Starting phenix.real_space_refine on Fri Sep 11 12:43:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o24_12698/09_2026/7o24_12698.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o24_12698/09_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_12698/09_2026/7o24_12698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o24_12698/09_2026/7o24_12698.map" model { file = "/net/cci-nas-00/data/ceres_data/7o24_12698/09_2026/7o24_12698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o24_12698/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 2.36, per 1000 atoms: 0.25 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: 1.03 Conformation dependent library (CDL) restraints added in 217.8 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: 1.27 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: 1.75 Time building geometry restraints manager: 1.26 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: 5.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.470 Find NCS groups from input model: 0.180 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.890 ------------------------------------------------------------------------------- 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 : 0.657 7.670 13346 Z= 0.431 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 0.65677 / 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 : 0.377 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: 0.0901 time to fit residues: 21.4509 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 : 0.339 ------------------------------------------------------------------------------- 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 = 0.3034 r_free = 0.3034 target = 0.062463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.050975 restraints weight = 49051.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.052629 restraints weight = 27774.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.053761 restraints weight = 17990.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.054582 restraints weight = 12794.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.055193 restraints weight = 9696.308| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0974 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 : 0.605 6.685 13346 Z= 0.326 Chirality : 0.044 0.189 1545 Planarity : 0.004 0.046 1534 Dihedral : 16.438 59.874 1652 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.26 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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: -0.07 (0.26), residues: 1072 helix: 1.37 (0.25), residues: 426 sheet: 0.10 (0.38), residues: 178 loop : -1.48 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 282 TYR 0.009 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 0.60479 / 0.33 (13346) hydrogen bonds : bond 0.05259 / 3.55 ( 445) hydrogen bonds : angle 4.46754 / 3.17 ( 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 153 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8840 (m-30) cc_final: 0.8507 (t70) REVERT: A 252 LEU cc_start: 0.8906 (mm) cc_final: 0.8667 (mm) REVERT: A 287 PHE cc_start: 0.8826 (t80) cc_final: 0.7691 (t80) REVERT: A 289 ASN cc_start: 0.9364 (m-40) cc_final: 0.8720 (m110) REVERT: A 301 LEU cc_start: 0.9041 (mp) cc_final: 0.8658 (mp) REVERT: A 375 ASP cc_start: 0.9447 (m-30) cc_final: 0.9216 (m-30) REVERT: A 505 MET cc_start: 0.9299 (tpt) cc_final: 0.8459 (tpt) REVERT: A 509 LEU cc_start: 0.9654 (mp) cc_final: 0.9045 (mp) REVERT: B 271 PHE cc_start: 0.9258 (p90) cc_final: 0.9048 (p90) REVERT: B 443 ASN cc_start: 0.8986 (t0) cc_final: 0.8702 (p0) REVERT: B 462 ASN cc_start: 0.8661 (t0) cc_final: 0.8249 (t0) REVERT: B 541 ARG cc_start: 0.8992 (mtt-85) cc_final: 0.8597 (mtt-85) REVERT: B 551 TRP cc_start: 0.8688 (m100) cc_final: 0.8212 (m-90) REVERT: C 634 ILE cc_start: 0.8655 (mp) cc_final: 0.8193 (mp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0706 time to fit residues: 16.4569 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 : 0.227 ------------------------------------------------------------------------------- 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: 0.0010 chunk 100 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS ** 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 = 0.3039 r_free = 0.3039 target = 0.062795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.051285 restraints weight = 48934.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.052941 restraints weight = 27947.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.054055 restraints weight = 18136.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.054901 restraints weight = 12910.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.055512 restraints weight = 9782.418| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9637 Z= 0.144 Angle : 0.600 7.883 13346 Z= 0.322 Chirality : 0.043 0.181 1545 Planarity : 0.004 0.053 1534 Dihedral : 16.369 59.898 1652 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.26 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: -0.10 (0.25), residues: 1072 helix: 1.38 (0.25), residues: 426 sheet: -0.02 (0.38), residues: 179 loop : -1.48 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 451 TYR 0.016 0.001 TYR A 316 PHE 0.018 0.001 PHE A 488 TRP 0.010 0.001 TRP A 548 HIS 0.005 0.001 HIS C 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 9637) covalent geometry : angle 0.60005 / 0.32 (13346) hydrogen bonds : bond 0.04698 / 3.14 ( 445) hydrogen bonds : angle 4.36329 / 3.10 ( 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 : 0.368 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8854 (m-30) cc_final: 0.8530 (t70) REVERT: A 213 MET cc_start: 0.7192 (mmt) cc_final: 0.6689 (mmm) REVERT: A 252 LEU cc_start: 0.8935 (mm) cc_final: 0.8658 (mm) REVERT: A 287 PHE cc_start: 0.8808 (t80) cc_final: 0.7537 (t80) REVERT: A 289 ASN cc_start: 0.9305 (m-40) cc_final: 0.8623 (m110) REVERT: A 301 LEU cc_start: 0.9025 (mp) cc_final: 0.8621 (mp) REVERT: A 505 MET cc_start: 0.9224 (tpt) cc_final: 0.8386 (tpt) REVERT: A 509 LEU cc_start: 0.9656 (mp) cc_final: 0.9043 (mp) REVERT: B 271 PHE cc_start: 0.9253 (p90) cc_final: 0.9023 (p90) REVERT: B 443 ASN cc_start: 0.8986 (t0) cc_final: 0.8660 (p0) REVERT: B 462 ASN cc_start: 0.8765 (t0) cc_final: 0.8306 (t0) REVERT: B 541 ARG cc_start: 0.8971 (mtt-85) cc_final: 0.8581 (mtt-85) REVERT: C 634 ILE cc_start: 0.8721 (mp) cc_final: 0.8211 (mp) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.0702 time to fit residues: 15.3190 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 : 0.343 ------------------------------------------------------------------------------- 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: 8.9990 chunk 85 optimal weight: 6.9990 chunk 75 optimal weight: 0.0980 chunk 7 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS B 187 GLN B 378 GLN C 619 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.063065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.051484 restraints weight = 49221.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.053170 restraints weight = 27942.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.054345 restraints weight = 18053.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.055179 restraints weight = 12748.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.055610 restraints weight = 9605.156| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1522 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= 0.130 Angle : 0.569 6.567 13346 Z= 0.308 Chirality : 0.042 0.183 1545 Planarity : 0.004 0.034 1534 Dihedral : 16.195 59.238 1652 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.36 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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: -0.09 (0.25), residues: 1072 helix: 1.43 (0.25), residues: 427 sheet: 0.02 (0.38), residues: 179 loop : -1.53 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 684 TYR 0.016 0.001 TYR A 316 PHE 0.010 0.001 PHE A 488 TRP 0.012 0.001 TRP C 683 HIS 0.007 0.001 HIS C 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 9637) covalent geometry : angle 0.56926 / 0.31 (13346) hydrogen bonds : bond 0.04200 / 2.81 ( 445) hydrogen bonds : angle 4.19816 / 2.99 ( 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 : 0.350 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8870 (m-30) cc_final: 0.8530 (t70) REVERT: A 131 ASP cc_start: 0.9439 (t0) cc_final: 0.9190 (t70) REVERT: A 213 MET cc_start: 0.7010 (mmt) cc_final: 0.6569 (mmm) REVERT: A 252 LEU cc_start: 0.8916 (mm) cc_final: 0.8500 (mm) REVERT: A 287 PHE cc_start: 0.8781 (t80) cc_final: 0.7509 (t80) REVERT: A 289 ASN cc_start: 0.9286 (m-40) cc_final: 0.8570 (m110) REVERT: A 301 LEU cc_start: 0.9012 (mp) cc_final: 0.8726 (mp) REVERT: A 375 ASP cc_start: 0.9355 (m-30) cc_final: 0.9105 (m-30) REVERT: A 505 MET cc_start: 0.9219 (tpt) cc_final: 0.8346 (tpt) REVERT: A 509 LEU cc_start: 0.9677 (mp) cc_final: 0.9102 (mp) REVERT: B 271 PHE cc_start: 0.9232 (p90) cc_final: 0.8971 (p90) REVERT: B 443 ASN cc_start: 0.8981 (t0) cc_final: 0.8652 (p0) REVERT: B 462 ASN cc_start: 0.8777 (t0) cc_final: 0.8296 (t0) REVERT: B 541 ARG cc_start: 0.8958 (mtt-85) cc_final: 0.8558 (mtt-85) REVERT: B 551 TRP cc_start: 0.8704 (m100) cc_final: 0.8222 (m-90) REVERT: C 634 ILE cc_start: 0.8672 (mp) cc_final: 0.8172 (mp) REVERT: C 694 LYS cc_start: 0.8856 (tppp) cc_final: 0.8634 (ptpt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.0724 time to fit residues: 16.6136 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 : 0.334 ------------------------------------------------------------------------------- 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: 10.0000 chunk 10 optimal weight: 0.0010 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 overall best weight: 2.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 GLN A 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.061952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.050712 restraints weight = 49794.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.052357 restraints weight = 28211.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.053476 restraints weight = 18268.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.054290 restraints weight = 12969.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.054727 restraints weight = 9784.779| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9637 Z= 0.175 Angle : 0.612 8.741 13346 Z= 0.329 Chirality : 0.043 0.194 1545 Planarity : 0.004 0.035 1534 Dihedral : 16.208 59.916 1652 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.29 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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: -0.22 (0.25), residues: 1072 helix: 1.33 (0.25), residues: 427 sheet: -0.21 (0.37), residues: 179 loop : -1.56 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 684 TYR 0.012 0.001 TYR A 316 PHE 0.008 0.001 PHE C 595 TRP 0.009 0.001 TRP A 548 HIS 0.003 0.001 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 ( 9637) covalent geometry : angle 0.61221 / 0.33 (13346) hydrogen bonds : bond 0.04538 / 3.04 ( 445) hydrogen bonds : angle 4.26921 / 3.04 ( 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 145 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8886 (m-30) cc_final: 0.8550 (t70) REVERT: A 131 ASP cc_start: 0.9467 (t0) cc_final: 0.9224 (t70) REVERT: A 213 MET cc_start: 0.7059 (mmt) cc_final: 0.6671 (mmm) REVERT: A 252 LEU cc_start: 0.8887 (mm) cc_final: 0.8684 (mm) REVERT: A 287 PHE cc_start: 0.8811 (t80) cc_final: 0.7569 (t80) REVERT: A 289 ASN cc_start: 0.9242 (m-40) cc_final: 0.8572 (m110) REVERT: A 375 ASP cc_start: 0.9342 (m-30) cc_final: 0.9107 (m-30) REVERT: A 505 MET cc_start: 0.9198 (tpt) cc_final: 0.8286 (tpt) REVERT: A 509 LEU cc_start: 0.9686 (mp) cc_final: 0.9104 (mp) REVERT: B 271 PHE cc_start: 0.9292 (p90) cc_final: 0.8978 (p90) REVERT: B 462 ASN cc_start: 0.8886 (t0) cc_final: 0.8337 (t0) REVERT: B 541 ARG cc_start: 0.8975 (mtt-85) cc_final: 0.8557 (mtt-85) REVERT: B 555 LEU cc_start: 0.9357 (mt) cc_final: 0.9115 (mt) REVERT: C 595 PHE cc_start: 0.8845 (m-10) cc_final: 0.8578 (m-10) REVERT: C 634 ILE cc_start: 0.8662 (mp) cc_final: 0.8167 (mp) REVERT: C 654 LYS cc_start: 0.8733 (pptt) cc_final: 0.8304 (pptt) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.0742 time to fit residues: 16.3623 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 : 0.358 ------------------------------------------------------------------------------- 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: 0.9980 chunk 91 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 95 optimal weight: 0.0370 chunk 15 optimal weight: 6.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.062426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.051054 restraints weight = 50184.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.052731 restraints weight = 28644.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.053878 restraints weight = 18470.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.054691 restraints weight = 13057.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.055292 restraints weight = 9875.519| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9637 Z= 0.139 Angle : 0.584 7.580 13346 Z= 0.312 Chirality : 0.042 0.178 1545 Planarity : 0.004 0.043 1534 Dihedral : 16.176 59.865 1652 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.82 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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 (0.26), residues: 1072 helix: 1.36 (0.25), residues: 428 sheet: -0.09 (0.37), residues: 179 loop : -1.57 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 684 TYR 0.016 0.001 TYR A 316 PHE 0.015 0.001 PHE C 651 TRP 0.012 0.001 TRP C 683 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 9637) covalent geometry : angle 0.58412 / 0.31 (13346) hydrogen bonds : bond 0.04190 / 2.79 ( 445) hydrogen bonds : angle 4.15205 / 2.96 ( 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 146 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8872 (m-30) cc_final: 0.8533 (t70) REVERT: A 131 ASP cc_start: 0.9440 (t0) cc_final: 0.9144 (t70) REVERT: A 251 ASP cc_start: 0.8034 (t0) cc_final: 0.7786 (t0) REVERT: A 252 LEU cc_start: 0.8875 (mm) cc_final: 0.8653 (mm) REVERT: A 287 PHE cc_start: 0.8803 (t80) cc_final: 0.7563 (t80) REVERT: A 289 ASN cc_start: 0.9278 (m-40) cc_final: 0.8569 (m110) REVERT: A 301 LEU cc_start: 0.8970 (mp) cc_final: 0.8642 (mp) REVERT: A 375 ASP cc_start: 0.9324 (m-30) cc_final: 0.9085 (m-30) REVERT: A 505 MET cc_start: 0.9182 (tpt) cc_final: 0.8304 (tpt) REVERT: A 509 LEU cc_start: 0.9674 (mp) cc_final: 0.9145 (mp) REVERT: B 271 PHE cc_start: 0.9282 (p90) cc_final: 0.8923 (p90) REVERT: B 389 LEU cc_start: 0.8959 (tp) cc_final: 0.8707 (pp) REVERT: B 462 ASN cc_start: 0.8862 (t0) cc_final: 0.8347 (t0) REVERT: B 541 ARG cc_start: 0.8937 (mtt-85) cc_final: 0.8539 (mtt-85) REVERT: B 551 TRP cc_start: 0.8731 (m100) cc_final: 0.8276 (m-90) REVERT: C 634 ILE cc_start: 0.8649 (mp) cc_final: 0.8145 (mp) REVERT: C 694 LYS cc_start: 0.8942 (tppp) cc_final: 0.8643 (ptpt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0710 time to fit residues: 15.8011 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 : 0.352 ------------------------------------------------------------------------------- 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: 8.9990 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 0.1980 chunk 98 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 0.0770 chunk 13 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.061866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.050501 restraints weight = 50617.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.052156 restraints weight = 28763.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.053273 restraints weight = 18586.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.054077 restraints weight = 13196.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.054592 restraints weight = 10040.864| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1935 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= 0.162 Angle : 0.600 8.997 13346 Z= 0.323 Chirality : 0.042 0.188 1545 Planarity : 0.004 0.044 1534 Dihedral : 16.231 59.739 1652 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.10 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: -0.23 (0.25), residues: 1072 helix: 1.31 (0.25), residues: 428 sheet: -0.14 (0.37), residues: 179 loop : -1.59 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 451 TYR 0.015 0.001 TYR A 316 PHE 0.013 0.001 PHE C 651 TRP 0.014 0.001 TRP C 683 HIS 0.003 0.001 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 9637) covalent geometry : angle 0.59960 / 0.32 (13346) hydrogen bonds : bond 0.04302 / 2.86 ( 445) hydrogen bonds : angle 4.20386 / 3.00 ( 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 141 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8894 (m-30) cc_final: 0.8551 (t70) REVERT: A 131 ASP cc_start: 0.9449 (t0) cc_final: 0.9151 (t70) REVERT: A 213 MET cc_start: 0.6982 (mmt) cc_final: 0.6247 (mmm) REVERT: A 251 ASP cc_start: 0.8029 (t0) cc_final: 0.7807 (t0) REVERT: A 287 PHE cc_start: 0.8815 (t80) cc_final: 0.7587 (t80) REVERT: A 289 ASN cc_start: 0.9228 (m-40) cc_final: 0.8555 (m110) REVERT: A 375 ASP cc_start: 0.9315 (m-30) cc_final: 0.9077 (m-30) REVERT: A 505 MET cc_start: 0.9190 (tpt) cc_final: 0.8319 (tpt) REVERT: A 509 LEU cc_start: 0.9677 (mp) cc_final: 0.9148 (mp) REVERT: B 271 PHE cc_start: 0.9303 (p90) cc_final: 0.8995 (p90) REVERT: B 389 LEU cc_start: 0.8925 (tp) cc_final: 0.8696 (pp) REVERT: B 462 ASN cc_start: 0.8871 (t0) cc_final: 0.8298 (t0) REVERT: B 541 ARG cc_start: 0.8927 (mtt-85) cc_final: 0.8555 (mtt-85) REVERT: C 634 ILE cc_start: 0.8633 (mp) cc_final: 0.8144 (mp) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.0749 time to fit residues: 16.0776 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 : 0.341 ------------------------------------------------------------------------------- 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: 7.9990 chunk 30 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS B 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.062262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.050965 restraints weight = 49854.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.052601 restraints weight = 28515.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.053703 restraints weight = 18443.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.054496 restraints weight = 13139.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.055023 restraints weight = 9952.140| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9637 Z= 0.144 Angle : 0.605 14.620 13346 Z= 0.319 Chirality : 0.042 0.181 1545 Planarity : 0.004 0.044 1534 Dihedral : 16.241 59.669 1652 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.64 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -0.22 (0.26), residues: 1072 helix: 1.32 (0.25), residues: 428 sheet: -0.10 (0.38), residues: 179 loop : -1.60 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 451 TYR 0.010 0.001 TYR A 133 PHE 0.011 0.001 PHE C 651 TRP 0.027 0.002 TRP C 632 HIS 0.004 0.001 HIS C 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 9637) covalent geometry : angle 0.60466 / 0.32 (13346) hydrogen bonds : bond 0.04158 / 2.77 ( 445) hydrogen bonds : angle 4.16483 / 2.98 ( 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 146 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8882 (m-30) cc_final: 0.8541 (t70) REVERT: A 131 ASP cc_start: 0.9437 (t0) cc_final: 0.9097 (t70) REVERT: A 213 MET cc_start: 0.6975 (mmt) cc_final: 0.6258 (mmm) REVERT: A 251 ASP cc_start: 0.8034 (t0) cc_final: 0.7810 (t0) REVERT: A 287 PHE cc_start: 0.8772 (t80) cc_final: 0.7555 (t80) REVERT: A 289 ASN cc_start: 0.9258 (m-40) cc_final: 0.8543 (m110) REVERT: A 375 ASP cc_start: 0.9283 (m-30) cc_final: 0.9045 (m-30) REVERT: A 505 MET cc_start: 0.9153 (tpt) cc_final: 0.8296 (tpt) REVERT: A 509 LEU cc_start: 0.9664 (mp) cc_final: 0.9191 (mp) REVERT: B 271 PHE cc_start: 0.9289 (p90) cc_final: 0.8930 (p90) REVERT: B 389 LEU cc_start: 0.8895 (tp) cc_final: 0.8689 (pp) REVERT: B 462 ASN cc_start: 0.8885 (t0) cc_final: 0.8321 (t0) REVERT: B 541 ARG cc_start: 0.8912 (mtt-85) cc_final: 0.8531 (mtt-85) REVERT: B 551 TRP cc_start: 0.8775 (m100) cc_final: 0.8286 (m-90) REVERT: C 595 PHE cc_start: 0.8868 (m-10) cc_final: 0.8614 (m-10) REVERT: C 694 LYS cc_start: 0.8948 (tppp) cc_final: 0.8632 (ptpt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0777 time to fit residues: 17.2719 Evaluate side-chains 110 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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: 3.9990 chunk 96 optimal weight: 10.0000 chunk 74 optimal weight: 0.1980 chunk 34 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 28 optimal weight: 0.0370 chunk 61 optimal weight: 2.9990 overall best weight: 1.2464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.062822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.051363 restraints weight = 48680.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.053054 restraints weight = 27511.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.054197 restraints weight = 17726.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.055004 restraints weight = 12551.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.055580 restraints weight = 9479.526| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2039 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= 0.126 Angle : 0.586 10.335 13346 Z= 0.310 Chirality : 0.042 0.179 1545 Planarity : 0.004 0.045 1534 Dihedral : 16.210 58.959 1652 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.82 % Favored : 95.99 % 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: -0.17 (0.26), residues: 1072 helix: 1.37 (0.26), residues: 428 sheet: -0.04 (0.38), residues: 179 loop : -1.59 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 684 TYR 0.008 0.001 TYR B 202 PHE 0.013 0.001 PHE C 651 TRP 0.021 0.002 TRP C 683 HIS 0.002 0.001 HIS C 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 ( 9637) covalent geometry : angle 0.58575 / 0.31 (13346) hydrogen bonds : bond 0.03895 / 2.58 ( 445) hydrogen bonds : angle 4.06406 / 2.91 ( 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 147 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8888 (m-30) cc_final: 0.8542 (t70) REVERT: A 131 ASP cc_start: 0.9434 (t0) cc_final: 0.9096 (t70) REVERT: A 213 MET cc_start: 0.6891 (mmt) cc_final: 0.6162 (mmm) REVERT: A 251 ASP cc_start: 0.8044 (t0) cc_final: 0.7825 (t0) REVERT: A 287 PHE cc_start: 0.8797 (t80) cc_final: 0.7562 (t80) REVERT: A 289 ASN cc_start: 0.9279 (m-40) cc_final: 0.8579 (m110) REVERT: A 301 LEU cc_start: 0.9030 (mp) cc_final: 0.8729 (mp) REVERT: A 375 ASP cc_start: 0.9303 (m-30) cc_final: 0.9063 (m-30) REVERT: A 505 MET cc_start: 0.9170 (tpt) cc_final: 0.8332 (tpt) REVERT: A 509 LEU cc_start: 0.9660 (mp) cc_final: 0.9208 (mp) REVERT: B 271 PHE cc_start: 0.9297 (p90) cc_final: 0.8889 (p90) REVERT: B 389 LEU cc_start: 0.8868 (tp) cc_final: 0.8667 (pp) REVERT: B 462 ASN cc_start: 0.8860 (t0) cc_final: 0.8316 (t0) REVERT: B 541 ARG cc_start: 0.8925 (mtt-85) cc_final: 0.8522 (mtt-85) REVERT: B 551 TRP cc_start: 0.8646 (m100) cc_final: 0.8198 (m-90) REVERT: C 631 GLN cc_start: 0.8669 (pm20) cc_final: 0.8368 (tm-30) REVERT: C 694 LYS cc_start: 0.8947 (tppp) cc_final: 0.8608 (ptpt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.0703 time to fit residues: 15.8247 Evaluate side-chains 114 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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: 3.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.061980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.050501 restraints weight = 49366.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.052171 restraints weight = 28051.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.053317 restraints weight = 18107.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.054029 restraints weight = 12832.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.054617 restraints weight = 9912.764| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9637 Z= 0.159 Angle : 0.610 9.085 13346 Z= 0.325 Chirality : 0.043 0.219 1545 Planarity : 0.004 0.044 1534 Dihedral : 16.222 59.717 1652 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.01 % Favored : 95.80 % 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: -0.24 (0.26), residues: 1072 helix: 1.30 (0.26), residues: 432 sheet: -0.11 (0.38), residues: 179 loop : -1.64 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 384 TYR 0.014 0.001 TYR A 316 PHE 0.010 0.001 PHE C 651 TRP 0.025 0.002 TRP B 548 HIS 0.004 0.001 HIS B 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 ( 9637) covalent geometry : angle 0.60984 / 0.32 (13346) hydrogen bonds : bond 0.04213 / 2.77 ( 445) hydrogen bonds : angle 4.22596 / 3.02 ( 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 142 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8900 (m-30) cc_final: 0.8548 (t70) REVERT: A 131 ASP cc_start: 0.9455 (t0) cc_final: 0.9135 (t70) REVERT: A 213 MET cc_start: 0.7060 (mmt) cc_final: 0.6346 (mmm) REVERT: A 287 PHE cc_start: 0.8806 (t80) cc_final: 0.7570 (t80) REVERT: A 289 ASN cc_start: 0.9262 (m-40) cc_final: 0.8602 (m110) REVERT: A 375 ASP cc_start: 0.9319 (m-30) cc_final: 0.9078 (m-30) REVERT: A 505 MET cc_start: 0.9175 (tpt) cc_final: 0.8350 (tpt) REVERT: A 509 LEU cc_start: 0.9666 (mp) cc_final: 0.9136 (mp) REVERT: B 271 PHE cc_start: 0.9317 (p90) cc_final: 0.8944 (p90) REVERT: B 462 ASN cc_start: 0.8864 (t0) cc_final: 0.8271 (t0) REVERT: B 541 ARG cc_start: 0.8920 (mtt-85) cc_final: 0.8544 (mtt-85) REVERT: C 631 GLN cc_start: 0.8696 (pm20) cc_final: 0.8428 (tm-30) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.0751 time to fit residues: 16.1194 Evaluate side-chains 107 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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: 0.7980 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.0270 chunk 53 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- 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** A 325 HIS C 619 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.063202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.051733 restraints weight = 47889.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.053411 restraints weight = 27201.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.054549 restraints weight = 17606.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.055263 restraints weight = 12472.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.055858 restraints weight = 9595.582| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.002 0.034 9637 Z= 0.122 Angle : 0.599 9.873 13346 Z= 0.312 Chirality : 0.042 0.216 1545 Planarity : 0.004 0.044 1534 Dihedral : 16.160 58.989 1652 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.73 % Favored : 96.08 % 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: -0.19 (0.26), residues: 1072 helix: 1.28 (0.26), residues: 433 sheet: 0.08 (0.38), residues: 178 loop : -1.61 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 684 TYR 0.009 0.001 TYR B 202 PHE 0.012 0.001 PHE C 651 TRP 0.025 0.002 TRP C 683 HIS 0.006 0.001 HIS C 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 9637) covalent geometry : angle 0.59885 / 0.31 (13346) hydrogen bonds : bond 0.03766 / 2.47 ( 445) hydrogen bonds : angle 4.11539 / 2.95 ( 1186) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1393.31 seconds wall clock time: 24 minutes 59.56 seconds (1499.56 seconds total)