Starting phenix.real_space_refine (version: dev) on Mon Apr 4 23:54:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvq_23540/04_2022/7lvq_23540_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvq_23540/04_2022/7lvq_23540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvq_23540/04_2022/7lvq_23540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvq_23540/04_2022/7lvq_23540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvq_23540/04_2022/7lvq_23540_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvq_23540/04_2022/7lvq_23540_updated.pdb" } resolution = 2.9 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= 0.004 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 "B TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 9767 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3458 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 441, 3446 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Conformer: "B" Number of residues, atoms: 441, 3446 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} bond proxies already assigned to first conformer: 3510 Chain: "B" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3376 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 19, 'TRANS': 408, 'PCIS': 1} Chain: "K" Number of atoms: 2778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2778 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 11, 'TRANS': 344} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GTP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 108 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 108 " occ=0.50 Time building chain proxies: 7.38, per 1000 atoms: 0.76 Number of scatterers: 9767 At special positions: 0 Unit cell: (110.37, 75.561, 112.068, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 8 15.00 Mg 2 11.99 O 1909 8.00 N 1663 7.00 C 6123 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: 4.28 Conformation dependent library (CDL) restraints added in 2.0 seconds 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2276 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 11 sheets defined 39.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 11 through 28 Processing helix chain 'A' and resid 37 through 40 Processing helix chain 'A' and resid 72 through 79 removed outlier: 4.372A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.570A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 225 through 238 removed outlier: 4.686A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 243 No H-bonds generated for 'chain 'A' and resid 240 through 243' Processing helix chain 'A' and resid 278 through 281 No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.651A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 383 through 399 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.227A pdb=" N GLU A 420 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 removed outlier: 4.135A pdb=" N ASP B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B 27 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS B 28 " --> pdb=" O ILE B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 73 through 77 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 102 through 105 No H-bonds generated for 'chain 'B' and resid 102 through 105' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 143 through 158 Processing helix chain 'B' and resid 181 through 192 Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 222 through 240 removed outlier: 3.765A pdb=" N ALA B 231 " --> pdb=" O HIS B 227 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 372 through 389 removed outlier: 4.429A pdb=" N LYS B 379 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 removed outlier: 4.194A pdb=" N THR B 399 " --> pdb=" O HIS B 396 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY B 400 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 423 Processing helix chain 'K' and resid 405 through 410 Processing helix chain 'K' and resid 455 through 472 removed outlier: 4.858A pdb=" N ALA K 464 " --> pdb=" O GLU K 460 " (cutoff:3.500A) Proline residue: K 465 - end of helix Processing helix chain 'K' and resid 488 through 492 Processing helix chain 'K' and resid 501 through 514 Processing helix chain 'K' and resid 577 through 590 Processing helix chain 'K' and resid 653 through 680 removed outlier: 4.088A pdb=" N GLY K 658 " --> pdb=" O ARG K 654 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN K 680 " --> pdb=" O SER K 676 " (cutoff:3.500A) Processing helix chain 'K' and resid 688 through 690 No H-bonds generated for 'chain 'K' and resid 688 through 690' Processing helix chain 'K' and resid 692 through 696 Processing helix chain 'K' and resid 698 through 701 No H-bonds generated for 'chain 'K' and resid 698 through 701' Processing helix chain 'K' and resid 717 through 735 removed outlier: 5.555A pdb=" N GLU K 721 " --> pdb=" O SER K 718 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG K 734 " --> pdb=" O THR K 731 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 65 through 68 removed outlier: 8.302A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ILE A 5 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE A 135 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE A 7 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL A 137 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A 9 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS A 139 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 269 through 272 Processing sheet with id= D, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.616A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N CYS B 129 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL B 5 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N GLN B 131 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 12.614A pdb=" N ILE B 7 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N PHE B 133 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 12.349A pdb=" N ALA B 9 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N LEU B 135 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LEU B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N HIS B 137 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE B 167 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU B 198 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N SER B 168 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR B 200 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 51 through 53 Processing sheet with id= F, first strand: chain 'K' and resid 391 through 393 Processing sheet with id= G, first strand: chain 'K' and resid 395 through 401 removed outlier: 4.378A pdb=" N LEU K 611 " --> pdb=" O ILE K 634 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU K 525 " --> pdb=" O VAL K 574 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 416 through 419 Processing sheet with id= I, first strand: chain 'K' and resid 530 through 533 Processing sheet with id= J, first strand: chain 'K' and resid 555 through 559 removed outlier: 4.332A pdb=" N ARG K 555 " --> pdb=" O GLU K 567 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 612 through 616 385 hydrogen bonds defined for protein. 939 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: 2.85 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1652 1.28 - 1.42: 2653 1.42 - 1.55: 5561 1.55 - 1.68: 16 1.68 - 1.81: 101 Bond restraints: 9983 Sorted by residual: bond pdb=" C VAL B 169 " pdb=" N MET B 170 " ideal model delta sigma weight residual 1.331 1.153 0.177 1.48e-02 4.57e+03 1.44e+02 bond pdb=" C HIS K 427 " pdb=" N PRO K 428 " ideal model delta sigma weight residual 1.337 1.408 -0.071 1.11e-02 8.12e+03 4.13e+01 bond pdb=" C22 TA1 B 502 " pdb=" O09 TA1 B 502 " ideal model delta sigma weight residual 1.335 1.457 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C12 TA1 B 502 " pdb=" O04 TA1 B 502 " ideal model delta sigma weight residual 1.337 1.454 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C27 TA1 B 502 " pdb=" O11 TA1 B 502 " ideal model delta sigma weight residual 1.329 1.445 -0.116 2.00e-02 2.50e+03 3.39e+01 ... (remaining 9978 not shown) Histogram of bond angle deviations from ideal: 87.35 - 97.20: 14 97.20 - 107.04: 366 107.04 - 116.88: 6658 116.88 - 126.72: 6398 126.72 - 136.56: 126 Bond angle restraints: 13562 Sorted by residual: angle pdb=" C PRO B 357 " pdb=" N PRO B 358 " pdb=" CA PRO B 358 " ideal model delta sigma weight residual 120.03 126.43 -6.40 9.90e-01 1.02e+00 4.18e+01 angle pdb=" N TYR A 103 " pdb=" CA TYR A 103 " pdb=" C TYR A 103 " ideal model delta sigma weight residual 111.82 104.64 7.18 1.16e+00 7.43e-01 3.83e+01 angle pdb=" C LYS A 112 " pdb=" N GLU A 113 " pdb=" CA GLU A 113 " ideal model delta sigma weight residual 126.45 136.03 -9.58 1.77e+00 3.19e-01 2.93e+01 angle pdb=" CA HIS K 427 " pdb=" C HIS K 427 " pdb=" O HIS K 427 " ideal model delta sigma weight residual 120.69 114.60 6.09 1.13e+00 7.83e-01 2.90e+01 angle pdb=" N GLU B 22 " pdb=" CA GLU B 22 " pdb=" C GLU B 22 " ideal model delta sigma weight residual 113.20 107.73 5.47 1.21e+00 6.83e-01 2.05e+01 ... (remaining 13557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 5811 35.22 - 70.44: 96 70.44 - 105.66: 7 105.66 - 140.88: 2 140.88 - 176.10: 2 Dihedral angle restraints: 5918 sinusoidal: 2369 harmonic: 3549 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -114.63 -176.10 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -37.18 141.77 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" O5' GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PA GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 274.12 144.48 129.65 1 2.00e+01 2.50e-03 3.93e+01 ... (remaining 5915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 1261 0.126 - 0.252: 215 0.252 - 0.377: 14 0.377 - 0.503: 2 0.503 - 0.629: 1 Chirality restraints: 1493 Sorted by residual: chirality pdb=" C18 TA1 B 502 " pdb=" C10 TA1 B 502 " pdb=" C17 TA1 B 502 " pdb=" C20 TA1 B 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.53 -0.63 2.00e-01 2.50e+01 9.89e+00 chirality pdb=" CA ARG B 276 " pdb=" N ARG B 276 " pdb=" C ARG B 276 " pdb=" CB ARG B 276 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CB VAL A 68 " pdb=" CA VAL A 68 " pdb=" CG1 VAL A 68 " pdb=" CG2 VAL A 68 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 1490 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS K 427 " 0.037 2.00e-02 2.50e+03 7.66e-02 5.87e+01 pdb=" C HIS K 427 " -0.132 2.00e-02 2.50e+03 pdb=" O HIS K 427 " 0.050 2.00e-02 2.50e+03 pdb=" N PRO K 428 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 401 " 0.509 9.50e-02 1.11e+02 2.28e-01 3.23e+01 pdb=" NE ARG K 401 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG K 401 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG K 401 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG K 401 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 275 " -0.023 2.00e-02 2.50e+03 4.52e-02 2.05e+01 pdb=" C SER B 275 " 0.078 2.00e-02 2.50e+03 pdb=" O SER B 275 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG B 276 " -0.028 2.00e-02 2.50e+03 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 60 2.52 - 3.11: 7426 3.11 - 3.71: 14686 3.71 - 4.30: 21617 4.30 - 4.90: 37086 Nonbonded interactions: 80875 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.920 2.170 nonbonded pdb=" OG SER K 528 " pdb=" OG1 THR K 610 " model vdw 2.002 2.440 nonbonded pdb=" O06 TA1 B 502 " pdb=" O07 TA1 B 502 " model vdw 2.057 2.440 nonbonded pdb=" OE2 GLU A 71 " pdb="MG MG A 502 " model vdw 2.071 2.170 nonbonded pdb=" O SER B 275 " pdb=" OG SER B 275 " model vdw 2.106 2.440 ... (remaining 80870 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 6123 2.51 5 N 1663 2.21 5 O 1909 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.670 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: 14.630 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 32.400 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 0.024 0.197 9983 Z= 1.593 Angle : 1.332 12.921 13562 Z= 0.749 Chirality : 0.094 0.629 1493 Planarity : 0.011 0.228 1752 Dihedral : 14.763 176.104 3642 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.39 % Favored : 93.52 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.20 (0.20), residues: 1223 helix: -2.02 (0.20), residues: 477 sheet: -1.60 (0.31), residues: 234 loop : -2.33 (0.24), residues: 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 220 time to evaluate : 1.083 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 222 average time/residue: 1.0952 time to fit residues: 263.1307 Evaluate side-chains 179 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1063 time to fit residues: 1.7463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.0770 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 109 optimal weight: 10.0000 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN K 549 GLN K 588 ASN K 649 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 9983 Z= 0.235 Angle : 0.607 8.634 13562 Z= 0.307 Chirality : 0.045 0.202 1493 Planarity : 0.005 0.051 1752 Dihedral : 9.779 165.503 1369 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.60 (0.22), residues: 1223 helix: -0.33 (0.23), residues: 478 sheet: -0.86 (0.31), residues: 238 loop : -1.79 (0.25), residues: 507 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 238 time to evaluate : 1.128 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 247 average time/residue: 1.0003 time to fit residues: 269.3457 Evaluate side-chains 224 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 215 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.0955 time to fit residues: 2.3293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 chunk 74 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN B 52 ASN B 100 ASN B 131 GLN B 348 ASN B 384 GLN K 649 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 9983 Z= 0.221 Angle : 0.574 7.858 13562 Z= 0.287 Chirality : 0.044 0.194 1493 Planarity : 0.005 0.045 1752 Dihedral : 9.318 162.291 1369 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.95 (0.24), residues: 1223 helix: 0.29 (0.25), residues: 476 sheet: -0.54 (0.32), residues: 231 loop : -1.49 (0.26), residues: 516 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 226 time to evaluate : 1.211 Fit side-chains outliers start: 26 outliers final: 15 residues processed: 234 average time/residue: 1.0691 time to fit residues: 270.9539 Evaluate side-chains 222 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 207 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 7 residues processed: 8 average time/residue: 0.2651 time to fit residues: 4.3554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN A 372 GLN B 43 GLN B 52 ASN B 131 GLN B 191 GLN B 195 ASN B 348 ASN K 649 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 9983 Z= 0.263 Angle : 0.577 9.500 13562 Z= 0.288 Chirality : 0.045 0.211 1493 Planarity : 0.005 0.041 1752 Dihedral : 9.215 159.117 1369 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.68 (0.24), residues: 1223 helix: 0.49 (0.25), residues: 480 sheet: -0.38 (0.33), residues: 231 loop : -1.34 (0.26), residues: 512 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 229 time to evaluate : 0.981 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 244 average time/residue: 1.0878 time to fit residues: 286.7839 Evaluate side-chains 237 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 219 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 10 residues processed: 9 average time/residue: 0.4709 time to fit residues: 6.5501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 99 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 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 ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN A 372 GLN B 52 ASN B 131 GLN B 348 ASN K 649 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9983 Z= 0.234 Angle : 0.556 8.604 13562 Z= 0.280 Chirality : 0.044 0.197 1493 Planarity : 0.004 0.039 1752 Dihedral : 9.027 153.700 1369 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.43 (0.24), residues: 1223 helix: 0.68 (0.25), residues: 479 sheet: -0.20 (0.33), residues: 231 loop : -1.20 (0.27), residues: 513 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 221 time to evaluate : 1.165 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 18 residues processed: 237 average time/residue: 1.1034 time to fit residues: 282.7931 Evaluate side-chains 231 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 213 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 10 residues processed: 9 average time/residue: 0.8937 time to fit residues: 10.4458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 0.0870 chunk 28 optimal weight: 0.2980 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 356 ASN A 372 GLN B 52 ASN B 131 GLN B 298 ASN B 348 ASN K 649 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9983 Z= 0.201 Angle : 0.547 8.300 13562 Z= 0.274 Chirality : 0.043 0.188 1493 Planarity : 0.004 0.037 1752 Dihedral : 8.833 148.853 1369 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.24), residues: 1223 helix: 0.86 (0.25), residues: 477 sheet: -0.17 (0.33), residues: 236 loop : -1.10 (0.27), residues: 510 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 223 time to evaluate : 1.189 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 239 average time/residue: 1.1067 time to fit residues: 286.6992 Evaluate side-chains 233 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 218 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 5 average time/residue: 0.7326 time to fit residues: 5.6811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 372 GLN B 52 ASN B 131 GLN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 649 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9983 Z= 0.273 Angle : 0.575 8.047 13562 Z= 0.289 Chirality : 0.045 0.182 1493 Planarity : 0.004 0.038 1752 Dihedral : 8.865 146.570 1369 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.18 (0.24), residues: 1223 helix: 0.78 (0.25), residues: 479 sheet: 0.01 (0.34), residues: 238 loop : -1.00 (0.28), residues: 506 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 210 time to evaluate : 0.992 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 225 average time/residue: 1.1363 time to fit residues: 275.9900 Evaluate side-chains 222 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 6 average time/residue: 0.9152 time to fit residues: 7.4896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 0.0370 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 0.0000 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 372 GLN B 256 ASN K 588 ASN K 649 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9983 Z= 0.217 Angle : 0.565 11.626 13562 Z= 0.281 Chirality : 0.044 0.184 1493 Planarity : 0.004 0.037 1752 Dihedral : 8.766 142.858 1369 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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 (0.25), residues: 1223 helix: 0.86 (0.25), residues: 480 sheet: -0.04 (0.34), residues: 236 loop : -0.90 (0.28), residues: 507 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 206 time to evaluate : 1.125 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 217 average time/residue: 1.0861 time to fit residues: 255.3804 Evaluate side-chains 214 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 200 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.6573 time to fit residues: 4.4495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 47 optimal weight: 0.0040 chunk 85 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 102 optimal weight: 0.0270 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 overall best weight: 0.2650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 372 GLN B 52 ASN B 131 GLN B 165 ASN B 204 ASN ** K 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 649 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9983 Z= 0.158 Angle : 0.550 10.332 13562 Z= 0.274 Chirality : 0.043 0.193 1493 Planarity : 0.004 0.037 1752 Dihedral : 8.465 137.000 1369 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.25), residues: 1223 helix: 1.00 (0.25), residues: 480 sheet: 0.03 (0.34), residues: 236 loop : -0.91 (0.28), residues: 507 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 204 time to evaluate : 1.190 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 215 average time/residue: 1.0927 time to fit residues: 254.3118 Evaluate side-chains 210 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 200 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.1881 time to fit residues: 2.3745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 356 ASN A 372 GLN B 52 ASN B 131 GLN B 204 ASN ** K 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 649 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 9983 Z= 0.341 Angle : 0.627 9.902 13562 Z= 0.313 Chirality : 0.046 0.199 1493 Planarity : 0.005 0.040 1752 Dihedral : 8.831 140.228 1369 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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 (0.25), residues: 1223 helix: 0.80 (0.25), residues: 482 sheet: 0.17 (0.35), residues: 233 loop : -0.92 (0.28), residues: 508 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 204 time to evaluate : 1.127 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 214 average time/residue: 1.1281 time to fit residues: 261.5873 Evaluate side-chains 209 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 200 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.2545 time to fit residues: 1.9257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 98 optimal weight: 0.0970 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 5 optimal weight: 0.0670 chunk 69 optimal weight: 0.6980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 356 ASN A 372 GLN B 204 ASN ** K 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 649 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.138664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.112160 restraints weight = 16951.190| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.24 r_work: 0.3455 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work: 0.3424 rms_B_bonded: 2.05 restraints_weight: 0.1250 r_work: 0.3407 rms_B_bonded: 2.16 restraints_weight: 0.0625 r_work: 0.3389 rms_B_bonded: 2.31 restraints_weight: 0.0312 r_work: 0.3369 rms_B_bonded: 2.51 restraints_weight: 0.0156 r_work: 0.3347 rms_B_bonded: 2.75 restraints_weight: 0.0078 r_work: 0.3323 rms_B_bonded: 3.05 restraints_weight: 0.0039 r_work: 0.3296 rms_B_bonded: 3.41 restraints_weight: 0.0020 r_work: 0.3266 rms_B_bonded: 3.83 restraints_weight: 0.0010 r_work: 0.3232 rms_B_bonded: 4.32 restraints_weight: 0.0005 r_work: 0.3195 rms_B_bonded: 4.90 restraints_weight: 0.0002 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9983 Z= 0.178 Angle : 0.571 9.864 13562 Z= 0.283 Chirality : 0.043 0.201 1493 Planarity : 0.004 0.036 1752 Dihedral : 8.592 137.778 1369 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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 (0.25), residues: 1223 helix: 0.99 (0.25), residues: 478 sheet: -0.05 (0.34), residues: 236 loop : -0.83 (0.28), residues: 509 =============================================================================== Job complete usr+sys time: 4414.06 seconds wall clock time: 78 minutes 51.78 seconds (4731.78 seconds total)