Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 22:42:19 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvq_23540/12_2021/7lvq_23540_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvq_23540/12_2021/7lvq_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_23540/12_2021/7lvq_23540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvq_23540/12_2021/7lvq_23540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvq_23540/12_2021/7lvq_23540_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvq_23540/12_2021/7lvq_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 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-1.20rc4-4434/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 Amimo 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: 4.40 Conformation dependent library (CDL) restraints added in 1.9 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: 1.07 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: 2.74 Time building geometry restraints manager: 4.74 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=" C4 ANP K 802 " pdb=" C5 ANP K 802 " ideal model delta sigma weight residual 1.386 1.457 -0.071 1.00e-02 1.00e+04 5.04e+01 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=" C5 ANP K 802 " pdb=" C6 ANP K 802 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.54e+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=" C4 ANP K 802 " pdb=" N9 ANP K 802 " pdb=" C8 ANP K 802 " ideal model delta sigma weight residual 105.70 110.52 -4.82 4.55e-01 4.83e+00 1.12e+02 angle pdb=" C5 ANP K 802 " pdb=" C4 ANP K 802 " pdb=" N3 ANP K 802 " ideal model delta sigma weight residual 126.80 119.19 7.61 7.41e-01 1.82e+00 1.05e+02 angle pdb=" C5 ANP K 802 " pdb=" N7 ANP K 802 " pdb=" C8 ANP K 802 " ideal model delta sigma weight residual 103.67 107.51 -3.84 4.26e-01 5.51e+00 8.12e+01 angle pdb=" C4 ANP K 802 " pdb=" C5 ANP K 802 " pdb=" N7 ANP K 802 " ideal model delta sigma weight residual 110.73 106.95 3.78 4.52e-01 4.89e+00 6.98e+01 angle pdb=" N3 ANP K 802 " pdb=" C4 ANP K 802 " pdb=" N9 ANP K 802 " ideal model delta sigma weight residual 127.16 135.71 -8.55 1.06e+00 8.92e-01 6.52e+01 ... (remaining 13557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 5816 35.22 - 70.44: 97 70.44 - 105.66: 6 105.66 - 140.88: 2 140.88 - 176.10: 3 Dihedral angle restraints: 5924 sinusoidal: 2375 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 5921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 1264 0.126 - 0.252: 214 0.252 - 0.377: 14 0.377 - 0.503: 2 0.503 - 0.629: 1 Chirality restraints: 1495 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 1492 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 Write .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.690 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 31.920 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.730 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 63.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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= 1.590 Angle : 1.326 11.940 13562 Z= 0.775 Chirality : 0.094 0.629 1495 Planarity : 0.011 0.228 1752 Dihedral : 14.937 176.104 3648 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 : 1.001 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 222 average time/residue: 1.0950 time to fit residues: 262.7237 Evaluate side-chains 179 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0905 time to fit residues: 1.7481 ------------------------------------------------------------------------------- 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: 0.7756 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 9983 Z= 0.258 Angle : 0.634 9.176 13562 Z= 0.322 Chirality : 0.046 0.217 1495 Planarity : 0.005 0.055 1752 Dihedral : 10.491 165.322 1375 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 1.80 % 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: -1.66 (0.22), residues: 1223 helix: -0.36 (0.23), residues: 473 sheet: -0.93 (0.31), residues: 239 loop : -1.81 (0.25), residues: 511 *********************** 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 231 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 212 time to evaluate : 1.088 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 219 average time/residue: 1.0313 time to fit residues: 245.6231 Evaluate side-chains 209 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 201 time to evaluate : 1.323 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.1036 time to fit residues: 2.4015 ------------------------------------------------------------------------------- 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: 0.8980 chunk 34 optimal weight: 0.6980 chunk 91 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 131 GLN B 347 ASN B 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 9983 Z= 0.345 Angle : 0.628 8.948 13562 Z= 0.317 Chirality : 0.047 0.231 1495 Planarity : 0.005 0.049 1752 Dihedral : 10.246 165.980 1375 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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: -1.12 (0.23), residues: 1223 helix: 0.20 (0.24), residues: 471 sheet: -0.68 (0.31), residues: 238 loop : -1.60 (0.25), residues: 514 *********************** 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 280 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 244 time to evaluate : 1.131 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 17 residues processed: 256 average time/residue: 0.9839 time to fit residues: 273.1586 Evaluate side-chains 236 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 219 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 8 residues processed: 10 average time/residue: 0.1629 time to fit residues: 3.3564 ------------------------------------------------------------------------------- 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: 1.9990 chunk 82 optimal weight: 0.3980 chunk 57 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 73 optimal weight: 0.0980 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 0.0770 chunk 104 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 216 ASN A 356 ASN A 372 GLN B 131 GLN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 384 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3230 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= 0.180 Angle : 0.548 6.735 13562 Z= 0.278 Chirality : 0.043 0.174 1495 Planarity : 0.004 0.041 1752 Dihedral : 9.966 162.144 1375 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 3.61 % 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: -0.71 (0.24), residues: 1223 helix: 0.48 (0.25), residues: 478 sheet: -0.35 (0.33), residues: 231 loop : -1.39 (0.26), residues: 514 *********************** 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 257 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 219 time to evaluate : 1.164 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 18 residues processed: 236 average time/residue: 1.0631 time to fit residues: 271.7822 Evaluate side-chains 229 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 211 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 9 residues processed: 10 average time/residue: 0.3648 time to fit residues: 6.1859 ------------------------------------------------------------------------------- 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: 0.9980 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 216 ASN A 300 ASN A 356 ASN A 372 GLN B 43 GLN B 52 ASN B 131 GLN B 191 GLN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 384 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 9983 Z= 0.370 Angle : 0.622 7.881 13562 Z= 0.313 Chirality : 0.048 0.291 1495 Planarity : 0.005 0.042 1752 Dihedral : 10.078 163.743 1375 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 3.99 % 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: -0.61 (0.24), residues: 1223 helix: 0.50 (0.25), residues: 478 sheet: -0.18 (0.33), residues: 233 loop : -1.33 (0.26), residues: 512 *********************** 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 258 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 216 time to evaluate : 1.051 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 21 residues processed: 236 average time/residue: 1.0071 time to fit residues: 257.6809 Evaluate side-chains 235 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 214 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 11 residues processed: 11 average time/residue: 0.4655 time to fit residues: 7.0365 ------------------------------------------------------------------------------- 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: 0.9980 chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 117 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 0.0060 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 overall best weight: 0.5134 ------------------------------------------------------------------------------- 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 131 GLN B 165 ASN B 256 ASN B 348 ASN B 384 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3612 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= 0.206 Angle : 0.566 10.471 13562 Z= 0.284 Chirality : 0.044 0.215 1495 Planarity : 0.004 0.038 1752 Dihedral : 9.865 159.421 1375 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: -0.33 (0.24), residues: 1223 helix: 0.77 (0.25), residues: 475 sheet: -0.04 (0.34), residues: 231 loop : -1.20 (0.27), residues: 517 *********************** 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 251 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 221 time to evaluate : 1.160 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 238 average time/residue: 1.0129 time to fit residues: 262.5103 Evaluate side-chains 234 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 218 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 8 residues processed: 8 average time/residue: 0.4618 time to fit residues: 5.8904 ------------------------------------------------------------------------------- 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: 0.8980 chunk 85 optimal weight: 0.7980 chunk 98 optimal weight: 0.0040 chunk 65 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 131 GLN B 298 ASN B 348 ASN B 384 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 9983 Z= 0.232 Angle : 0.575 9.847 13562 Z= 0.288 Chirality : 0.044 0.215 1495 Planarity : 0.004 0.038 1752 Dihedral : 9.765 157.172 1375 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.60 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: -0.26 (0.25), residues: 1223 helix: 0.81 (0.25), residues: 479 sheet: -0.06 (0.34), residues: 236 loop : -1.13 (0.27), residues: 508 *********************** 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 247 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 217 time to evaluate : 1.074 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 234 average time/residue: 1.0203 time to fit residues: 259.7875 Evaluate side-chains 229 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 213 time to evaluate : 1.073 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.6257 time to fit residues: 4.3846 ------------------------------------------------------------------------------- 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: 0.5980 chunk 22 optimal weight: 0.0980 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 0.0370 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 0.0670 chunk 106 optimal weight: 0.0040 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 0.1608 ------------------------------------------------------------------------------- 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 204 ASN B 348 ASN K 549 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 9983 Z= 0.143 Angle : 0.541 9.279 13562 Z= 0.274 Chirality : 0.042 0.213 1495 Planarity : 0.004 0.037 1752 Dihedral : 9.460 151.444 1375 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 2.37 % 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: -0.03 (0.25), residues: 1223 helix: 1.02 (0.25), residues: 478 sheet: 0.05 (0.34), residues: 236 loop : -1.02 (0.28), residues: 509 *********************** 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 233 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 208 time to evaluate : 1.058 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 223 average time/residue: 1.0491 time to fit residues: 254.4688 Evaluate side-chains 216 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 204 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.2580 time to fit residues: 2.6367 ------------------------------------------------------------------------------- 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: 0.0870 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.0670 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 71 optimal weight: 0.0770 chunk 114 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 overall best weight: 0.3454 ------------------------------------------------------------------------------- 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 131 GLN B 191 GLN B 348 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3992 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= 0.172 Angle : 0.568 10.897 13562 Z= 0.285 Chirality : 0.044 0.255 1495 Planarity : 0.004 0.037 1752 Dihedral : 9.321 148.037 1375 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 1.61 % 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: 0.04 (0.25), residues: 1223 helix: 1.05 (0.25), residues: 481 sheet: 0.08 (0.34), residues: 236 loop : -0.94 (0.28), residues: 506 *********************** 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 229 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 212 time to evaluate : 1.106 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 225 average time/residue: 1.0029 time to fit residues: 245.7850 Evaluate side-chains 223 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 213 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.2118 time to fit residues: 1.8281 ------------------------------------------------------------------------------- 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: 0.5980 chunk 120 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 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 356 ASN A 372 GLN B 131 GLN B 204 ASN B 348 ASN B 375 GLN B 384 GLN B 423 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4014 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= 0.239 Angle : 0.583 10.272 13562 Z= 0.294 Chirality : 0.044 0.205 1495 Planarity : 0.004 0.038 1752 Dihedral : 9.354 146.570 1375 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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: 0.05 (0.25), residues: 1223 helix: 0.97 (0.25), residues: 484 sheet: 0.10 (0.35), residues: 236 loop : -0.85 (0.28), residues: 503 ********************** 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 234 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 216 time to evaluate : 0.980 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 228 average time/residue: 1.0904 time to fit residues: 270.5007 Evaluate side-chains 225 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 214 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.1747 time to fit residues: 2.1264 ------------------------------------------------------------------------------- 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: 0.7980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 131 GLN B 204 ASN B 348 ASN B 384 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.137923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110621 restraints weight = 16708.409| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.25 r_work: 0.3442 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work: 0.3411 rms_B_bonded: 2.07 restraints_weight: 0.1250 r_work: 0.3394 rms_B_bonded: 2.17 restraints_weight: 0.0625 r_work: 0.3376 rms_B_bonded: 2.32 restraints_weight: 0.0312 r_work: 0.3356 rms_B_bonded: 2.52 restraints_weight: 0.0156 r_work: 0.3334 rms_B_bonded: 2.77 restraints_weight: 0.0078 r_work: 0.3309 rms_B_bonded: 3.07 restraints_weight: 0.0039 r_work: 0.3282 rms_B_bonded: 3.43 restraints_weight: 0.0020 r_work: 0.3252 rms_B_bonded: 3.87 restraints_weight: 0.0010 r_work: 0.3218 rms_B_bonded: 4.38 restraints_weight: 0.0005 r_work: 0.3180 rms_B_bonded: 4.98 restraints_weight: 0.0002 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 9983 Z= 0.267 Angle : 0.605 9.530 13562 Z= 0.302 Chirality : 0.045 0.208 1495 Planarity : 0.004 0.038 1752 Dihedral : 9.416 146.440 1375 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 1.61 % 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: 0.06 (0.25), residues: 1223 helix: 0.95 (0.25), residues: 482 sheet: 0.17 (0.34), residues: 238 loop : -0.86 (0.29), residues: 503 =============================================================================== Job complete usr+sys time: 4202.05 seconds wall clock time: 78 minutes 3.10 seconds (4683.10 seconds total)