Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 11 17:29:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wle_32583/08_2023/7wle_32583.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wle_32583/08_2023/7wle_32583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wle_32583/08_2023/7wle_32583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wle_32583/08_2023/7wle_32583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wle_32583/08_2023/7wle_32583.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wle_32583/08_2023/7wle_32583.pdb" } resolution = 3.62 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= 0.001 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 6650 2.51 5 N 1690 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 295": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B ARG 295": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B ARG 685": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 10188 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5094 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 635} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5094 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 635} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 5.33, per 1000 atoms: 0.52 Number of scatterers: 10188 At special positions: 0 Unit cell: (84.056, 125.552, 123.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1806 8.00 N 1690 7.00 C 6650 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: 4.10 Conformation dependent library (CDL) restraints added in 1.7 seconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 64.3% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.603A pdb=" N GLN A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 57 through 69 removed outlier: 4.012A pdb=" N ALA A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.915A pdb=" N TYR A 78 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 109 removed outlier: 3.972A pdb=" N LEU A 107 " --> pdb=" O MET A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 Proline residue: A 123 - end of helix removed outlier: 3.921A pdb=" N VAL A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 155 removed outlier: 3.613A pdb=" N MET A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 206 removed outlier: 3.866A pdb=" N LEU A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 216 through 240 removed outlier: 3.924A pdb=" N ILE A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 268 through 292 Processing helix chain 'A' and resid 301 through 316 removed outlier: 3.662A pdb=" N ILE A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 345 through 351 removed outlier: 3.596A pdb=" N MET A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 370 Processing helix chain 'A' and resid 371 through 374 Processing helix chain 'A' and resid 380 through 396 removed outlier: 3.620A pdb=" N GLU A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 416 removed outlier: 3.508A pdb=" N THR A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 Processing helix chain 'A' and resid 448 through 458 removed outlier: 4.312A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 466 through 473 removed outlier: 4.311A pdb=" N ARG A 470 " --> pdb=" O CYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 515 removed outlier: 3.653A pdb=" N ALA A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ASP A 495 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 573 through 595 Processing helix chain 'A' and resid 669 through 685 Processing helix chain 'A' and resid 698 through 706 Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.567A pdb=" N ARG A 717 " --> pdb=" O ARG A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 removed outlier: 3.819A pdb=" N VAL A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.606A pdb=" N GLN B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.511A pdb=" N SER B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.999A pdb=" N ALA B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 109 removed outlier: 3.964A pdb=" N LEU B 107 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 130 Proline residue: B 123 - end of helix removed outlier: 3.960A pdb=" N VAL B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE B 130 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 155 removed outlier: 3.649A pdb=" N MET B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 206 removed outlier: 3.894A pdb=" N LEU B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 216 through 240 removed outlier: 3.672A pdb=" N ALA B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 268 through 292 Processing helix chain 'B' and resid 301 through 316 removed outlier: 3.683A pdb=" N ILE B 305 " --> pdb=" O PRO B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 344 No H-bonds generated for 'chain 'B' and resid 342 through 344' Processing helix chain 'B' and resid 345 through 351 removed outlier: 3.601A pdb=" N MET B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 370 Processing helix chain 'B' and resid 371 through 374 Processing helix chain 'B' and resid 380 through 396 removed outlier: 3.564A pdb=" N GLU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 Processing helix chain 'B' and resid 421 through 437 Processing helix chain 'B' and resid 448 through 458 removed outlier: 4.297A pdb=" N VAL B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 475 through 515 removed outlier: 3.792A pdb=" N ALA B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 494 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ASP B 495 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 669 through 685 Processing helix chain 'B' and resid 698 through 706 Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.547A pdb=" N ARG B 717 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 733 removed outlier: 3.825A pdb=" N VAL B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA2, first strand: chain 'A' and resid 530 through 532 removed outlier: 3.723A pdb=" N ASN A 519 " --> pdb=" O ARG A 549 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 549 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 547 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N SER A 523 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 12.636A pdb=" N VAL A 545 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS A 546 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A 658 " --> pdb=" O TYR A 691 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA4, first strand: chain 'B' and resid 530 through 532 removed outlier: 3.682A pdb=" N ASN B 519 " --> pdb=" O ARG B 549 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 549 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE B 547 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N SER B 523 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 12.675A pdb=" N VAL B 545 " --> pdb=" O SER B 523 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS B 546 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 658 " --> pdb=" O TYR B 691 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1614 1.32 - 1.44: 2671 1.44 - 1.56: 6041 1.56 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10390 Sorted by residual: bond pdb=" CA THR A 225 " pdb=" C THR A 225 " ideal model delta sigma weight residual 1.523 1.442 0.081 1.37e-02 5.33e+03 3.45e+01 bond pdb=" CA THR A 224 " pdb=" C THR A 224 " ideal model delta sigma weight residual 1.523 1.450 0.073 1.35e-02 5.49e+03 2.90e+01 bond pdb=" CA ALA A 228 " pdb=" C ALA A 228 " ideal model delta sigma weight residual 1.524 1.464 0.060 1.27e-02 6.20e+03 2.24e+01 bond pdb=" CA ALA A 227 " pdb=" C ALA A 227 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.37e-02 5.33e+03 2.15e+01 bond pdb=" N ALA A 228 " pdb=" CA ALA A 228 " ideal model delta sigma weight residual 1.459 1.410 0.049 1.19e-02 7.06e+03 1.69e+01 ... (remaining 10385 not shown) Histogram of bond angle deviations from ideal: 100.74 - 107.39: 302 107.39 - 114.04: 6127 114.04 - 120.70: 4418 120.70 - 127.35: 3199 127.35 - 134.00: 74 Bond angle restraints: 14120 Sorted by residual: angle pdb=" N GLY A 222 " pdb=" CA GLY A 222 " pdb=" C GLY A 222 " ideal model delta sigma weight residual 112.83 103.22 9.61 1.22e+00 6.72e-01 6.21e+01 angle pdb=" N ALA A 228 " pdb=" CA ALA A 228 " pdb=" C ALA A 228 " ideal model delta sigma weight residual 111.07 104.91 6.16 1.07e+00 8.73e-01 3.32e+01 angle pdb=" N ALA A 227 " pdb=" CA ALA A 227 " pdb=" C ALA A 227 " ideal model delta sigma weight residual 112.23 105.18 7.05 1.26e+00 6.30e-01 3.13e+01 angle pdb=" N THR A 225 " pdb=" CA THR A 225 " pdb=" C THR A 225 " ideal model delta sigma weight residual 112.23 105.81 6.42 1.26e+00 6.30e-01 2.60e+01 angle pdb=" N ALA A 226 " pdb=" CA ALA A 226 " pdb=" C ALA A 226 " ideal model delta sigma weight residual 112.89 108.24 4.65 1.24e+00 6.50e-01 1.41e+01 ... (remaining 14115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 5882 17.20 - 34.39: 242 34.39 - 51.59: 47 51.59 - 68.78: 3 68.78 - 85.98: 4 Dihedral angle restraints: 6178 sinusoidal: 2360 harmonic: 3818 Sorted by residual: dihedral pdb=" CA LEU A 694 " pdb=" C LEU A 694 " pdb=" N LEU A 695 " pdb=" CA LEU A 695 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU B 694 " pdb=" C LEU B 694 " pdb=" N LEU B 695 " pdb=" CA LEU B 695 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA LEU A 695 " pdb=" C LEU A 695 " pdb=" N GLN A 696 " pdb=" CA GLN A 696 " ideal model delta harmonic sigma weight residual -180.00 -161.84 -18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 6175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1464 0.055 - 0.110: 236 0.110 - 0.165: 12 0.165 - 0.220: 1 0.220 - 0.275: 1 Chirality restraints: 1714 Sorted by residual: chirality pdb=" CA PHE A 223 " pdb=" N PHE A 223 " pdb=" C PHE A 223 " pdb=" CB PHE A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA THR A 224 " pdb=" N THR A 224 " pdb=" C THR A 224 " pdb=" CB THR A 224 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA THR B 224 " pdb=" N THR B 224 " pdb=" C THR B 224 " pdb=" CB THR B 224 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 1711 not shown) Planarity restraints: 1756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 221 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C GLY A 221 " -0.034 2.00e-02 2.50e+03 pdb=" O GLY A 221 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 222 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 75 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO B 76 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 653 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO B 654 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 654 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 654 " -0.020 5.00e-02 4.00e+02 ... (remaining 1753 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2032 2.77 - 3.30: 10943 3.30 - 3.84: 17076 3.84 - 4.37: 19505 4.37 - 4.90: 32536 Nonbonded interactions: 82092 Sorted by model distance: nonbonded pdb=" O HIS A 135 " pdb=" OG1 THR A 410 " model vdw 2.240 2.440 nonbonded pdb=" O HIS B 135 " pdb=" OG1 THR B 410 " model vdw 2.248 2.440 nonbonded pdb=" NE2 GLN B 101 " pdb=" OG SER B 408 " model vdw 2.249 2.520 nonbonded pdb=" NE2 GLN A 101 " pdb=" OG SER A 408 " model vdw 2.260 2.520 nonbonded pdb=" O VAL B 453 " pdb=" ND2 ASN B 457 " model vdw 2.272 2.520 ... (remaining 82087 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 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: 7.330 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.690 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 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 0.081 10390 Z= 0.198 Angle : 0.499 9.614 14120 Z= 0.305 Chirality : 0.038 0.275 1714 Planarity : 0.004 0.039 1756 Dihedral : 9.906 85.978 3718 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer Outliers : 5.25 % 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: -3.62 (0.19), residues: 1316 helix: -1.46 (0.16), residues: 808 sheet: -2.61 (0.85), residues: 20 loop : -4.00 (0.21), residues: 488 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 409 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 17 residues processed: 450 average time/residue: 0.2688 time to fit residues: 158.9911 Evaluate side-chains 321 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 304 time to evaluate : 1.250 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.0980 time to fit residues: 4.7296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.0170 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 0.0980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN A 262 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN A 383 GLN A 446 GLN A 457 ASN A 474 GLN A 684 GLN B 34 GLN B 262 GLN B 318 ASN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN B 474 GLN B 535 HIS B 684 GLN B 689 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 10390 Z= 0.221 Angle : 0.662 10.610 14120 Z= 0.334 Chirality : 0.043 0.192 1714 Planarity : 0.004 0.034 1756 Dihedral : 3.764 22.763 1414 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.22), residues: 1316 helix: -0.15 (0.18), residues: 808 sheet: -0.24 (1.01), residues: 20 loop : -3.26 (0.25), residues: 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 321 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 12 residues processed: 340 average time/residue: 0.2501 time to fit residues: 114.2143 Evaluate side-chains 301 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 289 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1171 time to fit residues: 3.9115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.0670 chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 33 optimal weight: 0.0870 chunk 120 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 40 optimal weight: 0.0870 chunk 96 optimal weight: 1.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN A 723 HIS B 689 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 10390 Z= 0.199 Angle : 0.650 8.407 14120 Z= 0.329 Chirality : 0.042 0.146 1714 Planarity : 0.004 0.040 1756 Dihedral : 3.961 22.656 1414 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer Outliers : 2.76 % 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: -1.36 (0.23), residues: 1316 helix: 0.22 (0.18), residues: 806 sheet: 0.23 (1.04), residues: 20 loop : -2.92 (0.26), residues: 490 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 299 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 8 residues processed: 316 average time/residue: 0.2647 time to fit residues: 111.2799 Evaluate side-chains 288 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 280 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0949 time to fit residues: 2.9275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 62 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN A 457 ASN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 10390 Z= 0.239 Angle : 0.664 8.472 14120 Z= 0.340 Chirality : 0.042 0.161 1714 Planarity : 0.004 0.037 1756 Dihedral : 4.114 23.133 1414 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer Outliers : 2.85 % 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: -1.02 (0.23), residues: 1316 helix: 0.37 (0.18), residues: 808 sheet: 0.66 (1.03), residues: 20 loop : -2.57 (0.27), residues: 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 311 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 18 residues processed: 328 average time/residue: 0.2723 time to fit residues: 118.9125 Evaluate side-chains 303 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 285 time to evaluate : 1.210 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.1647 time to fit residues: 6.1651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 0.0170 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 0.0040 overall best weight: 0.4830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN A 457 ASN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 10390 Z= 0.218 Angle : 0.677 9.035 14120 Z= 0.342 Chirality : 0.043 0.163 1714 Planarity : 0.004 0.044 1756 Dihedral : 4.190 22.619 1414 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer Outliers : 2.22 % 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: -1.04 (0.23), residues: 1316 helix: 0.36 (0.18), residues: 828 sheet: 0.77 (1.03), residues: 20 loop : -2.73 (0.27), residues: 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 307 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 315 average time/residue: 0.2751 time to fit residues: 115.4640 Evaluate side-chains 297 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 285 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1015 time to fit residues: 3.6658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 10390 Z= 0.256 Angle : 0.699 8.629 14120 Z= 0.357 Chirality : 0.043 0.172 1714 Planarity : 0.004 0.039 1756 Dihedral : 4.279 23.971 1414 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 2.05 % 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: -0.98 (0.23), residues: 1316 helix: 0.44 (0.18), residues: 824 sheet: 0.82 (1.02), residues: 20 loop : -2.75 (0.27), residues: 472 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 285 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 6 residues processed: 298 average time/residue: 0.2578 time to fit residues: 103.1550 Evaluate side-chains 275 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 269 time to evaluate : 1.062 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1692 time to fit residues: 3.0119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN A 324 ASN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.096 10390 Z= 0.272 Angle : 0.734 8.668 14120 Z= 0.376 Chirality : 0.045 0.221 1714 Planarity : 0.004 0.040 1756 Dihedral : 4.391 23.587 1414 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer Outliers : 2.14 % 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: -0.85 (0.23), residues: 1316 helix: 0.48 (0.18), residues: 830 sheet: 0.81 (1.01), residues: 20 loop : -2.60 (0.28), residues: 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 279 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 290 average time/residue: 0.2740 time to fit residues: 107.6493 Evaluate side-chains 285 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 274 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0953 time to fit residues: 3.5082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 10390 Z= 0.288 Angle : 0.760 12.116 14120 Z= 0.388 Chirality : 0.045 0.212 1714 Planarity : 0.004 0.041 1756 Dihedral : 4.484 25.794 1414 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.24), residues: 1316 helix: 0.56 (0.19), residues: 810 sheet: 0.76 (1.00), residues: 20 loop : -2.40 (0.28), residues: 486 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 287 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 289 average time/residue: 0.2700 time to fit residues: 104.2682 Evaluate side-chains 284 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 278 time to evaluate : 1.081 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0976 time to fit residues: 2.6846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 121 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 76 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 GLN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 10390 Z= 0.278 Angle : 0.781 14.214 14120 Z= 0.395 Chirality : 0.045 0.215 1714 Planarity : 0.004 0.049 1756 Dihedral : 4.579 25.888 1414 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer Outliers : 1.25 % 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: -0.76 (0.23), residues: 1316 helix: 0.52 (0.18), residues: 832 sheet: 0.49 (0.97), residues: 20 loop : -2.49 (0.28), residues: 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 283 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 290 average time/residue: 0.2479 time to fit residues: 97.4177 Evaluate side-chains 285 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 277 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0943 time to fit residues: 2.8539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 121 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS B 322 ASN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 10390 Z= 0.290 Angle : 0.820 14.468 14120 Z= 0.414 Chirality : 0.046 0.214 1714 Planarity : 0.004 0.048 1756 Dihedral : 4.744 25.952 1414 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer Outliers : 0.18 % 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: -0.83 (0.23), residues: 1316 helix: 0.45 (0.18), residues: 842 sheet: 0.55 (0.91), residues: 20 loop : -2.53 (0.28), residues: 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 277 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 277 average time/residue: 0.2801 time to fit residues: 104.7195 Evaluate side-chains 268 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 267 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0922 time to fit residues: 1.7221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 92 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 75 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.123256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106220 restraints weight = 21177.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.109373 restraints weight = 10486.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.111375 restraints weight = 6207.762| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 10390 Z= 0.271 Angle : 0.825 13.900 14120 Z= 0.418 Chirality : 0.046 0.273 1714 Planarity : 0.005 0.052 1756 Dihedral : 4.774 25.817 1414 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer Outliers : 0.53 % 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: -0.82 (0.23), residues: 1316 helix: 0.44 (0.18), residues: 840 sheet: 0.72 (0.99), residues: 20 loop : -2.48 (0.29), residues: 456 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2638.25 seconds wall clock time: 48 minutes 28.18 seconds (2908.18 seconds total)