Starting phenix.real_space_refine on Fri Feb 14 08:16:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uic_42292/02_2025/8uic_42292.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uic_42292/02_2025/8uic_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/cci-nas-00/data/ceres_data/8uic_42292/02_2025/8uic_42292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uic_42292/02_2025/8uic_42292.map" model { file = "/net/cci-nas-00/data/ceres_data/8uic_42292/02_2025/8uic_42292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uic_42292/02_2025/8uic_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.74, per 1000 atoms: 0.58 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: 2.76 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: 1.02 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: 3.13 Time building geometry restraints manager: 3.06 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.310 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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: 31.420 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 1.167 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: 0.2253 time to fit residues: 63.4531 Evaluate side-chains 143 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.167975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.138049 restraints weight = 13246.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.142164 restraints weight = 7437.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.143822 restraints weight = 5088.926| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: K 83 ILE cc_start: 0.9008 (mm) cc_final: 0.8769 (mm) REVERT: K 92 MET cc_start: 0.8096 (ptm) cc_final: 0.7834 (ptm) REVERT: K 280 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7817 (ttpp) REVERT: T 449 ARG cc_start: 0.8703 (tpt90) cc_final: 0.8366 (tpt90) REVERT: T 746 TYR cc_start: 0.8553 (m-80) cc_final: 0.8337 (m-10) REVERT: T 822 MET cc_start: 0.8547 (ttp) cc_final: 0.8206 (ttt) outliers start: 24 outliers final: 18 residues processed: 160 average time/residue: 0.2032 time to fit residues: 47.8394 Evaluate side-chains 149 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.0670 chunk 85 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 0.3980 chunk 101 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.168900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.138113 restraints weight = 13436.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.142584 restraints weight = 7345.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.145419 restraints weight = 4995.768| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10171 Z= 0.165 Angle : 0.549 7.022 13730 Z= 0.291 Chirality : 0.040 0.180 1570 Planarity : 0.003 0.047 1712 Dihedral : 5.528 55.673 1317 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.62 % Allowed : 13.00 % Favored : 84.39 % 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: -0.54 (0.25), residues: 1199 helix: 0.85 (0.20), residues: 717 sheet: -0.47 (0.77), residues: 52 loop : -2.49 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 256 HIS 0.004 0.001 HIS K 414 PHE 0.020 0.001 PHE T 541 TYR 0.016 0.001 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 177 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: K 83 ILE cc_start: 0.9033 (mm) cc_final: 0.8794 (mm) REVERT: K 92 MET cc_start: 0.8057 (ptm) cc_final: 0.7803 (ptm) REVERT: K 280 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7809 (ttpp) REVERT: T 39 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7860 (tp40) REVERT: T 141 MET cc_start: 0.7408 (tmm) cc_final: 0.6890 (ptp) REVERT: T 319 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7498 (mm) REVERT: T 957 ASP cc_start: 0.8193 (t0) cc_final: 0.7866 (t0) outliers start: 29 outliers final: 23 residues processed: 161 average time/residue: 0.2122 time to fit residues: 49.8220 Evaluate side-chains 159 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 79 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.165348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.135032 restraints weight = 13294.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.139396 restraints weight = 7879.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.141205 restraints weight = 5258.663| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10171 Z= 0.255 Angle : 0.584 8.176 13730 Z= 0.306 Chirality : 0.043 0.298 1570 Planarity : 0.004 0.047 1712 Dihedral : 5.467 57.534 1317 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.62 % Allowed : 14.17 % Favored : 83.21 % 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: -0.46 (0.25), residues: 1199 helix: 0.97 (0.21), residues: 717 sheet: -1.24 (0.70), residues: 61 loop : -2.46 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 339 HIS 0.006 0.001 HIS K 329 PHE 0.019 0.001 PHE T 541 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 165 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: K 179 TYR cc_start: 0.8445 (p90) cc_final: 0.7924 (p90) REVERT: K 280 LYS cc_start: 0.8129 (ttmm) cc_final: 0.7833 (ttpp) REVERT: T 39 GLN cc_start: 0.8316 (tp40) cc_final: 0.8051 (tp40) REVERT: T 319 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7667 (mm) outliers start: 29 outliers final: 22 residues processed: 152 average time/residue: 0.2083 time to fit residues: 46.3640 Evaluate side-chains 150 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 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 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 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 50 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 28 ASN ** T 353 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 = 0.3982 r_free = 0.3982 target = 0.161519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132069 restraints weight = 13399.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.135666 restraints weight = 8253.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.137319 restraints weight = 5642.893| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10171 Z= 0.350 Angle : 0.638 8.943 13730 Z= 0.333 Chirality : 0.044 0.151 1570 Planarity : 0.004 0.049 1712 Dihedral : 5.621 58.739 1317 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.07 % Allowed : 15.97 % Favored : 80.96 % 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: -0.69 (0.25), residues: 1199 helix: 0.78 (0.20), residues: 729 sheet: -1.44 (0.70), residues: 61 loop : -2.62 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 339 HIS 0.005 0.001 HIS K 414 PHE 0.029 0.002 PHE T 826 TYR 0.018 0.002 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 167 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: K 179 TYR cc_start: 0.8518 (p90) cc_final: 0.8184 (p90) REVERT: K 257 GLU cc_start: 0.7606 (tp30) cc_final: 0.7401 (tp30) REVERT: K 280 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7843 (ttpp) REVERT: K 315 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.7313 (p0) REVERT: T 39 GLN cc_start: 0.8327 (tp40) cc_final: 0.7910 (tp40) REVERT: T 141 MET cc_start: 0.7514 (tmm) cc_final: 0.7126 (ptp) REVERT: T 449 ARG cc_start: 0.8724 (tpt90) cc_final: 0.8438 (tpt90) outliers start: 34 outliers final: 27 residues processed: 154 average time/residue: 0.2264 time to fit residues: 50.6870 Evaluate side-chains 155 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 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 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 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 116 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.162617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133147 restraints weight = 13494.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.138070 restraints weight = 8384.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.139296 restraints weight = 5426.239| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10171 Z= 0.277 Angle : 0.610 7.914 13730 Z= 0.318 Chirality : 0.043 0.313 1570 Planarity : 0.004 0.050 1712 Dihedral : 5.379 59.066 1314 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.61 % Allowed : 17.06 % Favored : 79.33 % 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: -0.61 (0.25), residues: 1199 helix: 0.83 (0.20), residues: 729 sheet: -1.40 (0.70), residues: 61 loop : -2.56 (0.29), residues: 409 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 0.023 0.002 PHE T 826 TYR 0.019 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 167 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: K 179 TYR cc_start: 0.8498 (p90) cc_final: 0.8189 (p90) REVERT: K 257 GLU cc_start: 0.7602 (tp30) cc_final: 0.7389 (tp30) REVERT: K 280 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7867 (ttpp) REVERT: K 315 ASN cc_start: 0.7633 (OUTLIER) cc_final: 0.7296 (p0) REVERT: T 371 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8234 (tp) REVERT: T 441 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8320 (mt) REVERT: T 449 ARG cc_start: 0.8677 (tpt90) cc_final: 0.8407 (tpt90) outliers start: 40 outliers final: 33 residues processed: 155 average time/residue: 0.2064 time to fit residues: 47.1199 Evaluate side-chains 161 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 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 K residue 382 MET Chi-restraints excluded: chain K residue 437 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 74 VAL 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 342 LEU Chi-restraints excluded: chain T residue 371 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 661 VAL Chi-restraints excluded: chain T residue 938 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.166250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.136593 restraints weight = 13569.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.140271 restraints weight = 8143.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141562 restraints weight = 5591.566| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10171 Z= 0.185 Angle : 0.566 10.236 13730 Z= 0.296 Chirality : 0.041 0.262 1570 Planarity : 0.003 0.048 1712 Dihedral : 5.118 58.605 1314 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.70 % Allowed : 17.51 % Favored : 78.79 % 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: -0.36 (0.25), residues: 1199 helix: 1.04 (0.20), residues: 725 sheet: -1.21 (0.71), residues: 61 loop : -2.49 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 339 HIS 0.004 0.001 HIS K 73 PHE 0.031 0.001 PHE T 826 TYR 0.021 0.001 TYR T 461 ARG 0.008 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 182 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: K 179 TYR cc_start: 0.8492 (p90) cc_final: 0.8156 (p90) REVERT: K 257 GLU cc_start: 0.7550 (tp30) cc_final: 0.7345 (tp30) REVERT: K 280 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7852 (ttpp) REVERT: K 315 ASN cc_start: 0.7470 (OUTLIER) cc_final: 0.7148 (p0) REVERT: T 141 MET cc_start: 0.7471 (tmm) cc_final: 0.6876 (ptp) REVERT: T 319 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7769 (mm) REVERT: T 371 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8177 (tp) REVERT: T 644 ASP cc_start: 0.7777 (t70) cc_final: 0.7174 (t0) REVERT: T 813 GLU cc_start: 0.7455 (mp0) cc_final: 0.7000 (mp0) outliers start: 41 outliers final: 30 residues processed: 166 average time/residue: 0.1907 time to fit residues: 46.9395 Evaluate side-chains 167 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 315 ASN Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 370 VAL 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 507 VAL Chi-restraints excluded: chain T residue 520 GLU Chi-restraints excluded: chain T residue 546 THR Chi-restraints excluded: chain T residue 562 LEU Chi-restraints excluded: chain T residue 709 ILE Chi-restraints excluded: chain T residue 938 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 107 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.167681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.138360 restraints weight = 13396.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143275 restraints weight = 8635.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144258 restraints weight = 5272.109| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10171 Z= 0.174 Angle : 0.583 17.129 13730 Z= 0.299 Chirality : 0.041 0.193 1570 Planarity : 0.003 0.048 1712 Dihedral : 5.016 57.511 1313 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.52 % Allowed : 17.87 % 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: -0.27 (0.25), residues: 1199 helix: 1.10 (0.20), residues: 730 sheet: -1.04 (0.72), residues: 61 loop : -2.49 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 339 HIS 0.004 0.001 HIS K 73 PHE 0.026 0.001 PHE T 826 TYR 0.021 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 176 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: K 179 TYR cc_start: 0.8491 (p90) cc_final: 0.8124 (p90) REVERT: K 280 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7839 (ttpp) REVERT: K 315 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.7072 (p0) REVERT: T 141 MET cc_start: 0.7426 (tmm) cc_final: 0.6783 (ptp) REVERT: T 319 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7836 (mm) REVERT: T 813 GLU cc_start: 0.7421 (mp0) cc_final: 0.6972 (mp0) outliers start: 39 outliers final: 31 residues processed: 158 average time/residue: 0.2104 time to fit residues: 49.5416 Evaluate side-chains 165 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 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 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 546 THR Chi-restraints excluded: chain T residue 562 LEU Chi-restraints excluded: chain T residue 938 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 9 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.166162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136977 restraints weight = 13394.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.140109 restraints weight = 8259.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141922 restraints weight = 5888.488| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10171 Z= 0.226 Angle : 0.610 16.471 13730 Z= 0.310 Chirality : 0.043 0.386 1570 Planarity : 0.003 0.049 1712 Dihedral : 5.021 57.043 1313 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.43 % Allowed : 18.32 % Favored : 78.25 % 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: -0.28 (0.25), residues: 1199 helix: 1.11 (0.20), residues: 729 sheet: -1.07 (0.72), residues: 61 loop : -2.51 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 339 HIS 0.007 0.001 HIS K 157 PHE 0.024 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 170 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: K 179 TYR cc_start: 0.8519 (p90) cc_final: 0.8184 (p90) REVERT: K 280 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7866 (ttpp) REVERT: K 315 ASN cc_start: 0.7434 (OUTLIER) cc_final: 0.7108 (p0) REVERT: T 141 MET cc_start: 0.7449 (tmm) cc_final: 0.6826 (ptp) REVERT: T 319 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7704 (mm) REVERT: T 371 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8175 (tp) REVERT: T 813 GLU cc_start: 0.7489 (mp0) cc_final: 0.7003 (mp0) outliers start: 38 outliers final: 33 residues processed: 155 average time/residue: 0.2017 time to fit residues: 45.6847 Evaluate side-chains 163 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 546 THR Chi-restraints excluded: chain T residue 562 LEU Chi-restraints excluded: chain T residue 661 VAL Chi-restraints excluded: chain T residue 938 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 36 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 374 ASN 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** T 940 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.164563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135365 restraints weight = 13518.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.139153 restraints weight = 8238.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.140563 restraints weight = 5820.316| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10171 Z= 0.272 Angle : 0.635 16.124 13730 Z= 0.323 Chirality : 0.044 0.387 1570 Planarity : 0.003 0.050 1712 Dihedral : 5.114 57.184 1313 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.70 % Allowed : 18.14 % Favored : 78.16 % 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: -0.33 (0.25), residues: 1199 helix: 1.08 (0.20), residues: 729 sheet: -1.11 (0.73), residues: 61 loop : -2.56 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 339 HIS 0.007 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 ********************** 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 168 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: K 179 TYR cc_start: 0.8564 (p90) cc_final: 0.8172 (p90) REVERT: K 280 LYS cc_start: 0.8114 (ttmm) cc_final: 0.7826 (ttpp) REVERT: K 315 ASN cc_start: 0.7491 (OUTLIER) cc_final: 0.7161 (p0) REVERT: T 141 MET cc_start: 0.7449 (tmm) cc_final: 0.6868 (ptp) REVERT: T 319 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7755 (mm) REVERT: T 371 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8224 (tp) REVERT: T 813 GLU cc_start: 0.7488 (mp0) cc_final: 0.7018 (mp0) outliers start: 41 outliers final: 34 residues processed: 153 average time/residue: 0.1957 time to fit residues: 44.1015 Evaluate side-chains 158 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 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 443 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 546 THR 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 52 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 374 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.166550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.137771 restraints weight = 13409.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.140500 restraints weight = 8380.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.141991 restraints weight = 5865.928| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10171 Z= 0.208 Angle : 0.615 16.074 13730 Z= 0.313 Chirality : 0.043 0.389 1570 Planarity : 0.003 0.049 1712 Dihedral : 5.034 56.521 1313 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.61 % Allowed : 18.59 % Favored : 77.80 % 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: -0.25 (0.25), residues: 1199 helix: 1.12 (0.20), residues: 730 sheet: -0.94 (0.75), residues: 61 loop : -2.51 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 339 HIS 0.006 0.001 HIS K 157 PHE 0.036 0.001 PHE T 826 TYR 0.025 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: 2692.59 seconds wall clock time: 49 minutes 21.58 seconds (2961.58 seconds total)