Starting phenix.real_space_refine on Fri Oct 11 13:02:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uic_42292/10_2024/8uic_42292.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uic_42292/10_2024/8uic_42292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uic_42292/10_2024/8uic_42292.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uic_42292/10_2024/8uic_42292.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uic_42292/10_2024/8uic_42292.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uic_42292/10_2024/8uic_42292.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.109 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 77 5.16 5 C 6436 2.51 5 N 1658 2.21 5 O 1798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 9971 Number of models: 1 Model: "" Number of chains: 3 Chain: "K" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3340 Classifications: {'peptide': 424} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 403} Chain breaks: 3 Chain: "T" Number of atoms: 6629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6629 Classifications: {'peptide': 803} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 788} Chain breaks: 9 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9956 SG CYS T 973 31.553 58.803 51.985 1.00 62.13 S ATOM 9956 SG CYS T 973 31.553 58.803 51.985 1.00 62.13 S Time building chain proxies: 6.06, per 1000 atoms: 0.61 Number of scatterers: 9971 At special positions: 0 Unit cell: (95.304, 95.304, 112.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 77 16.00 O 1798 8.00 N 1658 7.00 C 6436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 800 " pdb="ZN ZN K 800 " - pdb=" ND1 HIS K 70 " pdb="ZN ZN K 800 " - pdb=" NE2 HIS K 157 " pdb="ZN ZN K 800 " - pdb=" NE2 HIS K 68 " pdb="ZN ZN K 800 " - pdb=" SG CYS T 973 " pdb=" ZN K 801 " pdb="ZN ZN K 801 " - pdb=" SG CYS T 973 " pdb="ZN ZN K 801 " - pdb=" NE2 HIS K 73 " pdb="ZN ZN K 801 " - pdb=" NE2 HIS K 414 " Number of angles added : 3 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2356 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 6 sheets defined 65.3% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'K' and resid 41 through 45 removed outlier: 3.837A pdb=" N PHE K 45 " --> pdb=" O GLU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 83 Processing helix chain 'K' and resid 94 through 112 Proline residue: K 101 - end of helix Processing helix chain 'K' and resid 122 through 132 removed outlier: 4.031A pdb=" N LYS K 132 " --> pdb=" O ASP K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 230 removed outlier: 3.965A pdb=" N ASP K 220 " --> pdb=" O CYS K 216 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE K 221 " --> pdb=" O ARG K 217 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS K 224 " --> pdb=" O ASP K 220 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU K 227 " --> pdb=" O LYS K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 249 removed outlier: 3.664A pdb=" N LEU K 248 " --> pdb=" O ARG K 244 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS K 249 " --> pdb=" O ALA K 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 244 through 249' Processing helix chain 'K' and resid 250 through 259 Processing helix chain 'K' and resid 273 through 286 removed outlier: 3.884A pdb=" N TYR K 279 " --> pdb=" O ALA K 275 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE K 283 " --> pdb=" O TYR K 279 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR K 284 " --> pdb=" O LYS K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 315 removed outlier: 3.663A pdb=" N ILE K 313 " --> pdb=" O LYS K 310 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP K 314 " --> pdb=" O ALA K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 341 removed outlier: 3.594A pdb=" N GLN K 335 " --> pdb=" O GLY K 331 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS K 339 " --> pdb=" O GLN K 335 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 365 removed outlier: 3.774A pdb=" N LYS K 362 " --> pdb=" O THR K 358 " (cutoff:3.500A) Processing helix chain 'K' and resid 394 through 406 removed outlier: 3.637A pdb=" N ILE K 398 " --> pdb=" O ASP K 394 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET K 399 " --> pdb=" O ALA K 395 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 432 removed outlier: 3.702A pdb=" N SER K 425 " --> pdb=" O LYS K 421 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS K 426 " --> pdb=" O PHE K 422 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 19 removed outlier: 3.532A pdb=" N LEU T 19 " --> pdb=" O PHE T 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 40 removed outlier: 3.650A pdb=" N GLU T 32 " --> pdb=" O ASN T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 43 No H-bonds generated for 'chain 'T' and resid 41 through 43' Processing helix chain 'T' and resid 44 through 49 removed outlier: 3.694A pdb=" N GLN T 48 " --> pdb=" O ALA T 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 64 Processing helix chain 'T' and resid 73 through 86 removed outlier: 3.729A pdb=" N PHE T 77 " --> pdb=" O LYS T 73 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 98 removed outlier: 3.529A pdb=" N ARG T 94 " --> pdb=" O TRP T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 111 Processing helix chain 'T' and resid 117 through 131 removed outlier: 3.879A pdb=" N VAL T 131 " --> pdb=" O LYS T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 132 through 143 Processing helix chain 'T' and resid 144 through 155 removed outlier: 3.609A pdb=" N LEU T 148 " --> pdb=" O ILE T 144 " (cutoff:3.500A) Processing helix chain 'T' and resid 160 through 178 removed outlier: 4.572A pdb=" N GLN T 166 " --> pdb=" O ARG T 162 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL T 167 " --> pdb=" O GLU T 163 " (cutoff:3.500A) Processing helix chain 'T' and resid 181 through 200 removed outlier: 4.038A pdb=" N THR T 185 " --> pdb=" O ASP T 181 " (cutoff:3.500A) Proline residue: T 195 - end of helix removed outlier: 3.784A pdb=" N ASN T 199 " --> pdb=" O PRO T 195 " (cutoff:3.500A) Processing helix chain 'T' and resid 218 through 240 removed outlier: 3.849A pdb=" N LYS T 222 " --> pdb=" O GLU T 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU T 240 " --> pdb=" O GLN T 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 245 through 253 Processing helix chain 'T' and resid 255 through 267 removed outlier: 3.582A pdb=" N THR T 259 " --> pdb=" O ASP T 255 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP T 265 " --> pdb=" O TRP T 261 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N MET T 266 " --> pdb=" O LYS T 262 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR T 267 " --> pdb=" O LEU T 263 " (cutoff:3.500A) Processing helix chain 'T' and resid 269 through 293 removed outlier: 3.827A pdb=" N GLU T 274 " --> pdb=" O PRO T 270 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS T 275 " --> pdb=" O TYR T 271 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE T 276 " --> pdb=" O PHE T 272 " (cutoff:3.500A) Processing helix chain 'T' and resid 305 through 323 removed outlier: 3.939A pdb=" N ALA T 311 " --> pdb=" O GLU T 307 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS T 323 " --> pdb=" O LEU T 319 " (cutoff:3.500A) Processing helix chain 'T' and resid 325 through 343 removed outlier: 3.896A pdb=" N GLY T 343 " --> pdb=" O TRP T 339 " (cutoff:3.500A) Processing helix chain 'T' and resid 358 through 377 removed outlier: 4.297A pdb=" N GLN T 362 " --> pdb=" O THR T 358 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU T 363 " --> pdb=" O PHE T 359 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE T 364 " --> pdb=" O GLU T 360 " (cutoff:3.500A) Proline residue: T 370 - end of helix removed outlier: 3.683A pdb=" N TYR T 377 " --> pdb=" O PHE T 373 " (cutoff:3.500A) Processing helix chain 'T' and resid 394 through 399 removed outlier: 3.542A pdb=" N LEU T 398 " --> pdb=" O TYR T 394 " (cutoff:3.500A) Processing helix chain 'T' and resid 400 through 402 No H-bonds generated for 'chain 'T' and resid 400 through 402' Processing helix chain 'T' and resid 403 through 417 removed outlier: 3.677A pdb=" N LEU T 409 " --> pdb=" O GLN T 405 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP T 415 " --> pdb=" O TYR T 411 " (cutoff:3.500A) Processing helix chain 'T' and resid 432 through 443 Processing helix chain 'T' and resid 444 through 446 No H-bonds generated for 'chain 'T' and resid 444 through 446' Processing helix chain 'T' and resid 449 through 468 removed outlier: 3.727A pdb=" N VAL T 453 " --> pdb=" O ARG T 449 " (cutoff:3.500A) Processing helix chain 'T' and resid 505 through 523 Processing helix chain 'T' and resid 531 through 546 removed outlier: 4.462A pdb=" N THR T 546 " --> pdb=" O VAL T 542 " (cutoff:3.500A) Processing helix chain 'T' and resid 549 through 567 removed outlier: 3.716A pdb=" N THR T 553 " --> pdb=" O ASP T 549 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL T 554 " --> pdb=" O ALA T 550 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN T 555 " --> pdb=" O ARG T 551 " (cutoff:3.500A) Processing helix chain 'T' and resid 583 through 595 Proline residue: T 589 - end of helix removed outlier: 3.842A pdb=" N VAL T 592 " --> pdb=" O GLY T 588 " (cutoff:3.500A) Processing helix chain 'T' and resid 599 through 617 removed outlier: 3.625A pdb=" N ARG T 603 " --> pdb=" O MET T 599 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR T 605 " --> pdb=" O GLU T 601 " (cutoff:3.500A) Processing helix chain 'T' and resid 625 through 630 Processing helix chain 'T' and resid 632 through 643 removed outlier: 3.694A pdb=" N ILE T 636 " --> pdb=" O LYS T 632 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN T 643 " --> pdb=" O GLU T 639 " (cutoff:3.500A) Processing helix chain 'T' and resid 646 through 660 Processing helix chain 'T' and resid 663 through 670 Processing helix chain 'T' and resid 675 through 686 removed outlier: 4.329A pdb=" N HIS T 679 " --> pdb=" O ASP T 675 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR T 685 " --> pdb=" O LEU T 681 " (cutoff:3.500A) Processing helix chain 'T' and resid 690 through 707 removed outlier: 3.787A pdb=" N SER T 694 " --> pdb=" O ASP T 690 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU T 695 " --> pdb=" O ILE T 691 " (cutoff:3.500A) Processing helix chain 'T' and resid 710 through 712 No H-bonds generated for 'chain 'T' and resid 710 through 712' Processing helix chain 'T' and resid 713 through 724 Processing helix chain 'T' and resid 730 through 750 removed outlier: 3.516A pdb=" N LYS T 734 " --> pdb=" O HIS T 730 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER T 750 " --> pdb=" O TYR T 746 " (cutoff:3.500A) Processing helix chain 'T' and resid 777 through 794 removed outlier: 3.909A pdb=" N TYR T 793 " --> pdb=" O GLU T 789 " (cutoff:3.500A) Processing helix chain 'T' and resid 795 through 806 removed outlier: 3.638A pdb=" N GLU T 805 " --> pdb=" O LYS T 801 " (cutoff:3.500A) Processing helix chain 'T' and resid 809 through 823 removed outlier: 3.727A pdb=" N GLU T 813 " --> pdb=" O MET T 809 " (cutoff:3.500A) Processing helix chain 'T' and resid 873 through 880 Processing helix chain 'T' and resid 888 through 894 Processing helix chain 'T' and resid 913 through 919 removed outlier: 3.985A pdb=" N GLN T 917 " --> pdb=" O TYR T 914 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA T 919 " --> pdb=" O LYS T 916 " (cutoff:3.500A) Processing helix chain 'T' and resid 921 through 932 removed outlier: 3.582A pdb=" N GLU T 927 " --> pdb=" O ARG T 923 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU T 929 " --> pdb=" O PHE T 925 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE T 932 " --> pdb=" O GLU T 928 " (cutoff:3.500A) Processing helix chain 'T' and resid 934 through 949 removed outlier: 4.019A pdb=" N VAL T 938 " --> pdb=" O LEU T 934 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS T 941 " --> pdb=" O LEU T 937 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN T 942 " --> pdb=" O VAL T 938 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE T 945 " --> pdb=" O HIS T 941 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU T 949 " --> pdb=" O PHE T 945 " (cutoff:3.500A) Processing helix chain 'T' and resid 950 through 964 Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.771A pdb=" N ILE K 6 " --> pdb=" O CYS K 444 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 64 through 65 removed outlier: 6.505A pdb=" N VAL K 64 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N THR K 93 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE K 90 " --> pdb=" O ILE K 134 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL K 136 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N MET K 92 " --> pdb=" O VAL K 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'K' and resid 142 through 144 removed outlier: 4.121A pdb=" N LEU K 148 " --> pdb=" O VAL K 144 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE K 201 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL K 174 " --> pdb=" O ILE K 201 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N GLU K 203 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU K 412 " --> pdb=" O LEU K 200 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER K 202 " --> pdb=" O LEU K 412 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N HIS K 414 " --> pdb=" O SER K 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 320 through 323 removed outlier: 4.162A pdb=" N VAL K 348 " --> pdb=" O ALA K 383 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU K 385 " --> pdb=" O VAL K 348 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET K 350 " --> pdb=" O GLU K 385 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 265 through 266 removed outlier: 6.059A pdb=" N ILE K 265 " --> pdb=" O LYS K 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'K' and resid 370 through 371 removed outlier: 3.604A pdb=" N VAL K 370 " --> pdb=" O VAL K 378 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1452 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: 3.23 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1621 1.30 - 1.42: 2577 1.42 - 1.55: 5846 1.55 - 1.68: 0 1.68 - 1.81: 127 Bond restraints: 10171 Sorted by residual: bond pdb=" C VAL K 348 " pdb=" O VAL K 348 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.19e-02 7.06e+03 3.40e+01 bond pdb=" CA ALA K 318 " pdb=" CB ALA K 318 " ideal model delta sigma weight residual 1.529 1.471 0.057 1.66e-02 3.63e+03 1.19e+01 bond pdb=" N PRO K 351 " pdb=" CA PRO K 351 " ideal model delta sigma weight residual 1.469 1.426 0.043 1.28e-02 6.10e+03 1.13e+01 bond pdb=" C PRO K 351 " pdb=" O PRO K 351 " ideal model delta sigma weight residual 1.235 1.192 0.043 1.30e-02 5.92e+03 1.10e+01 bond pdb=" C ILE K 349 " pdb=" O ILE K 349 " ideal model delta sigma weight residual 1.236 1.199 0.037 1.19e-02 7.06e+03 9.74e+00 ... (remaining 10166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 13051 2.00 - 4.00: 527 4.00 - 6.00: 115 6.00 - 7.99: 31 7.99 - 9.99: 6 Bond angle restraints: 13730 Sorted by residual: angle pdb=" N PRO K 316 " pdb=" CA PRO K 316 " pdb=" C PRO K 316 " ideal model delta sigma weight residual 113.53 122.97 -9.44 1.39e+00 5.18e-01 4.62e+01 angle pdb=" C ASN K 315 " pdb=" CA ASN K 315 " pdb=" CB ASN K 315 " ideal model delta sigma weight residual 109.42 119.41 -9.99 1.57e+00 4.06e-01 4.05e+01 angle pdb=" CA MET K 319 " pdb=" C MET K 319 " pdb=" O MET K 319 " ideal model delta sigma weight residual 121.45 115.06 6.39 1.07e+00 8.73e-01 3.57e+01 angle pdb=" N LYS K 381 " pdb=" CA LYS K 381 " pdb=" C LYS K 381 " ideal model delta sigma weight residual 113.89 104.71 9.18 1.58e+00 4.01e-01 3.38e+01 angle pdb=" N LEU K 364 " pdb=" CA LEU K 364 " pdb=" C LEU K 364 " ideal model delta sigma weight residual 113.18 106.56 6.62 1.21e+00 6.83e-01 2.99e+01 ... (remaining 13725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 5293 17.13 - 34.26: 662 34.26 - 51.39: 127 51.39 - 68.52: 30 68.52 - 85.65: 15 Dihedral angle restraints: 6127 sinusoidal: 2513 harmonic: 3614 Sorted by residual: dihedral pdb=" CA VAL K 144 " pdb=" C VAL K 144 " pdb=" N ASP K 145 " pdb=" CA ASP K 145 " ideal model delta harmonic sigma weight residual -180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA LEU T 447 " pdb=" C LEU T 447 " pdb=" N ASP T 448 " pdb=" CA ASP T 448 " ideal model delta harmonic sigma weight residual -180.00 -153.73 -26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ASP T 255 " pdb=" C ASP T 255 " pdb=" N PHE T 256 " pdb=" CA PHE T 256 " ideal model delta harmonic sigma weight residual -180.00 -154.32 -25.68 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 6124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1298 0.071 - 0.141: 225 0.141 - 0.212: 35 0.212 - 0.282: 8 0.282 - 0.353: 4 Chirality restraints: 1570 Sorted by residual: chirality pdb=" CA PRO K 316 " pdb=" N PRO K 316 " pdb=" C PRO K 316 " pdb=" CB PRO K 316 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CB THR K 7 " pdb=" CA THR K 7 " pdb=" OG1 THR K 7 " pdb=" CG2 THR K 7 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA VAL K 378 " pdb=" N VAL K 378 " pdb=" C VAL K 378 " pdb=" CB VAL K 378 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 1567 not shown) Planarity restraints: 1712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE K 372 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C PHE K 372 " -0.060 2.00e-02 2.50e+03 pdb=" O PHE K 372 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU K 373 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 310 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C LYS K 310 " 0.050 2.00e-02 2.50e+03 pdb=" O LYS K 310 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA K 311 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU K 385 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C GLU K 385 " -0.046 2.00e-02 2.50e+03 pdb=" O GLU K 385 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR K 386 " 0.016 2.00e-02 2.50e+03 ... (remaining 1709 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 126 2.65 - 3.21: 9301 3.21 - 3.77: 14814 3.77 - 4.34: 19328 4.34 - 4.90: 32657 Nonbonded interactions: 76226 Sorted by model distance: nonbonded pdb=" OD2 ASP K 178 " pdb="ZN ZN K 800 " model vdw 2.082 2.230 nonbonded pdb=" OG1 THR K 96 " pdb=" O GLY K 160 " model vdw 2.209 3.040 nonbonded pdb=" OD2 ASP K 72 " pdb="ZN ZN K 801 " model vdw 2.224 2.230 nonbonded pdb=" OH TYR K 153 " pdb=" OD2 ASP K 193 " model vdw 2.253 3.040 nonbonded pdb=" O GLU T 687 " pdb=" NH2 ARG T 693 " model vdw 2.261 3.120 ... (remaining 76221 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.500 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 : 0.007 0.070 10171 Z= 0.457 Angle : 0.971 9.993 13730 Z= 0.562 Chirality : 0.060 0.353 1570 Planarity : 0.005 0.056 1712 Dihedral : 16.026 85.653 3771 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 1.99 % Allowed : 0.90 % Favored : 97.11 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.94 % 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: -1.75 (0.23), residues: 1199 helix: -0.27 (0.19), residues: 701 sheet: -0.31 (0.81), residues: 49 loop : -2.69 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 256 HIS 0.008 0.001 HIS K 73 PHE 0.033 0.003 PHE K 267 TYR 0.034 0.002 TYR K 179 ARG 0.016 0.001 ARG T 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: K 92 MET cc_start: 0.8138 (ptm) cc_final: 0.7860 (ptm) REVERT: K 257 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7606 (tp30) REVERT: K 280 LYS cc_start: 0.8102 (ttmm) cc_final: 0.7749 (ttpp) REVERT: K 343 ASN cc_start: 0.8512 (t0) cc_final: 0.8285 (t0) REVERT: K 369 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8030 (mtpp) REVERT: K 371 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7220 (mm-30) REVERT: K 372 PHE cc_start: 0.8530 (m-80) cc_final: 0.8156 (m-80) REVERT: K 375 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7102 (mmt90) REVERT: T 39 GLN cc_start: 0.8214 (mm110) cc_final: 0.7994 (tp40) REVERT: T 746 TYR cc_start: 0.8712 (m-80) cc_final: 0.8475 (m-10) REVERT: T 822 MET cc_start: 0.8494 (ttp) cc_final: 0.8163 (ttp) REVERT: T 957 ASP cc_start: 0.8306 (t0) cc_final: 0.8071 (t0) outliers start: 22 outliers final: 4 residues processed: 192 average time/residue: 0.2293 time to fit residues: 63.5288 Evaluate side-chains 143 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 369 LYS Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain K residue 371 GLU Chi-restraints excluded: chain K residue 375 ARG Chi-restraints excluded: chain K residue 380 VAL Chi-restraints excluded: chain K residue 382 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 0.0030 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 374 ASN ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 566 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10171 Z= 0.182 Angle : 0.597 8.501 13730 Z= 0.315 Chirality : 0.042 0.263 1570 Planarity : 0.004 0.054 1712 Dihedral : 6.568 58.022 1330 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.17 % Allowed : 9.12 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.25), residues: 1199 helix: 0.54 (0.20), residues: 712 sheet: -0.54 (0.76), residues: 54 loop : -2.48 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 256 HIS 0.006 0.001 HIS K 414 PHE 0.030 0.001 PHE K 267 TYR 0.013 0.001 TYR T 461 ARG 0.005 0.000 ARG T 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: K 83 ILE cc_start: 0.8951 (mm) cc_final: 0.8735 (mm) REVERT: K 92 MET cc_start: 0.8208 (ptm) cc_final: 0.7926 (ptm) REVERT: K 179 TYR cc_start: 0.8401 (p90) cc_final: 0.8151 (p90) REVERT: K 280 LYS cc_start: 0.8188 (ttmm) cc_final: 0.7853 (ttpp) REVERT: K 343 ASN cc_start: 0.8510 (t0) cc_final: 0.8141 (t0) REVERT: T 39 GLN cc_start: 0.8040 (mm110) cc_final: 0.7839 (tp40) REVERT: T 449 ARG cc_start: 0.8713 (tpt90) cc_final: 0.8328 (tpt90) REVERT: T 746 TYR cc_start: 0.8684 (m-80) cc_final: 0.8445 (m-10) REVERT: T 822 MET cc_start: 0.8558 (ttp) cc_final: 0.8271 (ttt) outliers start: 24 outliers final: 18 residues processed: 160 average time/residue: 0.2159 time to fit residues: 50.8746 Evaluate side-chains 150 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain K residue 380 VAL Chi-restraints excluded: chain K residue 382 MET Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 112 HIS Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 276 ILE Chi-restraints excluded: chain T residue 310 LEU Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain T residue 520 GLU Chi-restraints excluded: chain T residue 562 LEU Chi-restraints excluded: chain T residue 955 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 329 HIS T 28 ASN T 102 ASN ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10171 Z= 0.306 Angle : 0.622 9.489 13730 Z= 0.327 Chirality : 0.043 0.208 1570 Planarity : 0.004 0.047 1712 Dihedral : 5.779 56.350 1317 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.71 % Allowed : 13.54 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.75 (0.25), residues: 1199 helix: 0.70 (0.20), residues: 720 sheet: -0.77 (0.75), residues: 54 loop : -2.60 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 256 HIS 0.006 0.001 HIS K 414 PHE 0.020 0.002 PHE K 267 TYR 0.016 0.002 TYR T 271 ARG 0.005 0.000 ARG T 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: K 92 MET cc_start: 0.8212 (ptm) cc_final: 0.7976 (ptm) REVERT: K 280 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7873 (ttpp) REVERT: K 343 ASN cc_start: 0.8543 (t0) cc_final: 0.8164 (t0) REVERT: T 78 MET cc_start: 0.7996 (tmm) cc_final: 0.7722 (tpp) REVERT: T 154 ASN cc_start: 0.7459 (m-40) cc_final: 0.7257 (m110) REVERT: T 449 ARG cc_start: 0.8812 (tpt90) cc_final: 0.8432 (tpt90) REVERT: T 746 TYR cc_start: 0.8704 (m-80) cc_final: 0.8494 (m-10) REVERT: T 955 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8185 (mm) outliers start: 30 outliers final: 24 residues processed: 155 average time/residue: 0.2080 time to fit residues: 47.1495 Evaluate side-chains 153 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 303 LYS Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain K residue 380 VAL Chi-restraints excluded: chain K residue 382 MET Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 158 LEU Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 276 ILE Chi-restraints excluded: chain T residue 319 LEU Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain T residue 520 GLU Chi-restraints excluded: chain T residue 562 LEU Chi-restraints excluded: chain T residue 938 VAL Chi-restraints excluded: chain T residue 955 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.8980 chunk 57 optimal weight: 0.0040 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 98 optimal weight: 0.9980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 GLN ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10171 Z= 0.159 Angle : 0.543 8.555 13730 Z= 0.286 Chirality : 0.041 0.282 1570 Planarity : 0.003 0.046 1712 Dihedral : 5.402 60.045 1317 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.71 % Allowed : 14.26 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.42 (0.25), residues: 1199 helix: 0.97 (0.20), residues: 718 sheet: -1.17 (0.71), residues: 61 loop : -2.40 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 339 HIS 0.007 0.001 HIS K 329 PHE 0.021 0.001 PHE K 267 TYR 0.016 0.001 TYR T 271 ARG 0.006 0.000 ARG T 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 179 TYR cc_start: 0.8508 (p90) cc_final: 0.8271 (p90) REVERT: K 280 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7898 (ttpp) REVERT: K 343 ASN cc_start: 0.8589 (t0) cc_final: 0.8210 (t0) REVERT: T 39 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7772 (tp40) REVERT: T 141 MET cc_start: 0.7603 (tmm) cc_final: 0.6866 (ptp) REVERT: T 319 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7404 (mm) outliers start: 30 outliers final: 24 residues processed: 154 average time/residue: 0.2043 time to fit residues: 45.8915 Evaluate side-chains 154 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain K residue 380 VAL Chi-restraints excluded: chain K residue 382 MET Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 158 LEU Chi-restraints excluded: chain T residue 171 MET Chi-restraints excluded: chain T residue 180 HIS Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 276 ILE Chi-restraints excluded: chain T residue 310 LEU Chi-restraints excluded: chain T residue 319 LEU Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain T residue 520 GLU Chi-restraints excluded: chain T residue 562 LEU Chi-restraints excluded: chain T residue 725 VAL Chi-restraints excluded: chain T residue 938 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.1980 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 329 HIS T 28 ASN T 154 ASN T 290 HIS ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10171 Z= 0.255 Angle : 0.586 8.131 13730 Z= 0.307 Chirality : 0.043 0.311 1570 Planarity : 0.003 0.047 1712 Dihedral : 5.405 58.828 1317 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.89 % Allowed : 15.97 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.40 (0.25), residues: 1199 helix: 1.03 (0.20), residues: 719 sheet: -1.30 (0.70), residues: 61 loop : -2.46 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 339 HIS 0.005 0.001 HIS K 414 PHE 0.028 0.002 PHE T 826 TYR 0.017 0.001 TYR T 461 ARG 0.007 0.000 ARG T 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 280 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7859 (ttpp) REVERT: K 315 ASN cc_start: 0.6298 (OUTLIER) cc_final: 0.5863 (p0) REVERT: K 343 ASN cc_start: 0.8592 (t0) cc_final: 0.8172 (t0) REVERT: T 39 GLN cc_start: 0.8237 (tp40) cc_final: 0.7887 (tp40) REVERT: T 78 MET cc_start: 0.7948 (tmm) cc_final: 0.7721 (tpp) REVERT: T 319 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7559 (mm) outliers start: 32 outliers final: 23 residues processed: 155 average time/residue: 0.1966 time to fit residues: 44.6487 Evaluate side-chains 149 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain K residue 380 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 158 LEU Chi-restraints excluded: chain T residue 180 HIS Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 276 ILE Chi-restraints excluded: chain T residue 310 LEU Chi-restraints excluded: chain T residue 319 LEU Chi-restraints excluded: chain T residue 342 LEU Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain T residue 520 GLU Chi-restraints excluded: chain T residue 562 LEU Chi-restraints excluded: chain T residue 938 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 2 GLN T 28 ASN ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10171 Z= 0.242 Angle : 0.581 9.264 13730 Z= 0.305 Chirality : 0.042 0.218 1570 Planarity : 0.003 0.048 1712 Dihedral : 5.215 60.749 1314 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.16 % Allowed : 17.33 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.30 (0.25), residues: 1199 helix: 1.10 (0.20), residues: 719 sheet: -1.27 (0.70), residues: 61 loop : -2.41 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 339 HIS 0.004 0.001 HIS K 414 PHE 0.031 0.001 PHE T 826 TYR 0.020 0.001 TYR T 461 ARG 0.008 0.000 ARG T 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 130 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 280 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7910 (ttpp) REVERT: K 315 ASN cc_start: 0.6289 (OUTLIER) cc_final: 0.5870 (p0) REVERT: K 343 ASN cc_start: 0.8603 (t0) cc_final: 0.8235 (t0) REVERT: T 78 MET cc_start: 0.8027 (tmm) cc_final: 0.7779 (tpp) REVERT: T 141 MET cc_start: 0.7520 (tmm) cc_final: 0.6968 (ptp) REVERT: T 319 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7562 (mm) REVERT: T 441 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8199 (mt) outliers start: 35 outliers final: 29 residues processed: 152 average time/residue: 0.2000 time to fit residues: 44.7015 Evaluate side-chains 160 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 39 TYR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 303 LYS Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain K residue 380 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 158 LEU Chi-restraints excluded: chain T residue 171 MET Chi-restraints excluded: chain T residue 180 HIS Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 276 ILE Chi-restraints excluded: chain T residue 310 LEU Chi-restraints excluded: chain T residue 319 LEU Chi-restraints excluded: chain T residue 342 LEU Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain T residue 441 LEU Chi-restraints excluded: chain T residue 507 VAL Chi-restraints excluded: chain T residue 520 GLU Chi-restraints excluded: chain T residue 562 LEU Chi-restraints excluded: chain T residue 938 VAL Chi-restraints excluded: chain T residue 955 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 27 ASN T 28 ASN T 39 GLN ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10171 Z= 0.224 Angle : 0.568 9.544 13730 Z= 0.299 Chirality : 0.042 0.218 1570 Planarity : 0.003 0.048 1712 Dihedral : 5.142 59.232 1314 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.06 % Allowed : 17.42 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.20 (0.25), residues: 1199 helix: 1.17 (0.20), residues: 719 sheet: -1.15 (0.71), residues: 61 loop : -2.37 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 339 HIS 0.004 0.001 HIS K 414 PHE 0.030 0.001 PHE T 826 TYR 0.019 0.001 TYR T 461 ARG 0.007 0.000 ARG T 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 135 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 280 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7933 (ttpp) REVERT: K 315 ASN cc_start: 0.6257 (OUTLIER) cc_final: 0.5834 (p0) REVERT: K 343 ASN cc_start: 0.8645 (t0) cc_final: 0.8260 (t0) REVERT: T 141 MET cc_start: 0.7539 (tmm) cc_final: 0.7027 (ptp) REVERT: T 319 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7572 (mm) REVERT: T 371 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7949 (tp) REVERT: T 548 MET cc_start: 0.8352 (pmm) cc_final: 0.8123 (pmm) REVERT: T 813 GLU cc_start: 0.7761 (mp0) cc_final: 0.7152 (mp0) outliers start: 45 outliers final: 33 residues processed: 162 average time/residue: 0.2069 time to fit residues: 49.0705 Evaluate side-chains 163 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 127 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 39 TYR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 303 LYS Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain K residue 382 MET Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 158 LEU Chi-restraints excluded: chain T residue 171 MET Chi-restraints excluded: chain T residue 180 HIS Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 276 ILE Chi-restraints excluded: chain T residue 310 LEU Chi-restraints excluded: chain T residue 319 LEU Chi-restraints excluded: chain T residue 342 LEU Chi-restraints excluded: chain T residue 371 LEU Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain T residue 460 LEU Chi-restraints excluded: chain T residue 507 VAL Chi-restraints excluded: chain T residue 520 GLU Chi-restraints excluded: chain T residue 562 LEU Chi-restraints excluded: chain T residue 661 VAL Chi-restraints excluded: chain T residue 938 VAL Chi-restraints excluded: chain T residue 955 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 28 ASN T 39 GLN ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10171 Z= 0.202 Angle : 0.572 9.000 13730 Z= 0.301 Chirality : 0.042 0.234 1570 Planarity : 0.003 0.048 1712 Dihedral : 5.048 59.817 1313 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.70 % Allowed : 17.96 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.23 (0.25), residues: 1199 helix: 1.16 (0.20), residues: 725 sheet: -1.01 (0.72), residues: 61 loop : -2.47 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 339 HIS 0.004 0.001 HIS K 73 PHE 0.027 0.001 PHE T 826 TYR 0.022 0.001 TYR T 461 ARG 0.009 0.000 ARG T 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 134 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 179 TYR cc_start: 0.8597 (p90) cc_final: 0.8326 (p90) REVERT: K 280 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7888 (ttpp) REVERT: K 315 ASN cc_start: 0.6212 (OUTLIER) cc_final: 0.5791 (p0) REVERT: K 343 ASN cc_start: 0.8642 (t0) cc_final: 0.8248 (t0) REVERT: T 141 MET cc_start: 0.7495 (tmm) cc_final: 0.7039 (ptp) REVERT: T 319 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7545 (mm) REVERT: T 371 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7887 (tp) REVERT: T 813 GLU cc_start: 0.7781 (mp0) cc_final: 0.7161 (mp0) REVERT: T 928 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7674 (tp30) outliers start: 41 outliers final: 32 residues processed: 158 average time/residue: 0.1992 time to fit residues: 45.9627 Evaluate side-chains 164 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 39 TYR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 303 LYS Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain K residue 382 MET Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 158 LEU Chi-restraints excluded: chain T residue 180 HIS Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 276 ILE Chi-restraints excluded: chain T residue 310 LEU Chi-restraints excluded: chain T residue 319 LEU Chi-restraints excluded: chain T residue 342 LEU Chi-restraints excluded: chain T residue 371 LEU Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain T residue 460 LEU Chi-restraints excluded: chain T residue 507 VAL Chi-restraints excluded: chain T residue 520 GLU Chi-restraints excluded: chain T residue 562 LEU Chi-restraints excluded: chain T residue 661 VAL Chi-restraints excluded: chain T residue 928 GLU Chi-restraints excluded: chain T residue 938 VAL Chi-restraints excluded: chain T residue 955 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 65 optimal weight: 0.0170 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 GLN ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10171 Z= 0.198 Angle : 0.580 10.390 13730 Z= 0.302 Chirality : 0.042 0.220 1570 Planarity : 0.003 0.049 1712 Dihedral : 5.048 58.814 1313 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.43 % Allowed : 17.60 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.20 (0.25), residues: 1199 helix: 1.18 (0.20), residues: 726 sheet: -0.94 (0.73), residues: 61 loop : -2.47 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 339 HIS 0.006 0.001 HIS K 157 PHE 0.033 0.001 PHE T 826 TYR 0.023 0.001 TYR T 461 ARG 0.010 0.000 ARG T 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 131 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 280 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7859 (ttpp) REVERT: K 315 ASN cc_start: 0.6193 (OUTLIER) cc_final: 0.5805 (p0) REVERT: K 343 ASN cc_start: 0.8584 (t0) cc_final: 0.8258 (t0) REVERT: T 141 MET cc_start: 0.7517 (tmm) cc_final: 0.7061 (ptp) REVERT: T 319 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7516 (mm) REVERT: T 371 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7932 (tp) REVERT: T 813 GLU cc_start: 0.7770 (mp0) cc_final: 0.7142 (mp0) outliers start: 38 outliers final: 33 residues processed: 153 average time/residue: 0.2059 time to fit residues: 46.4354 Evaluate side-chains 164 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 39 TYR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 303 LYS Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain K residue 382 MET Chi-restraints excluded: chain K residue 437 MET Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 158 LEU Chi-restraints excluded: chain T residue 180 HIS Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 276 ILE Chi-restraints excluded: chain T residue 310 LEU Chi-restraints excluded: chain T residue 319 LEU Chi-restraints excluded: chain T residue 342 LEU Chi-restraints excluded: chain T residue 371 LEU Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain T residue 460 LEU Chi-restraints excluded: chain T residue 507 VAL Chi-restraints excluded: chain T residue 520 GLU Chi-restraints excluded: chain T residue 562 LEU Chi-restraints excluded: chain T residue 661 VAL Chi-restraints excluded: chain T residue 938 VAL Chi-restraints excluded: chain T residue 955 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 39 GLN ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10171 Z= 0.227 Angle : 0.611 17.801 13730 Z= 0.312 Chirality : 0.042 0.215 1570 Planarity : 0.003 0.050 1712 Dihedral : 5.055 59.105 1313 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.25 % Allowed : 18.14 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.20 (0.25), residues: 1199 helix: 1.19 (0.20), residues: 725 sheet: -0.97 (0.73), residues: 61 loop : -2.49 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 339 HIS 0.006 0.001 HIS K 157 PHE 0.035 0.001 PHE T 826 TYR 0.024 0.001 TYR T 461 ARG 0.012 0.000 ARG T 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 125 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 163 MET cc_start: 0.8380 (ptt) cc_final: 0.8162 (ptt) REVERT: K 179 TYR cc_start: 0.8606 (p90) cc_final: 0.8400 (p90) REVERT: K 280 LYS cc_start: 0.8210 (ttmm) cc_final: 0.7908 (ttpp) REVERT: K 315 ASN cc_start: 0.6214 (OUTLIER) cc_final: 0.5794 (p0) REVERT: K 343 ASN cc_start: 0.8593 (t0) cc_final: 0.8271 (t0) REVERT: T 141 MET cc_start: 0.7540 (tmm) cc_final: 0.7070 (ptp) REVERT: T 319 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7554 (mm) REVERT: T 371 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7929 (tp) REVERT: T 813 GLU cc_start: 0.7796 (mp0) cc_final: 0.7169 (mp0) outliers start: 36 outliers final: 33 residues processed: 146 average time/residue: 0.2077 time to fit residues: 44.8614 Evaluate side-chains 160 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 124 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 39 TYR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 303 LYS Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain K residue 382 MET Chi-restraints excluded: chain K residue 437 MET Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 158 LEU Chi-restraints excluded: chain T residue 180 HIS Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 276 ILE Chi-restraints excluded: chain T residue 310 LEU Chi-restraints excluded: chain T residue 319 LEU Chi-restraints excluded: chain T residue 342 LEU Chi-restraints excluded: chain T residue 371 LEU Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain T residue 460 LEU Chi-restraints excluded: chain T residue 507 VAL Chi-restraints excluded: chain T residue 520 GLU Chi-restraints excluded: chain T residue 562 LEU Chi-restraints excluded: chain T residue 661 VAL Chi-restraints excluded: chain T residue 938 VAL Chi-restraints excluded: chain T residue 955 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 39 GLN ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.164251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135064 restraints weight = 13218.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.137620 restraints weight = 7948.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.139937 restraints weight = 5746.852| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10171 Z= 0.277 Angle : 0.634 17.290 13730 Z= 0.324 Chirality : 0.043 0.207 1570 Planarity : 0.003 0.051 1712 Dihedral : 5.151 59.159 1313 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 3.43 % Allowed : 18.14 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1199 helix: 1.15 (0.20), residues: 725 sheet: -1.06 (0.74), residues: 61 loop : -2.51 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 339 HIS 0.008 0.001 HIS K 157 PHE 0.036 0.001 PHE T 826 TYR 0.024 0.001 TYR T 461 ARG 0.011 0.000 ARG T 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1911.49 seconds wall clock time: 35 minutes 53.88 seconds (2153.88 seconds total)