Starting phenix.real_space_refine on Fri Mar 14 00:50:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o24_12698/03_2025/7o24_12698.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o24_12698/03_2025/7o24_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_12698/03_2025/7o24_12698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o24_12698/03_2025/7o24_12698.map" model { file = "/net/cci-nas-00/data/ceres_data/7o24_12698/03_2025/7o24_12698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o24_12698/03_2025/7o24_12698.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 3, 'GLU:plan': 5, '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: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 2} 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: 6.38, per 1000 atoms: 0.68 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: 2.63 Conformation dependent library (CDL) restraints added in 996.1 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: 3.47 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: 3.03 Time building geometry restraints manager: 3.05 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=" 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=" N ASP C 668 " pdb=" CA ASP C 668 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.22e-02 6.72e+03 6.15e+00 bond pdb=" CA GLN A 478 " pdb=" C GLN A 478 " ideal model delta sigma weight residual 1.520 1.548 -0.028 1.48e-02 4.57e+03 3.64e+00 bond pdb=" N LYS B 535 " pdb=" CA LYS B 535 " ideal model delta sigma weight residual 1.460 1.440 0.020 1.17e-02 7.31e+03 3.03e+00 bond pdb=" C ASP C 598 " pdb=" O ASP C 598 " ideal model delta sigma weight residual 1.234 1.248 -0.014 1.30e-02 5.92e+03 1.17e+00 ... (remaining 9632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 12949 1.53 - 3.07: 323 3.07 - 4.60: 46 4.60 - 6.14: 24 6.14 - 7.67: 4 Bond angle restraints: 13346 Sorted by residual: angle pdb=" N ASP C 668 " pdb=" CA ASP C 668 " pdb=" C ASP C 668 " ideal model delta sigma weight residual 112.88 109.10 3.78 1.29e+00 6.01e-01 8.59e+00 angle pdb=" C GLN B 378 " pdb=" CA GLN B 378 " pdb=" CB GLN B 378 " ideal model delta sigma weight residual 110.42 115.82 -5.40 1.99e+00 2.53e-01 7.37e+00 angle pdb=" CA LYS A 132 " pdb=" CB LYS A 132 " pdb=" CG LYS A 132 " ideal model delta sigma weight residual 114.10 119.42 -5.32 2.00e+00 2.50e-01 7.09e+00 angle pdb=" CA ARG C 684 " pdb=" CB ARG C 684 " pdb=" CG ARG C 684 " ideal model delta sigma weight residual 114.10 119.41 -5.31 2.00e+00 2.50e-01 7.06e+00 angle pdb=" N GLU C 650 " pdb=" CA GLU C 650 " pdb=" CB GLU C 650 " ideal model delta sigma weight residual 110.16 114.07 -3.91 1.48e+00 4.57e-01 6.98e+00 ... (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: 1088 0.037 - 0.073: 316 0.073 - 0.110: 107 0.110 - 0.147: 30 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.810 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.003 0.035 9637 Z= 0.194 Angle : 0.615 7.670 13346 Z= 0.331 Chirality : 0.041 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (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 TRP 0.020 0.001 TRP A 137 HIS 0.010 0.001 HIS C 619 PHE 0.016 0.001 PHE A 294 TYR 0.015 0.001 TYR A 133 ARG 0.006 0.000 ARG C 684 *********************** 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 : 1.054 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: 0.7514 (t80) REVERT: A 289 ASN cc_start: 0.9348 (m-40) cc_final: 0.8670 (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: 0.2122 time to fit residues: 49.5584 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 : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 chunk 44 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 52 optimal weight: 0.0060 chunk 64 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3071 r_free = 0.3071 target = 0.064124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.052439 restraints weight = 47645.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.054152 restraints weight = 26825.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.055319 restraints weight = 17338.568| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9637 Z= 0.163 Angle : 0.562 6.213 13346 Z= 0.293 Chirality : 0.041 0.145 1545 Planarity : 0.004 0.044 1534 Dihedral : 16.141 59.936 1652 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.99 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1072 helix: 1.46 (0.26), residues: 428 sheet: 0.23 (0.39), residues: 178 loop : -1.43 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 548 HIS 0.009 0.001 HIS C 619 PHE 0.009 0.001 PHE A 488 TYR 0.010 0.001 TYR B 202 ARG 0.003 0.000 ARG C 684 *********************** 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 162 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8893 (m-30) cc_final: 0.8546 (t70) REVERT: A 252 LEU cc_start: 0.8944 (mm) cc_final: 0.8596 (mm) REVERT: A 287 PHE cc_start: 0.8785 (t80) cc_final: 0.7634 (t80) REVERT: A 289 ASN cc_start: 0.9362 (m-40) cc_final: 0.8683 (m110) REVERT: A 301 LEU cc_start: 0.9027 (mp) cc_final: 0.8649 (mp) REVERT: A 375 ASP cc_start: 0.9441 (m-30) cc_final: 0.9237 (m-30) REVERT: A 505 MET cc_start: 0.9268 (tpt) cc_final: 0.8451 (tpt) REVERT: A 509 LEU cc_start: 0.9637 (mp) cc_final: 0.9010 (mp) REVERT: B 251 ASP cc_start: 0.7830 (p0) cc_final: 0.7531 (p0) REVERT: B 443 ASN cc_start: 0.9006 (t0) cc_final: 0.8639 (p0) REVERT: B 462 ASN cc_start: 0.8632 (t0) cc_final: 0.8238 (t0) REVERT: B 541 ARG cc_start: 0.8968 (mtt-85) cc_final: 0.8516 (mtt-85) REVERT: C 634 ILE cc_start: 0.8681 (mp) cc_final: 0.8244 (mp) REVERT: C 694 LYS cc_start: 0.8974 (tppt) cc_final: 0.8656 (ptpt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1775 time to fit residues: 42.4161 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 : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 0.9990 chunk 43 optimal weight: 0.0050 chunk 24 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS B 187 GLN ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.064205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.052625 restraints weight = 48902.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.054326 restraints weight = 27977.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.055465 restraints weight = 18155.255| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9637 Z= 0.168 Angle : 0.553 8.029 13346 Z= 0.287 Chirality : 0.040 0.154 1545 Planarity : 0.004 0.045 1534 Dihedral : 15.975 59.591 1652 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.80 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1072 helix: 1.46 (0.26), residues: 428 sheet: 0.24 (0.38), residues: 178 loop : -1.40 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 551 HIS 0.005 0.001 HIS C 719 PHE 0.007 0.001 PHE C 595 TYR 0.014 0.001 TYR A 316 ARG 0.005 0.001 ARG B 451 *********************** 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 157 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8867 (m-30) cc_final: 0.8542 (t70) REVERT: A 131 ASP cc_start: 0.9267 (t70) cc_final: 0.9063 (t70) REVERT: A 213 MET cc_start: 0.6949 (mmt) cc_final: 0.6488 (mmm) REVERT: A 251 ASP cc_start: 0.8077 (t0) cc_final: 0.7833 (t0) REVERT: A 252 LEU cc_start: 0.8914 (mm) cc_final: 0.8584 (mm) REVERT: A 287 PHE cc_start: 0.8770 (t80) cc_final: 0.7554 (t80) REVERT: A 289 ASN cc_start: 0.9300 (m-40) cc_final: 0.8620 (m110) REVERT: A 301 LEU cc_start: 0.9080 (mp) cc_final: 0.8847 (mp) REVERT: A 375 ASP cc_start: 0.9410 (m-30) cc_final: 0.9206 (m-30) REVERT: A 505 MET cc_start: 0.9184 (tpt) cc_final: 0.8354 (tpt) REVERT: A 509 LEU cc_start: 0.9642 (mp) cc_final: 0.9031 (mp) REVERT: B 251 ASP cc_start: 0.7830 (p0) cc_final: 0.7570 (p0) REVERT: B 271 PHE cc_start: 0.9201 (p90) cc_final: 0.8942 (p90) REVERT: B 443 ASN cc_start: 0.9014 (t0) cc_final: 0.8652 (p0) REVERT: B 462 ASN cc_start: 0.8721 (t0) cc_final: 0.8309 (t0) REVERT: B 530 MET cc_start: 0.8654 (mmp) cc_final: 0.7958 (tpp) REVERT: B 541 ARG cc_start: 0.8950 (mtt-85) cc_final: 0.8510 (mtt-85) REVERT: B 555 LEU cc_start: 0.9271 (mt) cc_final: 0.8989 (mt) REVERT: C 634 ILE cc_start: 0.8720 (mp) cc_final: 0.8237 (mp) REVERT: C 715 ILE cc_start: 0.7481 (tp) cc_final: 0.7241 (pt) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1730 time to fit residues: 40.3042 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 : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 GLN A 285 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.060279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.049262 restraints weight = 50556.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.050854 restraints weight = 28561.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.051958 restraints weight = 18467.648| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9637 Z= 0.304 Angle : 0.643 9.406 13346 Z= 0.340 Chirality : 0.043 0.158 1545 Planarity : 0.004 0.048 1534 Dihedral : 16.105 59.841 1652 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.29 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1072 helix: 1.28 (0.25), residues: 425 sheet: -0.24 (0.37), residues: 181 loop : -1.49 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 548 HIS 0.005 0.002 HIS B 431 PHE 0.013 0.002 PHE A 488 TYR 0.018 0.002 TYR A 316 ARG 0.008 0.001 ARG C 684 *********************** 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 139 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8982 (m-30) cc_final: 0.8635 (t70) REVERT: A 213 MET cc_start: 0.7098 (mmt) cc_final: 0.6742 (mmm) REVERT: A 251 ASP cc_start: 0.8033 (t0) cc_final: 0.7785 (t0) REVERT: A 287 PHE cc_start: 0.8859 (t80) cc_final: 0.7689 (t80) REVERT: A 289 ASN cc_start: 0.9254 (m-40) cc_final: 0.8610 (m110) REVERT: A 505 MET cc_start: 0.9210 (tpt) cc_final: 0.8905 (tpt) REVERT: B 271 PHE cc_start: 0.9328 (p90) cc_final: 0.9073 (p90) REVERT: B 462 ASN cc_start: 0.8872 (t0) cc_final: 0.8276 (t0) REVERT: B 541 ARG cc_start: 0.8959 (mtt-85) cc_final: 0.8587 (mtt-85) REVERT: C 634 ILE cc_start: 0.8606 (mp) cc_final: 0.8166 (mp) REVERT: C 654 LYS cc_start: 0.8780 (pptt) cc_final: 0.8341 (pptt) REVERT: C 704 ASN cc_start: 0.8331 (m-40) cc_final: 0.8089 (m-40) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1767 time to fit residues: 36.6639 Evaluate side-chains 99 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 78 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.062551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.051256 restraints weight = 48860.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.052917 restraints weight = 27626.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.054058 restraints weight = 17761.591| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9637 Z= 0.172 Angle : 0.577 8.529 13346 Z= 0.296 Chirality : 0.041 0.142 1545 Planarity : 0.004 0.046 1534 Dihedral : 15.995 59.750 1652 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.54 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.26), residues: 1072 helix: 1.50 (0.26), residues: 420 sheet: -0.11 (0.37), residues: 184 loop : -1.48 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 137 HIS 0.005 0.001 HIS C 719 PHE 0.009 0.001 PHE A 294 TYR 0.008 0.001 TYR B 202 ARG 0.011 0.000 ARG C 684 *********************** 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 : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8897 (m-30) cc_final: 0.8566 (t70) REVERT: A 131 ASP cc_start: 0.9272 (t70) cc_final: 0.9065 (t70) REVERT: A 213 MET cc_start: 0.7006 (mmt) cc_final: 0.6687 (mmm) REVERT: A 251 ASP cc_start: 0.8008 (t0) cc_final: 0.7708 (t0) REVERT: A 252 LEU cc_start: 0.8898 (mm) cc_final: 0.8614 (mm) REVERT: A 287 PHE cc_start: 0.8808 (t80) cc_final: 0.7619 (t80) REVERT: A 289 ASN cc_start: 0.9259 (m-40) cc_final: 0.8609 (m110) REVERT: A 375 ASP cc_start: 0.9377 (m-30) cc_final: 0.9128 (m-30) REVERT: A 505 MET cc_start: 0.9189 (tpt) cc_final: 0.8397 (tpt) REVERT: A 509 LEU cc_start: 0.9675 (mp) cc_final: 0.9141 (mp) REVERT: B 271 PHE cc_start: 0.9266 (p90) cc_final: 0.8941 (p90) REVERT: B 273 TRP cc_start: 0.8699 (t-100) cc_final: 0.8452 (t-100) REVERT: B 389 LEU cc_start: 0.8929 (tp) cc_final: 0.8685 (pp) REVERT: B 462 ASN cc_start: 0.8851 (t0) cc_final: 0.8322 (t0) REVERT: B 541 ARG cc_start: 0.8934 (mtt-85) cc_final: 0.8530 (mtt-85) REVERT: C 634 ILE cc_start: 0.8665 (mp) cc_final: 0.8193 (mp) REVERT: C 694 LYS cc_start: 0.8998 (tppt) cc_final: 0.8730 (ptpt) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1914 time to fit residues: 41.1046 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 : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.049992 restraints weight = 49663.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.051638 restraints weight = 28098.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.052725 restraints weight = 18092.207| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9637 Z= 0.239 Angle : 0.598 8.032 13346 Z= 0.313 Chirality : 0.041 0.156 1545 Planarity : 0.004 0.038 1534 Dihedral : 15.978 59.649 1652 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.57 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.26), residues: 1072 helix: 1.33 (0.26), residues: 426 sheet: -0.29 (0.37), residues: 186 loop : -1.54 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 137 HIS 0.004 0.001 HIS A 431 PHE 0.009 0.001 PHE A 488 TYR 0.033 0.001 TYR A 434 ARG 0.011 0.001 ARG C 684 *********************** 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 136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8979 (m-30) cc_final: 0.8613 (t70) REVERT: A 131 ASP cc_start: 0.9290 (t70) cc_final: 0.9086 (t70) REVERT: A 213 MET cc_start: 0.7108 (mmt) cc_final: 0.6769 (mmm) REVERT: A 252 LEU cc_start: 0.8893 (mm) cc_final: 0.8586 (mm) REVERT: A 287 PHE cc_start: 0.8806 (t80) cc_final: 0.7645 (t80) REVERT: A 289 ASN cc_start: 0.9252 (m-40) cc_final: 0.8660 (m110) REVERT: A 375 ASP cc_start: 0.9361 (m-30) cc_final: 0.9112 (m-30) REVERT: A 505 MET cc_start: 0.9184 (tpt) cc_final: 0.8486 (tpt) REVERT: A 509 LEU cc_start: 0.9677 (mp) cc_final: 0.9129 (mp) REVERT: B 271 PHE cc_start: 0.9325 (p90) cc_final: 0.9056 (p90) REVERT: B 273 TRP cc_start: 0.8713 (t-100) cc_final: 0.8489 (t-100) REVERT: B 389 LEU cc_start: 0.8932 (tp) cc_final: 0.8701 (pp) REVERT: B 462 ASN cc_start: 0.8819 (t0) cc_final: 0.8197 (t0) REVERT: B 541 ARG cc_start: 0.8914 (mtt-85) cc_final: 0.8571 (mtt-85) REVERT: C 694 LYS cc_start: 0.9003 (tppt) cc_final: 0.8695 (ptpt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1745 time to fit residues: 35.4024 Evaluate side-chains 104 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.060273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.049275 restraints weight = 50999.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.050879 restraints weight = 28709.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.051976 restraints weight = 18525.984| |-----------------------------------------------------------------------------| r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9637 Z= 0.273 Angle : 0.625 8.314 13346 Z= 0.326 Chirality : 0.042 0.151 1545 Planarity : 0.004 0.037 1534 Dihedral : 16.087 59.926 1652 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.38 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1072 helix: 1.20 (0.25), residues: 432 sheet: -0.41 (0.37), residues: 177 loop : -1.63 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 137 HIS 0.004 0.001 HIS B 506 PHE 0.008 0.001 PHE B 398 TYR 0.023 0.002 TYR A 434 ARG 0.006 0.001 ARG C 684 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8979 (m-30) cc_final: 0.8639 (t70) REVERT: A 213 MET cc_start: 0.7204 (mmt) cc_final: 0.6866 (mmm) REVERT: A 251 ASP cc_start: 0.7987 (t0) cc_final: 0.7752 (t0) REVERT: A 252 LEU cc_start: 0.8894 (mm) cc_final: 0.8636 (mm) REVERT: A 287 PHE cc_start: 0.8818 (t80) cc_final: 0.7662 (t80) REVERT: A 289 ASN cc_start: 0.9245 (m-40) cc_final: 0.8656 (m110) REVERT: A 375 ASP cc_start: 0.9336 (m-30) cc_final: 0.9085 (m-30) REVERT: A 505 MET cc_start: 0.9170 (tpt) cc_final: 0.8490 (tpt) REVERT: A 509 LEU cc_start: 0.9657 (mp) cc_final: 0.9130 (mp) REVERT: B 271 PHE cc_start: 0.9337 (p90) cc_final: 0.9065 (p90) REVERT: B 389 LEU cc_start: 0.8921 (tp) cc_final: 0.8692 (pp) REVERT: B 462 ASN cc_start: 0.8870 (t0) cc_final: 0.8237 (t0) REVERT: B 541 ARG cc_start: 0.8882 (mtt-85) cc_final: 0.8543 (mtt-85) REVERT: C 585 MET cc_start: 0.7696 (pmm) cc_final: 0.5587 (mmt) REVERT: C 694 LYS cc_start: 0.9021 (tppt) cc_final: 0.8691 (ptpt) REVERT: C 744 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7199 (tt0) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1807 time to fit residues: 36.0878 Evaluate side-chains 100 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** 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 = 0.2977 r_free = 0.2977 target = 0.060205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.049101 restraints weight = 51472.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.050724 restraints weight = 28560.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.051832 restraints weight = 18162.276| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9637 Z= 0.276 Angle : 0.638 8.653 13346 Z= 0.334 Chirality : 0.042 0.165 1545 Planarity : 0.004 0.037 1534 Dihedral : 16.155 59.507 1652 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.85 % Favored : 94.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.26), residues: 1072 helix: 1.21 (0.26), residues: 425 sheet: -0.57 (0.37), residues: 182 loop : -1.62 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 632 HIS 0.004 0.001 HIS B 506 PHE 0.010 0.001 PHE A 294 TYR 0.022 0.001 TYR A 434 ARG 0.010 0.001 ARG B 451 *********************** 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 137 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8972 (m-30) cc_final: 0.8624 (t70) REVERT: A 213 MET cc_start: 0.7196 (mmt) cc_final: 0.6875 (mmm) REVERT: A 252 LEU cc_start: 0.8889 (mm) cc_final: 0.8645 (mm) REVERT: A 287 PHE cc_start: 0.8806 (t80) cc_final: 0.7625 (t80) REVERT: A 289 ASN cc_start: 0.9238 (m-40) cc_final: 0.8675 (m110) REVERT: A 375 ASP cc_start: 0.9339 (m-30) cc_final: 0.9093 (m-30) REVERT: A 505 MET cc_start: 0.9179 (tpt) cc_final: 0.8529 (tpt) REVERT: A 509 LEU cc_start: 0.9664 (mp) cc_final: 0.9167 (mp) REVERT: B 271 PHE cc_start: 0.9351 (p90) cc_final: 0.9090 (p90) REVERT: B 389 LEU cc_start: 0.8921 (tp) cc_final: 0.8700 (pp) REVERT: B 462 ASN cc_start: 0.8886 (t0) cc_final: 0.8223 (t0) REVERT: B 541 ARG cc_start: 0.8853 (mtt-85) cc_final: 0.8532 (mtt-85) REVERT: C 585 MET cc_start: 0.7724 (pmm) cc_final: 0.5970 (mmt) REVERT: C 651 PHE cc_start: 0.8862 (t80) cc_final: 0.8126 (t80) REVERT: C 694 LYS cc_start: 0.9019 (tppt) cc_final: 0.8683 (ptpt) REVERT: C 744 GLN cc_start: 0.7398 (mm-40) cc_final: 0.7143 (tt0) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1633 time to fit residues: 33.5045 Evaluate side-chains 103 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 105 optimal weight: 0.0970 chunk 53 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.063269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.052091 restraints weight = 48898.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.053694 restraints weight = 27701.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.054812 restraints weight = 17967.621| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9637 Z= 0.163 Angle : 0.581 9.440 13346 Z= 0.296 Chirality : 0.041 0.180 1545 Planarity : 0.004 0.045 1534 Dihedral : 16.044 59.696 1652 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.82 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1072 helix: 1.42 (0.26), residues: 425 sheet: -0.10 (0.38), residues: 183 loop : -1.61 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 137 HIS 0.006 0.001 HIS C 619 PHE 0.010 0.001 PHE A 294 TYR 0.019 0.001 TYR A 434 ARG 0.009 0.000 ARG B 451 *********************** 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 148 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8896 (m-30) cc_final: 0.8557 (t70) REVERT: A 131 ASP cc_start: 0.9225 (t70) cc_final: 0.8983 (t70) REVERT: A 213 MET cc_start: 0.7046 (mmt) cc_final: 0.6711 (mmm) REVERT: A 251 ASP cc_start: 0.7874 (t0) cc_final: 0.7615 (t0) REVERT: A 252 LEU cc_start: 0.8887 (mm) cc_final: 0.8573 (mm) REVERT: A 287 PHE cc_start: 0.8711 (t80) cc_final: 0.7551 (t80) REVERT: A 289 ASN cc_start: 0.9227 (m-40) cc_final: 0.8625 (m110) REVERT: A 375 ASP cc_start: 0.9285 (m-30) cc_final: 0.9039 (m-30) REVERT: A 505 MET cc_start: 0.9086 (tpt) cc_final: 0.8367 (tpt) REVERT: A 509 LEU cc_start: 0.9624 (mp) cc_final: 0.9121 (mp) REVERT: B 271 PHE cc_start: 0.9268 (p90) cc_final: 0.8822 (p90) REVERT: B 389 LEU cc_start: 0.8854 (tp) cc_final: 0.8651 (pp) REVERT: B 462 ASN cc_start: 0.8782 (t0) cc_final: 0.8220 (t0) REVERT: B 505 MET cc_start: 0.9446 (tmm) cc_final: 0.9215 (tmm) REVERT: B 541 ARG cc_start: 0.8854 (mtt-85) cc_final: 0.8415 (mtt-85) REVERT: C 585 MET cc_start: 0.7672 (pmm) cc_final: 0.6074 (mmt) REVERT: C 631 GLN cc_start: 0.8558 (pm20) cc_final: 0.8124 (tm-30) REVERT: C 634 ILE cc_start: 0.8638 (mp) cc_final: 0.8284 (mp) REVERT: C 651 PHE cc_start: 0.8787 (t80) cc_final: 0.8004 (t80) REVERT: C 694 LYS cc_start: 0.9046 (tppt) cc_final: 0.8709 (ptpt) REVERT: C 741 LEU cc_start: 0.8921 (mt) cc_final: 0.8642 (mt) REVERT: C 744 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7116 (tt0) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1652 time to fit residues: 36.7282 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 : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 94 optimal weight: 0.0010 chunk 91 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.060744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.049396 restraints weight = 51465.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.051020 restraints weight = 28707.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.052158 restraints weight = 18462.195| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9637 Z= 0.260 Angle : 0.612 8.203 13346 Z= 0.319 Chirality : 0.042 0.173 1545 Planarity : 0.004 0.039 1534 Dihedral : 16.097 59.656 1652 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.94 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1072 helix: 1.29 (0.26), residues: 433 sheet: -0.42 (0.37), residues: 178 loop : -1.64 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 273 HIS 0.005 0.001 HIS B 431 PHE 0.009 0.001 PHE A 294 TYR 0.019 0.002 TYR A 434 ARG 0.008 0.001 ARG B 451 ********************** 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 134 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8924 (m-30) cc_final: 0.8572 (t70) REVERT: A 213 MET cc_start: 0.7133 (mmt) cc_final: 0.6831 (mmm) REVERT: A 252 LEU cc_start: 0.8869 (mm) cc_final: 0.8622 (mm) REVERT: A 287 PHE cc_start: 0.8824 (t80) cc_final: 0.7624 (t80) REVERT: A 289 ASN cc_start: 0.9227 (m-40) cc_final: 0.8688 (m110) REVERT: A 375 ASP cc_start: 0.9344 (m-30) cc_final: 0.9099 (m-30) REVERT: A 505 MET cc_start: 0.9174 (tpt) cc_final: 0.8556 (tpt) REVERT: A 509 LEU cc_start: 0.9663 (mp) cc_final: 0.9148 (mp) REVERT: B 271 PHE cc_start: 0.9314 (p90) cc_final: 0.8987 (p90) REVERT: B 462 ASN cc_start: 0.8833 (t0) cc_final: 0.8175 (t0) REVERT: B 505 MET cc_start: 0.9451 (tmm) cc_final: 0.9228 (tmm) REVERT: B 541 ARG cc_start: 0.8878 (mtt-85) cc_final: 0.8551 (mtt-85) REVERT: C 585 MET cc_start: 0.7463 (pmm) cc_final: 0.6171 (mmt) REVERT: C 651 PHE cc_start: 0.8858 (t80) cc_final: 0.8121 (t80) REVERT: C 694 LYS cc_start: 0.9036 (tppt) cc_final: 0.8703 (ptpt) REVERT: C 744 GLN cc_start: 0.7379 (mm-40) cc_final: 0.7118 (tt0) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1650 time to fit residues: 33.2873 Evaluate side-chains 100 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.059109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.048137 restraints weight = 50691.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.049684 restraints weight = 28740.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.050733 restraints weight = 18614.326| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 9637 Z= 0.359 Angle : 0.701 11.026 13346 Z= 0.367 Chirality : 0.044 0.170 1545 Planarity : 0.005 0.045 1534 Dihedral : 16.319 62.976 1652 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.88 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1072 helix: 0.93 (0.25), residues: 430 sheet: -0.81 (0.37), residues: 177 loop : -1.73 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 273 HIS 0.006 0.002 HIS B 431 PHE 0.013 0.002 PHE B 398 TYR 0.024 0.002 TYR A 316 ARG 0.007 0.001 ARG B 451 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2524.65 seconds wall clock time: 44 minutes 54.87 seconds (2694.87 seconds total)