Starting phenix.real_space_refine on Thu Feb 13 21:17:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o24_12698/02_2025/7o24_12698.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o24_12698/02_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_12698/02_2025/7o24_12698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o24_12698/02_2025/7o24_12698.map" model { file = "/net/cci-nas-00/data/ceres_data/7o24_12698/02_2025/7o24_12698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o24_12698/02_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-5592/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: 6.81, per 1000 atoms: 0.73 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: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.32 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: 3.33 Time building geometry restraints manager: 2.86 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: 3.680 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.850 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.700 ------------------------------------------------------------------------------- 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 : 1.002 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: 0.2073 time to fit residues: 47.9342 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 : 0.951 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.052438 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 = 26824.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.055331 restraints weight = 17339.047| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 0.971 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8892 (m-30) cc_final: 0.8546 (t70) REVERT: A 252 LEU cc_start: 0.8941 (mm) cc_final: 0.8595 (mm) REVERT: A 287 PHE cc_start: 0.8788 (t80) cc_final: 0.7637 (t80) REVERT: A 289 ASN cc_start: 0.9362 (m-40) cc_final: 0.8684 (m110) REVERT: A 301 LEU cc_start: 0.9027 (mp) cc_final: 0.8648 (mp) REVERT: A 375 ASP cc_start: 0.9440 (m-30) cc_final: 0.9237 (m-30) REVERT: A 505 MET cc_start: 0.9270 (tpt) cc_final: 0.8453 (tpt) REVERT: A 509 LEU cc_start: 0.9637 (mp) cc_final: 0.9012 (mp) REVERT: B 251 ASP cc_start: 0.7833 (p0) cc_final: 0.7534 (p0) REVERT: B 443 ASN cc_start: 0.9001 (t0) cc_final: 0.8636 (p0) REVERT: B 462 ASN cc_start: 0.8632 (t0) cc_final: 0.8238 (t0) REVERT: B 541 ARG cc_start: 0.8969 (mtt-85) cc_final: 0.8514 (mtt-85) REVERT: C 634 ILE cc_start: 0.8688 (mp) cc_final: 0.8249 (mp) REVERT: C 694 LYS cc_start: 0.8973 (tppt) cc_final: 0.8655 (ptpt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1768 time to fit residues: 41.9578 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 : 0.944 ------------------------------------------------------------------------------- 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: 0.0670 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- 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 285 GLN A 325 HIS B 187 GLN ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.064853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.053137 restraints weight = 48433.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.054848 restraints weight = 27615.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.056068 restraints weight = 17918.851| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1724 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= 0.162 Angle : 0.550 8.135 13346 Z= 0.285 Chirality : 0.040 0.148 1545 Planarity : 0.004 0.045 1534 Dihedral : 15.967 59.606 1652 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.80 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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: 0.09 (0.26), residues: 1072 helix: 1.44 (0.26), residues: 429 sheet: 0.27 (0.38), residues: 178 loop : -1.38 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 551 HIS 0.004 0.001 HIS C 719 PHE 0.008 0.001 PHE A 488 TYR 0.012 0.001 TYR A 316 ARG 0.007 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 161 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8875 (m-30) cc_final: 0.8556 (t70) REVERT: A 131 ASP cc_start: 0.9264 (t70) cc_final: 0.9059 (t70) REVERT: A 213 MET cc_start: 0.6826 (mmt) cc_final: 0.6317 (mmm) REVERT: A 251 ASP cc_start: 0.8072 (t0) cc_final: 0.7843 (t0) REVERT: A 252 LEU cc_start: 0.8918 (mm) cc_final: 0.8603 (mm) REVERT: A 287 PHE cc_start: 0.8759 (t80) cc_final: 0.7538 (t80) REVERT: A 289 ASN cc_start: 0.9308 (m-40) cc_final: 0.8630 (m110) REVERT: A 301 LEU cc_start: 0.9075 (mp) cc_final: 0.8854 (mp) REVERT: A 375 ASP cc_start: 0.9422 (m-30) cc_final: 0.9214 (m-30) REVERT: A 505 MET cc_start: 0.9185 (tpt) cc_final: 0.8362 (tpt) REVERT: A 509 LEU cc_start: 0.9635 (mp) cc_final: 0.9051 (mp) REVERT: B 251 ASP cc_start: 0.7813 (p0) cc_final: 0.7567 (p0) REVERT: B 271 PHE cc_start: 0.9184 (p90) cc_final: 0.8913 (p90) REVERT: B 443 ASN cc_start: 0.8989 (t0) cc_final: 0.8618 (p0) REVERT: B 462 ASN cc_start: 0.8703 (t0) cc_final: 0.8330 (t0) REVERT: B 530 MET cc_start: 0.8790 (mmp) cc_final: 0.8133 (tpp) REVERT: B 541 ARG cc_start: 0.8942 (mtt-85) cc_final: 0.8494 (mtt-85) REVERT: B 555 LEU cc_start: 0.9265 (mt) cc_final: 0.8978 (mt) REVERT: C 634 ILE cc_start: 0.8720 (mp) cc_final: 0.8231 (mp) REVERT: C 715 ILE cc_start: 0.7456 (tp) cc_final: 0.7219 (pt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1763 time to fit residues: 42.2250 Evaluate side-chains 115 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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: 1.9990 chunk 8 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 77 optimal weight: 0.0370 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- 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 325 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 GLN B 390 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.061536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.050330 restraints weight = 49820.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.051969 restraints weight = 28343.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.053104 restraints weight = 18378.847| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1844 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= 0.257 Angle : 0.597 7.839 13346 Z= 0.316 Chirality : 0.042 0.157 1545 Planarity : 0.004 0.047 1534 Dihedral : 15.979 59.856 1652 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.92 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.26), residues: 1072 helix: 1.49 (0.26), residues: 420 sheet: -0.13 (0.36), residues: 184 loop : -1.38 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 683 HIS 0.004 0.001 HIS B 506 PHE 0.018 0.002 PHE A 488 TYR 0.018 0.001 TYR A 316 ARG 0.006 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 143 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8932 (m-30) cc_final: 0.8589 (t70) REVERT: A 213 MET cc_start: 0.7044 (mmt) cc_final: 0.6655 (mmm) REVERT: A 251 ASP cc_start: 0.8034 (t0) cc_final: 0.7774 (t0) REVERT: A 252 LEU cc_start: 0.8895 (mm) cc_final: 0.8663 (mm) REVERT: A 287 PHE cc_start: 0.8811 (t80) cc_final: 0.7612 (t80) REVERT: A 289 ASN cc_start: 0.9254 (m-40) cc_final: 0.8584 (m110) REVERT: A 505 MET cc_start: 0.9196 (tpt) cc_final: 0.8429 (tpt) REVERT: A 509 LEU cc_start: 0.9682 (mp) cc_final: 0.9071 (mp) REVERT: B 271 PHE cc_start: 0.9278 (p90) cc_final: 0.8960 (p90) REVERT: B 462 ASN cc_start: 0.8810 (t0) cc_final: 0.8262 (t0) REVERT: B 541 ARG cc_start: 0.8968 (mtt-85) cc_final: 0.8546 (mtt-85) REVERT: C 634 ILE cc_start: 0.8645 (mp) cc_final: 0.8196 (mp) REVERT: C 654 LYS cc_start: 0.8786 (pptt) cc_final: 0.8364 (pptt) REVERT: C 704 ASN cc_start: 0.8362 (m-40) cc_final: 0.8124 (m-40) REVERT: C 744 GLN cc_start: 0.7467 (mm-40) cc_final: 0.7240 (tt0) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1718 time to fit residues: 36.8084 Evaluate side-chains 108 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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: 6.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 B 390 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.060513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.049486 restraints weight = 50537.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.051066 restraints weight = 28780.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.052166 restraints weight = 18660.151| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9637 Z= 0.274 Angle : 0.626 8.065 13346 Z= 0.327 Chirality : 0.042 0.160 1545 Planarity : 0.004 0.038 1534 Dihedral : 16.072 59.712 1652 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.10 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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: -0.29 (0.26), residues: 1072 helix: 1.21 (0.25), residues: 433 sheet: -0.29 (0.37), residues: 181 loop : -1.54 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 137 HIS 0.005 0.001 HIS B 506 PHE 0.009 0.001 PHE B 398 TYR 0.016 0.002 TYR A 316 ARG 0.011 0.001 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 134 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8983 (m-30) cc_final: 0.8623 (t70) REVERT: A 213 MET cc_start: 0.7098 (mmt) cc_final: 0.6773 (mmm) REVERT: A 251 ASP cc_start: 0.8003 (t0) cc_final: 0.7743 (t0) REVERT: A 252 LEU cc_start: 0.8883 (mm) cc_final: 0.8655 (mm) REVERT: A 287 PHE cc_start: 0.8838 (t80) cc_final: 0.7691 (t80) REVERT: A 289 ASN cc_start: 0.9251 (m-40) cc_final: 0.8621 (m110) REVERT: A 375 ASP cc_start: 0.9348 (m-30) cc_final: 0.9100 (m-30) REVERT: A 505 MET cc_start: 0.9178 (tpt) cc_final: 0.8430 (tpt) REVERT: A 509 LEU cc_start: 0.9683 (mp) cc_final: 0.9130 (mp) REVERT: B 271 PHE cc_start: 0.9337 (p90) cc_final: 0.9062 (p90) REVERT: B 273 TRP cc_start: 0.8699 (t-100) cc_final: 0.8475 (t-100) REVERT: B 389 LEU cc_start: 0.8931 (tp) cc_final: 0.8693 (pp) REVERT: B 462 ASN cc_start: 0.8882 (t0) cc_final: 0.8236 (t0) REVERT: B 541 ARG cc_start: 0.8900 (mtt-85) cc_final: 0.8550 (mtt-85) REVERT: C 634 ILE cc_start: 0.8624 (mp) cc_final: 0.8151 (mp) REVERT: C 694 LYS cc_start: 0.9055 (ttmm) cc_final: 0.8757 (ptpt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1748 time to fit residues: 34.9222 Evaluate side-chains 101 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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: 6.9990 chunk 2 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 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 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN ** B 125 GLN ** 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 = 0.2947 r_free = 0.2947 target = 0.058863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.047937 restraints weight = 51556.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.049518 restraints weight = 28851.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.050517 restraints weight = 18430.168| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9637 Z= 0.361 Angle : 0.703 10.880 13346 Z= 0.372 Chirality : 0.044 0.163 1545 Planarity : 0.004 0.040 1534 Dihedral : 16.177 59.841 1652 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.50 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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: -0.66 (0.25), residues: 1072 helix: 0.96 (0.25), residues: 431 sheet: -0.66 (0.37), residues: 177 loop : -1.70 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 137 HIS 0.007 0.002 HIS B 431 PHE 0.013 0.002 PHE B 398 TYR 0.021 0.002 TYR A 316 ARG 0.012 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 126 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.990 Fit side-chains REVERT: A 107 ASP cc_start: 0.8988 (m-30) cc_final: 0.8635 (t70) REVERT: A 131 ASP cc_start: 0.9496 (t0) cc_final: 0.9254 (t70) REVERT: A 213 MET cc_start: 0.7064 (mmt) cc_final: 0.6807 (mmm) REVERT: A 287 PHE cc_start: 0.8782 (t80) cc_final: 0.7669 (t80) REVERT: A 289 ASN cc_start: 0.9233 (m-40) cc_final: 0.8676 (m110) REVERT: A 375 ASP cc_start: 0.9350 (m-30) cc_final: 0.9120 (m-30) REVERT: A 388 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8762 (mp0) REVERT: A 505 MET cc_start: 0.9214 (tpt) cc_final: 0.8963 (tpt) REVERT: B 389 LEU cc_start: 0.8940 (tp) cc_final: 0.8688 (pp) REVERT: B 396 PHE cc_start: 0.9392 (m-80) cc_final: 0.9189 (m-80) REVERT: B 462 ASN cc_start: 0.8963 (t0) cc_final: 0.8300 (t0) REVERT: B 541 ARG cc_start: 0.8849 (mtt-85) cc_final: 0.8509 (mtt-85) REVERT: C 585 MET cc_start: 0.7739 (pmm) cc_final: 0.5764 (mmt) REVERT: C 694 LYS cc_start: 0.9026 (ttmm) cc_final: 0.8673 (ptpt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1696 time to fit residues: 32.1840 Evaluate side-chains 90 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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: 3.9990 chunk 83 optimal weight: 0.0000 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 0.0970 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.3020 r_free = 0.3020 target = 0.062039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.050749 restraints weight = 49240.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.052412 restraints weight = 27622.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.053551 restraints weight = 17787.218| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2450 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= 0.169 Angle : 0.587 8.695 13346 Z= 0.303 Chirality : 0.041 0.153 1545 Planarity : 0.004 0.035 1534 Dihedral : 16.032 59.853 1652 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.73 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1072 helix: 1.43 (0.26), residues: 426 sheet: -0.36 (0.37), residues: 186 loop : -1.59 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 632 HIS 0.003 0.001 HIS C 619 PHE 0.009 0.001 PHE C 651 TYR 0.015 0.001 TYR A 316 ARG 0.002 0.000 ARG A 451 *********************** 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 149 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8940 (m-30) cc_final: 0.8591 (t70) REVERT: A 131 ASP cc_start: 0.9417 (t0) cc_final: 0.9151 (t70) REVERT: A 213 MET cc_start: 0.7040 (mmt) cc_final: 0.6720 (mmm) REVERT: A 252 LEU cc_start: 0.8893 (mm) cc_final: 0.8631 (mm) REVERT: A 287 PHE cc_start: 0.8763 (t80) cc_final: 0.7570 (t80) REVERT: A 289 ASN cc_start: 0.9235 (m-40) cc_final: 0.8683 (m110) REVERT: A 375 ASP cc_start: 0.9337 (m-30) cc_final: 0.9107 (m-30) REVERT: A 388 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8734 (mp0) REVERT: A 505 MET cc_start: 0.9131 (tpt) cc_final: 0.8448 (tpt) REVERT: A 509 LEU cc_start: 0.9642 (mp) cc_final: 0.9160 (mp) REVERT: B 273 TRP cc_start: 0.8655 (t-100) cc_final: 0.8311 (t-100) REVERT: B 389 LEU cc_start: 0.8885 (tp) cc_final: 0.8670 (pp) REVERT: B 462 ASN cc_start: 0.8799 (t0) cc_final: 0.8200 (t0) REVERT: B 505 MET cc_start: 0.9459 (tmm) cc_final: 0.9229 (tmm) REVERT: B 541 ARG cc_start: 0.8841 (mtt-85) cc_final: 0.8432 (mtt-85) REVERT: C 585 MET cc_start: 0.7698 (pmm) cc_final: 0.5843 (mmt) REVERT: C 595 PHE cc_start: 0.8901 (m-10) cc_final: 0.8684 (m-10) REVERT: C 631 GLN cc_start: 0.8604 (pm20) cc_final: 0.8185 (tm-30) REVERT: C 651 PHE cc_start: 0.8801 (t80) cc_final: 0.8498 (t80) REVERT: C 694 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8738 (ptpt) REVERT: C 741 LEU cc_start: 0.8889 (mt) cc_final: 0.8686 (mt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1899 time to fit residues: 41.3410 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 : 1.096 ------------------------------------------------------------------------------- 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: 0.0060 chunk 32 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- 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 = 0.3013 r_free = 0.3013 target = 0.061713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.050553 restraints weight = 49624.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.052204 restraints weight = 27771.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.053341 restraints weight = 17821.611| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2478 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= 0.200 Angle : 0.592 8.636 13346 Z= 0.308 Chirality : 0.041 0.184 1545 Planarity : 0.004 0.074 1534 Dihedral : 16.021 59.885 1652 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.92 % Favored : 95.90 % 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 (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: -0.27 (0.26), residues: 1072 helix: 1.35 (0.26), residues: 433 sheet: -0.27 (0.38), residues: 181 loop : -1.67 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 273 HIS 0.003 0.001 HIS A 259 PHE 0.012 0.001 PHE C 595 TYR 0.011 0.001 TYR B 202 ARG 0.023 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 139 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8928 (m-30) cc_final: 0.8587 (t70) REVERT: A 131 ASP cc_start: 0.9439 (t0) cc_final: 0.9161 (t70) REVERT: A 213 MET cc_start: 0.7116 (mmt) cc_final: 0.6790 (mmm) REVERT: A 251 ASP cc_start: 0.7945 (t0) cc_final: 0.7738 (t0) REVERT: A 252 LEU cc_start: 0.8883 (mm) cc_final: 0.8626 (mm) REVERT: A 287 PHE cc_start: 0.8788 (t80) cc_final: 0.7594 (t80) REVERT: A 289 ASN cc_start: 0.9222 (m-40) cc_final: 0.8675 (m110) REVERT: A 375 ASP cc_start: 0.9318 (m-30) cc_final: 0.9092 (m-30) REVERT: A 388 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8755 (mp0) REVERT: A 505 MET cc_start: 0.9142 (tpt) cc_final: 0.8467 (tpt) REVERT: A 509 LEU cc_start: 0.9661 (mp) cc_final: 0.9163 (mp) REVERT: B 273 TRP cc_start: 0.8722 (t-100) cc_final: 0.8350 (t-100) REVERT: B 389 LEU cc_start: 0.8907 (tp) cc_final: 0.8687 (pp) REVERT: B 462 ASN cc_start: 0.8818 (t0) cc_final: 0.8197 (t0) REVERT: B 505 MET cc_start: 0.9456 (tmm) cc_final: 0.9215 (tmm) REVERT: B 541 ARG cc_start: 0.8847 (mtt-85) cc_final: 0.8440 (mtt-85) REVERT: C 585 MET cc_start: 0.7748 (pmm) cc_final: 0.5999 (mmt) REVERT: C 651 PHE cc_start: 0.8832 (t80) cc_final: 0.8478 (t80) REVERT: C 694 LYS cc_start: 0.9029 (ttmm) cc_final: 0.8710 (ptpt) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1855 time to fit residues: 38.1404 Evaluate side-chains 109 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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: 0.9980 chunk 55 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 105 optimal weight: 0.0670 chunk 53 optimal weight: 9.9990 chunk 31 optimal weight: 0.1980 chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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** A 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.063646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.052271 restraints weight = 48259.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.053973 restraints weight = 27035.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.055099 restraints weight = 17382.120| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9637 Z= 0.158 Angle : 0.579 9.113 13346 Z= 0.295 Chirality : 0.041 0.173 1545 Planarity : 0.004 0.036 1534 Dihedral : 15.958 59.579 1652 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.64 % Favored : 96.18 % 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: -0.14 (0.26), residues: 1072 helix: 1.45 (0.26), residues: 430 sheet: -0.01 (0.38), residues: 178 loop : -1.67 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 137 HIS 0.002 0.000 HIS C 719 PHE 0.008 0.001 PHE C 682 TYR 0.010 0.001 TYR B 202 ARG 0.007 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 150 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8896 (m-30) cc_final: 0.8547 (t70) REVERT: A 131 ASP cc_start: 0.9412 (t0) cc_final: 0.9130 (t70) REVERT: A 213 MET cc_start: 0.7061 (mmt) cc_final: 0.6710 (mmm) REVERT: A 251 ASP cc_start: 0.7971 (t0) cc_final: 0.7704 (t0) REVERT: A 252 LEU cc_start: 0.8879 (mm) cc_final: 0.8589 (mm) REVERT: A 287 PHE cc_start: 0.8732 (t80) cc_final: 0.7503 (t80) REVERT: A 289 ASN cc_start: 0.9238 (m-40) cc_final: 0.8665 (m110) REVERT: A 375 ASP cc_start: 0.9308 (m-30) cc_final: 0.9080 (m-30) REVERT: A 388 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8776 (mp0) REVERT: A 505 MET cc_start: 0.9089 (tpt) cc_final: 0.8351 (tpt) REVERT: A 509 LEU cc_start: 0.9632 (mp) cc_final: 0.9129 (mp) REVERT: B 273 TRP cc_start: 0.8707 (t-100) cc_final: 0.8286 (t-100) REVERT: B 389 LEU cc_start: 0.8881 (tp) cc_final: 0.8665 (pp) REVERT: B 462 ASN cc_start: 0.8753 (t0) cc_final: 0.8174 (t0) REVERT: B 505 MET cc_start: 0.9464 (tmm) cc_final: 0.8968 (tmm) REVERT: B 541 ARG cc_start: 0.8877 (mtt-85) cc_final: 0.8431 (mtt-85) REVERT: B 551 TRP cc_start: 0.8631 (m100) cc_final: 0.8116 (m-90) REVERT: C 585 MET cc_start: 0.7727 (pmm) cc_final: 0.6113 (mmt) REVERT: C 631 GLN cc_start: 0.8681 (pm20) cc_final: 0.8231 (tm-30) REVERT: C 634 ILE cc_start: 0.8664 (mp) cc_final: 0.8316 (mp) REVERT: C 651 PHE cc_start: 0.8815 (t80) cc_final: 0.8005 (t80) REVERT: C 694 LYS cc_start: 0.9052 (ttmm) cc_final: 0.8746 (ptpt) REVERT: C 741 LEU cc_start: 0.8917 (mt) cc_final: 0.8691 (mt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1779 time to fit residues: 39.4782 Evaluate side-chains 119 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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: 7.9990 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.062791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.051579 restraints weight = 50345.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.053197 restraints weight = 28388.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.054334 restraints weight = 18358.282| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2658 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= 0.184 Angle : 0.570 6.568 13346 Z= 0.295 Chirality : 0.041 0.180 1545 Planarity : 0.004 0.039 1534 Dihedral : 15.943 59.985 1652 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.01 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1072 helix: 1.52 (0.26), residues: 430 sheet: -0.03 (0.37), residues: 180 loop : -1.62 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 137 HIS 0.003 0.001 HIS C 719 PHE 0.007 0.001 PHE A 396 TYR 0.031 0.001 TYR A 434 ARG 0.007 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 145 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8884 (m-30) cc_final: 0.8551 (t70) REVERT: A 131 ASP cc_start: 0.9422 (t0) cc_final: 0.9121 (t70) REVERT: A 213 MET cc_start: 0.7121 (mmt) cc_final: 0.6788 (mmm) REVERT: A 252 LEU cc_start: 0.8900 (mm) cc_final: 0.8585 (mm) REVERT: A 287 PHE cc_start: 0.8717 (t80) cc_final: 0.7514 (t80) REVERT: A 289 ASN cc_start: 0.9208 (m-40) cc_final: 0.8641 (m110) REVERT: A 354 GLU cc_start: 0.6972 (tp30) cc_final: 0.6769 (tp30) REVERT: A 375 ASP cc_start: 0.9282 (m-30) cc_final: 0.9038 (m-30) REVERT: A 388 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8786 (mp0) REVERT: A 505 MET cc_start: 0.9092 (tpt) cc_final: 0.8329 (tpt) REVERT: A 509 LEU cc_start: 0.9651 (mp) cc_final: 0.9083 (mp) REVERT: B 271 PHE cc_start: 0.9163 (p90) cc_final: 0.8963 (p90) REVERT: B 273 TRP cc_start: 0.8724 (t-100) cc_final: 0.8306 (t-100) REVERT: B 462 ASN cc_start: 0.8778 (t0) cc_final: 0.8166 (t0) REVERT: B 505 MET cc_start: 0.9440 (tmm) cc_final: 0.9224 (tmm) REVERT: B 541 ARG cc_start: 0.8873 (mtt-85) cc_final: 0.8463 (mtt-85) REVERT: B 555 LEU cc_start: 0.9364 (mt) cc_final: 0.9143 (mt) REVERT: C 585 MET cc_start: 0.7635 (pmm) cc_final: 0.6177 (mmt) REVERT: C 631 GLN cc_start: 0.8678 (pm20) cc_final: 0.8270 (tm-30) REVERT: C 634 ILE cc_start: 0.8654 (mp) cc_final: 0.8292 (mp) REVERT: C 651 PHE cc_start: 0.8836 (t80) cc_final: 0.8048 (t80) REVERT: C 694 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8723 (ptpt) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1810 time to fit residues: 38.8450 Evaluate side-chains 111 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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: 5.9990 chunk 60 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 166 GLN ** A 187 GLN ** 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 = 0.3005 r_free = 0.3005 target = 0.061408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.050258 restraints weight = 49620.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.051887 restraints weight = 27738.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.053011 restraints weight = 17787.881| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9637 Z= 0.235 Angle : 0.604 8.759 13346 Z= 0.314 Chirality : 0.042 0.177 1545 Planarity : 0.004 0.040 1534 Dihedral : 16.042 59.971 1652 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.38 % Favored : 95.43 % Rotamer: Outliers : 0.11 % Allowed : 0.23 % 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: -0.26 (0.26), residues: 1072 helix: 1.39 (0.26), residues: 432 sheet: -0.27 (0.38), residues: 178 loop : -1.70 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 137 HIS 0.006 0.001 HIS C 619 PHE 0.010 0.001 PHE C 595 TYR 0.025 0.001 TYR A 434 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: 2531.63 seconds wall clock time: 46 minutes 30.34 seconds (2790.34 seconds total)