Starting phenix.real_space_refine (version: dev) on Mon Dec 12 06:23:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o24_12698/12_2022/7o24_12698.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o24_12698/12_2022/7o24_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o24_12698/12_2022/7o24_12698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o24_12698/12_2022/7o24_12698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o24_12698/12_2022/7o24_12698.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o24_12698/12_2022/7o24_12698.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 436": "OE1" <-> "OE2" Residue "A GLU 492": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 5.85, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.19 Conformation dependent library (CDL) restraints added in 1.5 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: 2.88 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: 3.11 Time building geometry restraints manager: 4.53 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: 99.99 - 106.81: 591 106.81 - 113.64: 5445 113.64 - 120.47: 3538 120.47 - 127.30: 3578 127.30 - 134.12: 194 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: 4841 16.98 - 33.97: 485 33.97 - 50.95: 176 50.95 - 67.93: 66 67.93 - 84.92: 14 Dihedral angle restraints: 5582 sinusoidal: 2368 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 5579 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 2.520 nonbonded pdb=" O VAL C 621 " pdb=" OG1 THR C 627 " model vdw 2.222 2.440 nonbonded pdb=" OG1 THR A 199 " pdb=" O ALA A 270 " model vdw 2.244 2.440 nonbonded pdb=" O LEU A 533 " pdb=" OG1 THR A 536 " model vdw 2.249 2.440 nonbonded pdb=" O THR A 550 " pdb=" OG SER A 553 " model vdw 2.253 2.440 ... (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 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 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. 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: 3.180 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: 13.850 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.080 Process input model: 30.480 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 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 : 17.151 84.917 3492 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.17 % Favored : 96.64 % Rotamer Outliers : 1.38 % 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 165 average time/residue: 0.2034 time to fit residues: 47.3417 Evaluate side-chains 119 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2916 time to fit residues: 3.9884 ------------------------------------------------------------------------------- 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: 7.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.3980 chunk 100 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 325 HIS A 447 ASN ** C 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9637 Z= 0.159 Angle : 0.548 6.491 13346 Z= 0.284 Chirality : 0.040 0.145 1545 Planarity : 0.004 0.044 1534 Dihedral : 15.795 59.972 1606 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.08 % Favored : 96.74 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1072 helix: 1.62 (0.26), residues: 427 sheet: 0.24 (0.38), residues: 178 loop : -1.52 (0.27), residues: 467 *********************** 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 159 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.1663 time to fit residues: 39.5546 Evaluate side-chains 110 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 99 optimal weight: 0.3980 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 325 HIS A 447 ASN B 187 GLN B 378 GLN ** C 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1563 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= 0.251 Angle : 0.600 8.179 13346 Z= 0.314 Chirality : 0.041 0.150 1545 Planarity : 0.004 0.048 1534 Dihedral : 15.756 59.929 1606 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.48 % Favored : 95.34 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1072 helix: 1.46 (0.26), residues: 428 sheet: -0.08 (0.37), residues: 178 loop : -1.62 (0.27), residues: 466 *********************** 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 147 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 0.981 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.1785 time to fit residues: 38.9218 Evaluate side-chains 103 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.0170 chunk 52 optimal weight: 0.0770 chunk 11 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 28 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 325 HIS A 447 ASN B 125 GLN B 378 GLN B 443 ASN C 619 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9637 Z= 0.151 Angle : 0.564 8.044 13346 Z= 0.287 Chirality : 0.041 0.230 1545 Planarity : 0.004 0.045 1534 Dihedral : 15.640 59.464 1606 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.26 % Favored : 96.55 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1072 helix: 1.62 (0.26), residues: 429 sheet: 0.15 (0.37), residues: 178 loop : -1.56 (0.27), residues: 465 *********************** 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 160 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1843 time to fit residues: 43.5315 Evaluate side-chains 109 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.0970 chunk 91 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 96 optimal weight: 40.0000 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 overall best weight: 3.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 325 HIS A 447 ASN B 378 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 9637 Z= 0.300 Angle : 0.632 11.556 13346 Z= 0.329 Chirality : 0.041 0.156 1545 Planarity : 0.004 0.038 1534 Dihedral : 15.651 59.975 1606 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.29 % Favored : 95.52 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1072 helix: 1.53 (0.26), residues: 428 sheet: -0.17 (0.37), residues: 180 loop : -1.68 (0.27), residues: 464 *********************** 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 138 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.1797 time to fit residues: 36.7669 Evaluate side-chains 100 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.062 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.0020 chunk 107 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 447 ASN C 619 HIS ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 9637 Z= 0.157 Angle : 0.564 8.543 13346 Z= 0.287 Chirality : 0.040 0.172 1545 Planarity : 0.004 0.039 1534 Dihedral : 15.604 59.721 1606 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.54 % Favored : 96.27 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1072 helix: 1.66 (0.26), residues: 427 sheet: 0.09 (0.38), residues: 179 loop : -1.65 (0.27), residues: 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.1723 time to fit residues: 37.5802 Evaluate side-chains 110 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 0.0270 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 63 optimal weight: 7.9990 chunk 32 optimal weight: 0.0070 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 447 ASN B 474 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 9637 Z= 0.151 Angle : 0.561 8.670 13346 Z= 0.281 Chirality : 0.040 0.152 1545 Planarity : 0.004 0.037 1534 Dihedral : 15.519 59.440 1606 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.64 % Favored : 96.18 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1072 helix: 1.70 (0.26), residues: 427 sheet: 0.13 (0.38), residues: 181 loop : -1.63 (0.27), residues: 464 *********************** 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 150 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.161 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.1739 time to fit residues: 38.7330 Evaluate side-chains 115 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 0.0050 chunk 93 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 447 ASN B 378 GLN B 443 ASN ** C 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9637 Z= 0.182 Angle : 0.564 8.659 13346 Z= 0.288 Chirality : 0.040 0.179 1545 Planarity : 0.004 0.039 1534 Dihedral : 15.525 59.779 1606 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.20 % Favored : 95.62 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1072 helix: 1.71 (0.26), residues: 427 sheet: 0.11 (0.38), residues: 178 loop : -1.64 (0.27), residues: 467 *********************** 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 fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 1.055 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1755 time to fit residues: 36.3248 Evaluate side-chains 108 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 0.0970 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 447 ASN B 378 GLN ** C 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 9637 Z= 0.230 Angle : 0.601 8.872 13346 Z= 0.309 Chirality : 0.041 0.179 1545 Planarity : 0.004 0.039 1534 Dihedral : 15.635 59.997 1606 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.13 % Favored : 94.68 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1072 helix: 1.51 (0.26), residues: 435 sheet: -0.10 (0.38), residues: 180 loop : -1.72 (0.27), residues: 457 *********************** 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 140 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.096 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.1813 time to fit residues: 37.5489 Evaluate side-chains 107 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 447 ASN A 506 HIS B 378 GLN B 443 ASN ** C 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 9637 Z= 0.237 Angle : 0.608 8.993 13346 Z= 0.313 Chirality : 0.041 0.181 1545 Planarity : 0.004 0.039 1534 Dihedral : 15.717 59.822 1606 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.04 % Favored : 94.78 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1072 helix: 1.46 (0.26), residues: 433 sheet: -0.13 (0.38), residues: 178 loop : -1.78 (0.27), residues: 461 ********************** 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 131 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.110 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1748 time to fit residues: 34.4892 Evaluate side-chains 104 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 447 ASN ** C 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.063034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.051744 restraints weight = 48748.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.053371 restraints weight = 27477.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.054496 restraints weight = 17784.275| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2552 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= 0.164 Angle : 0.574 7.442 13346 Z= 0.290 Chirality : 0.041 0.180 1545 Planarity : 0.004 0.039 1534 Dihedral : 15.665 59.569 1606 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.20 % Favored : 95.62 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.26), residues: 1072 helix: 1.55 (0.26), residues: 433 sheet: 0.09 (0.38), residues: 178 loop : -1.73 (0.27), residues: 461 =============================================================================== Job complete usr+sys time: 1796.98 seconds wall clock time: 33 minutes 44.25 seconds (2024.25 seconds total)