cc_final: 0.9115 (m-30) REVERT: A 505 MET cc_start: 0.9211 (tpt) cc_final: 0.8513 (tpt) REVERT: A 509 LEU cc_start: 0.9688 (mp) cc_final: 0.9132 (mp) REVERT: B 271 PHE cc_start: 0.9349 (p90) cc_final: 0.9137 (p90) REVERT: B 389 LEU cc_start: 0.8977 (tp) cc_final: 0.8716 (pp) REVERT: B 462 ASN cc_start: 0.8914 (t0) cc_final: 0.8309 (t0) REVERT: B 541 ARG cc_start: 0.8930 (mtt-85) cc_final: 0.8510 (mtt-85) REVERT: B 551 TRP cc_start: 0.8759 (m100) cc_final: 0.8259 (m-90) REVERT: C 634 ILE cc_start: 0.8609 (mp) cc_final: 0.8126 (mp) REVERT: C 651 PHE cc_start: 0.8853 (t80) cc_final: 0.8576 (t80) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.0682 time to fit residues: 14.2175 Evaluate side-chains 102 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 11 optimal weight: 9.9990 chunk 57 optimal weight: 0.3980 chunk 25 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.060084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.049037 restraints weight = 51242.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.050627 restraints weight = 29066.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.051704 restraints weight = 18851.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.052458 restraints weight = 13385.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.053002 restraints weight = 10210.999| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9637 Z= 0.202 Angle : 0.648 9.697 13346 Z= 0.349 Chirality : 0.044 0.191 1545 Planarity : 0.004 0.051 1534 Dihedral : 16.415 59.499 1652 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.85 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.25), residues: 1072 helix: 1.03 (0.25), residues: 432 sheet: -0.41 (0.38), residues: 179 loop : -1.71 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 282 TYR 0.017 0.001 TYR A 316 PHE 0.009 0.001 PHE B 398 TRP 0.016 0.002 TRP C 683 HIS 0.006 0.001 HIS B 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 ( 9637) covalent geometry : angle 0.64824 / 0.35 (13346) hydrogen bonds : bond 0.04826 / 3.21 ( 445) hydrogen bonds : angle 4.45587 / 3.17 ( 1186) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8927 (m-30) cc_final: 0.8581 (t70) REVERT: A 131 ASP cc_start: 0.9482 (t0) cc_final: 0.9206 (t70) REVERT: A 251 ASP cc_start: 0.8013 (t0) cc_final: 0.7806 (t0) REVERT: A 287 PHE cc_start: 0.8846 (t80) cc_final: 0.7620 (t80) REVERT: A 289 ASN cc_start: 0.9222 (m-40) cc_final: 0.8604 (m110) REVERT: A 375 ASP cc_start: 0.9290 (m-30) cc_final: 0.9071 (m-30) REVERT: A 505 MET cc_start: 0.9225 (tpt) cc_final: 0.8469 (tpt) REVERT: A 509 LEU cc_start: 0.9672 (mp) cc_final: 0.9134 (mp) REVERT: B 271 PHE cc_start: 0.9358 (p90) cc_final: 0.9128 (p90) REVERT: B 389 LEU cc_start: 0.8917 (tp) cc_final: 0.8682 (pp) REVERT: B 462 ASN cc_start: 0.8920 (t0) cc_final: 0.8296 (t0) REVERT: B 541 ARG cc_start: 0.8888 (mtt-85) cc_final: 0.8531 (mtt-85) REVERT: B 551 TRP cc_start: 0.8802 (m100) cc_final: 0.8303 (m-90) REVERT: C 694 LYS cc_start: 0.9025 (tppt) cc_final: 0.8735 (ptpt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0618 time to fit residues: 12.4308 Evaluate side-chains 98 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.061039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.049783 restraints weight = 49527.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.051400 restraints weight = 28109.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.052502 restraints weight = 18221.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.053250 restraints weight = 12949.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.053824 restraints weight = 9903.564| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9637 Z= 0.147 Angle : 0.612 8.758 13346 Z= 0.328 Chirality : 0.043 0.187 1545 Planarity : 0.004 0.053 1534 Dihedral : 16.356 59.994 1652 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.82 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.26), residues: 1072 helix: 1.12 (0.25), residues: 434 sheet: -0.29 (0.38), residues: 179 loop : -1.72 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 282 TYR 0.016 0.001 TYR A 316 PHE 0.012 0.001 PHE A 488 TRP 0.020 0.002 TRP C 683 HIS 0.003 0.001 HIS B 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 ( 9637) covalent geometry : angle 0.61171 / 0.33 (13346) hydrogen bonds : bond 0.04368 / 2.89 ( 445) hydrogen bonds : angle 4.30576 / 3.07 ( 1186) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8892 (m-30) cc_final: 0.8532 (t70) REVERT: A 131 ASP cc_start: 0.9449 (t0) cc_final: 0.9135 (t70) REVERT: A 181 ILE cc_start: 0.9435 (mt) cc_final: 0.9167 (pt) REVERT: A 213 MET cc_start: 0.7516 (mmt) cc_final: 0.7038 (mmm) REVERT: A 251 ASP cc_start: 0.8019 (t0) cc_final: 0.7804 (t0) REVERT: A 287 PHE cc_start: 0.8811 (t80) cc_final: 0.7595 (t80) REVERT: A 289 ASN cc_start: 0.9215 (m-40) cc_final: 0.8597 (m110) REVERT: A 375 ASP cc_start: 0.9288 (m-30) cc_final: 0.9066 (m-30) REVERT: A 505 MET cc_start: 0.9204 (tpt) cc_final: 0.8468 (tpt) REVERT: A 509 LEU cc_start: 0.9667 (mp) cc_final: 0.9186 (mp) REVERT: B 271 PHE cc_start: 0.9336 (p90) cc_final: 0.8979 (p90) REVERT: B 273 TRP cc_start: 0.8712 (t-100) cc_final: 0.8485 (t-100) REVERT: B 389 LEU cc_start: 0.8877 (tp) cc_final: 0.8662 (pp) REVERT: B 462 ASN cc_start: 0.8908 (t0) cc_final: 0.8309 (t0) REVERT: B 541 ARG cc_start: 0.8860 (mtt-85) cc_final: 0.8472 (mtt-85) REVERT: B 551 TRP cc_start: 0.8761 (m100) cc_final: 0.8301 (m-90) REVERT: C 595 PHE cc_start: 0.8914 (m-10) cc_final: 0.8672 (m-10) REVERT: C 694 LYS cc_start: 0.9035 (tppt) cc_final: 0.8740 (ptpt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0584 time to fit residues: 12.4267 Evaluate side-chains 106 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 67 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.061855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.050552 restraints weight = 49221.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.052199 restraints weight = 27932.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.053260 restraints weight = 17996.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.054044 restraints weight = 12865.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.054646 restraints weight = 9795.266| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9637 Z= 0.133 Angle : 0.599 8.694 13346 Z= 0.320 Chirality : 0.043 0.187 1545 Planarity : 0.004 0.044 1534 Dihedral : 16.304 59.907 1652 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.38 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.26), residues: 1072 helix: 1.18 (0.25), residues: 433 sheet: -0.20 (0.38), residues: 179 loop : -1.73 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 451 TYR 0.012 0.001 TYR A 133 PHE 0.011 0.001 PHE C 651 TRP 0.034 0.002 TRP C 632 HIS 0.004 0.001 HIS C 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 9637) covalent geometry : angle 0.59907 / 0.32 (13346) hydrogen bonds : bond 0.04155 / 2.74 ( 445) hydrogen bonds : angle 4.19543 / 3.01 ( 1186) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8875 (m-30) cc_final: 0.8523 (t70) REVERT: A 131 ASP cc_start: 0.9429 (t0) cc_final: 0.9098 (t70) REVERT: A 213 MET cc_start: 0.7254 (mmt) cc_final: 0.7033 (mmm) REVERT: A 251 ASP cc_start: 0.8003 (t0) cc_final: 0.7775 (t0) REVERT: A 287 PHE cc_start: 0.8765 (t80) cc_final: 0.7546 (t80) REVERT: A 289 ASN cc_start: 0.9246 (m-40) cc_final: 0.8613 (m110) REVERT: A 301 LEU cc_start: 0.8971 (mp) cc_final: 0.8657 (mp) REVERT: A 375 ASP cc_start: 0.9273 (m-30) cc_final: 0.9051 (m-30) REVERT: A 505 MET cc_start: 0.9183 (tpt) cc_final: 0.8458 (tpt) REVERT: A 509 LEU cc_start: 0.9664 (mp) cc_final: 0.9150 (mp) REVERT: B 271 PHE cc_start: 0.9320 (p90) cc_final: 0.8913 (p90) REVERT: B 273 TRP cc_start: 0.8741 (t-100) cc_final: 0.8495 (t-100) REVERT: B 389 LEU cc_start: 0.8865 (tp) cc_final: 0.8658 (pp) REVERT: B 462 ASN cc_start: 0.8896 (t0) cc_final: 0.8316 (t0) REVERT: B 541 ARG cc_start: 0.8858 (mtt-85) cc_final: 0.8467 (mtt-85) REVERT: C 632 TRP cc_start: 0.6709 (m-10) cc_final: 0.6325 (m-10) REVERT: C 651 PHE cc_start: 0.8750 (t80) cc_final: 0.8106 (t80) REVERT: C 694 LYS cc_start: 0.9034 (tppt) cc_final: 0.8738 (ptpt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0566 time to fit residues: 12.5957 Evaluate side-chains 113 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 91 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.060518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.049374 restraints weight = 50034.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.050990 restraints weight = 28274.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.052095 restraints weight = 18226.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.052813 restraints weight = 12881.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.053376 restraints weight = 9854.537| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9637 Z= 0.192 Angle : 0.645 9.651 13346 Z= 0.345 Chirality : 0.043 0.198 1545 Planarity : 0.004 0.043 1534 Dihedral : 16.307 59.491 1652 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.85 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.26), residues: 1072 helix: 1.08 (0.25), residues: 432 sheet: -0.32 (0.38), residues: 177 loop : -1.76 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 684 TYR 0.017 0.001 TYR A 469 PHE 0.015 0.002 PHE A 396 TRP 0.023 0.002 TRP C 683 HIS 0.004 0.001 HIS C 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 ( 9637) covalent geometry : angle 0.64477 / 0.34 (13346) hydrogen bonds : bond 0.04625 / 3.05 ( 445) hydrogen bonds : angle 4.38380 / 3.13 ( 1186) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8912 (m-30) cc_final: 0.8548 (t70) REVERT: A 131 ASP cc_start: 0.9457 (t0) cc_final: 0.9160 (t70) REVERT: A 287 PHE cc_start: 0.8767 (t80) cc_final: 0.7579 (t80) REVERT: A 289 ASN cc_start: 0.9209 (m-40) cc_final: 0.8586 (m110) REVERT: A 375 ASP cc_start: 0.9292 (m-30) cc_final: 0.9070 (m-30) REVERT: A 505 MET cc_start: 0.9205 (tpt) cc_final: 0.8505 (tpt) REVERT: A 509 LEU cc_start: 0.9681 (mp) cc_final: 0.9149 (mp) REVERT: B 271 PHE cc_start: 0.9355 (p90) cc_final: 0.9011 (p90) REVERT: B 389 LEU cc_start: 0.8908 (tp) cc_final: 0.8698 (pp) REVERT: B 462 ASN cc_start: 0.8920 (t0) cc_final: 0.8310 (t0) REVERT: B 541 ARG cc_start: 0.8884 (mtt-85) cc_final: 0.8536 (mtt-85) REVERT: C 585 MET cc_start: 0.7737 (pmm) cc_final: 0.5645 (mmt) REVERT: C 629 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7721 (tm-30) REVERT: C 631 GLN cc_start: 0.8524 (pm20) cc_final: 0.8213 (tm-30) REVERT: C 651 PHE cc_start: 0.8770 (t80) cc_final: 0.8064 (t80) REVERT: C 694 LYS cc_start: 0.9058 (tppt) cc_final: 0.8758 (ptpt) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.0618 time to fit residues: 13.2522 Evaluate side-chains 105 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.0670 chunk 53 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 80 optimal weight: 0.0980 chunk 106 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 94 optimal weight: 0.0040 chunk 44 optimal weight: 0.0970 overall best weight: 0.2328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 HIS ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 HIS ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.063043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.051587 restraints weight = 48036.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.053248 restraints weight = 27321.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.054372 restraints weight = 17666.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.055120 restraints weight = 12503.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.055675 restraints weight = 9580.184| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9637 Z= 0.130 Angle : 0.617 9.643 13346 Z= 0.322 Chirality : 0.043 0.173 1545 Planarity : 0.004 0.044 1534 Dihedral : 16.177 59.074 1652 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.36 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.26), residues: 1072 helix: 1.20 (0.26), residues: 433 sheet: -0.07 (0.39), residues: 179 loop : -1.70 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 684 TYR 0.011 0.001 TYR B 202 PHE 0.009 0.001 PHE A 398 TRP 0.026 0.002 TRP C 683 HIS 0.006 0.001 HIS C 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 ( 9637) covalent geometry : angle 0.61736 / 0.32 (13346) hydrogen bonds : bond 0.03809 / 2.52 ( 445) hydrogen bonds : angle 4.08139 / 2.93 ( 1186) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1163.29 seconds wall clock time: 20 minutes 58.60 seconds (1258.60 seconds total)