Starting phenix.real_space_refine on Wed Aug 5 19:49:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gzr_34402/08_2026/8gzr_34402.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gzr_34402/08_2026/8gzr_34402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gzr_34402/08_2026/8gzr_34402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gzr_34402/08_2026/8gzr_34402.map" model { file = "/net/cci-nas-00/data/ceres_data/8gzr_34402/08_2026/8gzr_34402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gzr_34402/08_2026/8gzr_34402.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8gzr_34402/08_2026/8gzr_34402.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gzr_34402/08_2026/8gzr_34402.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.005 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: 7 Type Number sf(0) Gaussians Mn 3 7.51 5 Zn 2 6.06 5 P 37 5.49 5 S 65 5.16 5 C 6993 2.51 5 N 2027 2.21 5 O 2191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11318 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 7057 Classifications: {'peptide': 880} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 40, 'TRANS': 839} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 3474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3474 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 26, 'TRANS': 416} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 706 Classifications: {'RNAv2': 33} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 18, 'rna3p_pyr': 12} Link IDs: {'rna2p': 3, 'rna3p': 29} Chain breaks: 1 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 55 Unusual residues: {' MN': 2, ' ZN': 2, 'CDP': 1} Classifications: {'peptide': 1, 'undetermined': 5} Link IDs: {None: 5} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' MN': 1, 'CDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5788 SG CYS A 728 74.365 45.793 41.590 1.00 32.82 S ATOM 6763 SG CYS A 847 75.018 43.082 44.279 1.00 41.34 S ATOM 3533 SG CYS A 446 83.849 90.378 49.020 1.00 49.25 S ATOM 3549 SG CYS A 449 82.166 88.650 46.383 1.00 47.31 S Time building chain proxies: 2.57, per 1000 atoms: 0.23 Number of scatterers: 11318 At special positions: 0 Unit cell: (122.618, 108.533, 113.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Mn 3 24.99 S 65 16.00 P 37 15.00 O 2191 8.00 N 2027 7.00 C 6993 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: 0.87 Conformation dependent library (CDL) restraints added in 570.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" NE2 HIS A 714 " pdb="ZN ZN A1003 " - pdb=" NE2 HIS A 712 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 728 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 847 " pdb=" ZN A1004 " pdb="ZN ZN A1004 " - pdb=" NE2 HIS A 441 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 446 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 449 " Number of angles added : 2 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 13 sheets defined 46.6% alpha, 11.4% beta 10 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 8 through 19 removed outlier: 3.641A pdb=" N GLN A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.575A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 93 removed outlier: 3.947A pdb=" N GLY A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 153 through 169 removed outlier: 3.546A pdb=" N GLU A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 226 through 244 removed outlier: 3.627A pdb=" N PHE A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 328 through 333 removed outlier: 4.131A pdb=" N VAL A 333 " --> pdb=" O PRO A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'A' and resid 366 through 385 Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 412 through 416 Processing helix chain 'A' and resid 420 through 427 Processing helix chain 'A' and resid 428 through 443 removed outlier: 3.594A pdb=" N GLN A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 489 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.961A pdb=" N ILE A 517 " --> pdb=" O LYS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 540 Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 552 through 556 removed outlier: 3.625A pdb=" N MET A 556 " --> pdb=" O THR A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 571 Processing helix chain 'A' and resid 604 through 625 Processing helix chain 'A' and resid 629 through 634 Processing helix chain 'A' and resid 639 through 656 removed outlier: 4.622A pdb=" N ILE A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLU A 653 " --> pdb=" O THR A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 removed outlier: 4.089A pdb=" N PHE A 674 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 702 through 706 Processing helix chain 'A' and resid 730 through 739 removed outlier: 3.744A pdb=" N LEU A 734 " --> pdb=" O PRO A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 750 No H-bonds generated for 'chain 'A' and resid 748 through 750' Processing helix chain 'A' and resid 751 through 766 Processing helix chain 'A' and resid 769 through 782 Processing helix chain 'A' and resid 805 through 818 Processing helix chain 'A' and resid 832 through 836 Processing helix chain 'A' and resid 840 through 847 Processing helix chain 'A' and resid 853 through 862 Processing helix chain 'A' and resid 862 through 875 removed outlier: 3.613A pdb=" N ALA A 866 " --> pdb=" O ASN A 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.683A pdb=" N LYS B 185 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 removed outlier: 3.514A pdb=" N ALA B 207 " --> pdb=" O LYS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 236 Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 291 through 307 Processing helix chain 'B' and resid 349 through 354 removed outlier: 4.062A pdb=" N THR B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 379 removed outlier: 3.597A pdb=" N ASN B 379 " --> pdb=" O CYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 399 removed outlier: 4.978A pdb=" N GLN B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B 397 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 413 removed outlier: 3.698A pdb=" N GLU B 413 " --> pdb=" O ASP B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 413' Processing helix chain 'B' and resid 451 through 460 Processing helix chain 'B' and resid 486 through 497 removed outlier: 4.537A pdb=" N THR B 490 " --> pdb=" O HIS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'B' and resid 527 through 540 Processing helix chain 'B' and resid 544 through 553 Processing helix chain 'B' and resid 561 through 565 Processing helix chain 'B' and resid 598 through 602 removed outlier: 3.553A pdb=" N TYR B 602 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 616 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 127 removed outlier: 8.926A pdb=" N LYS A 125 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A 100 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N MET A 127 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLY A 102 " --> pdb=" O MET A 127 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLY A 75 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 99 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG A 76 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU A 144 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 78 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 309 removed outlier: 5.710A pdb=" N TYR A 304 " --> pdb=" O SER A 593 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER A 593 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 306 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN A 580 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 9.403A pdb=" N GLY A 455 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 740 through 742 removed outlier: 3.531A pdb=" N GLY A 745 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 340 through 342 Processing sheet with id=AA6, first strand: chain 'A' and resid 658 through 661 Processing sheet with id=AA7, first strand: chain 'A' and resid 712 through 717 Processing sheet with id=AA8, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AA9, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.220A pdb=" N LEU B 220 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP B 285 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 222 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 333 through 336 removed outlier: 6.178A pdb=" N GLN B 334 " --> pdb=" O TYR B 473 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE B 475 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU B 336 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 423 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR B 359 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR B 408 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TRP B 361 " --> pdb=" O THR B 408 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 428 through 435 removed outlier: 5.941A pdb=" N CYS B 429 " --> pdb=" O PRO B 447 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B 431 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 574 through 575 Processing sheet with id=AB4, first strand: chain 'B' and resid 581 through 583 443 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1806 1.31 - 1.45: 3380 1.45 - 1.58: 6280 1.58 - 1.72: 72 1.72 - 1.85: 112 Bond restraints: 11650 Sorted by residual: bond pdb=" C3' CDP A1006 " pdb=" C4' CDP A1006 " ideal model delta sigma weight residual 1.530 1.298 0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C3' CDP B 702 " pdb=" C4' CDP B 702 " ideal model delta sigma weight residual 1.530 1.308 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C4' CDP B 702 " pdb=" O4' CDP B 702 " ideal model delta sigma weight residual 1.431 1.617 -0.186 2.00e-02 2.50e+03 8.68e+01 bond pdb=" C4' CDP A1006 " pdb=" O4' CDP A1006 " ideal model delta sigma weight residual 1.431 1.614 -0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" C5 CDP B 702 " pdb=" C6 CDP B 702 " ideal model delta sigma weight residual 1.350 1.492 -0.142 2.00e-02 2.50e+03 5.02e+01 ... (remaining 11645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 15722 2.44 - 4.87: 192 4.87 - 7.31: 23 7.31 - 9.74: 3 9.74 - 12.18: 4 Bond angle restraints: 15944 Sorted by residual: angle pdb=" O1A CDP A1006 " pdb=" PA CDP A1006 " pdb=" O2A CDP A1006 " ideal model delta sigma weight residual 120.72 108.54 12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" O3A CDP A1006 " pdb=" PA CDP A1006 " pdb=" O5' CDP A1006 " ideal model delta sigma weight residual 98.38 110.39 -12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O1A CDP B 702 " pdb=" PA CDP B 702 " pdb=" O2A CDP B 702 " ideal model delta sigma weight residual 120.72 109.03 11.69 3.00e+00 1.11e-01 1.52e+01 angle pdb=" O3A CDP B 702 " pdb=" PA CDP B 702 " pdb=" O5' CDP B 702 " ideal model delta sigma weight residual 98.38 109.18 -10.80 3.00e+00 1.11e-01 1.30e+01 angle pdb=" O2B CDP B 702 " pdb=" PB CDP B 702 " pdb=" O3A CDP B 702 " ideal model delta sigma weight residual 100.97 109.43 -8.46 3.00e+00 1.11e-01 7.95e+00 ... (remaining 15939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 6098 16.29 - 32.57: 610 32.57 - 48.86: 187 48.86 - 65.14: 44 65.14 - 81.43: 15 Dihedral angle restraints: 6954 sinusoidal: 3141 harmonic: 3813 Sorted by residual: dihedral pdb=" C4' U C 6 " pdb=" C3' U C 6 " pdb=" C2' U C 6 " pdb=" C1' U C 6 " ideal model delta sinusoidal sigma weight residual 36.34 -37.39 73.73 1 3.10e+00 1.04e-01 7.19e+02 dihedral pdb=" C4' G C 5 " pdb=" C3' G C 5 " pdb=" C2' G C 5 " pdb=" C1' G C 5 " ideal model delta sinusoidal sigma weight residual 36.34 -34.93 71.27 1 3.10e+00 1.04e-01 6.78e+02 dihedral pdb=" C4' U C 7 " pdb=" C3' U C 7 " pdb=" C2' U C 7 " pdb=" C1' U C 7 " ideal model delta sinusoidal sigma weight residual 36.34 -34.65 70.99 1 3.10e+00 1.04e-01 6.74e+02 ... (remaining 6951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1516 0.065 - 0.129: 188 0.129 - 0.194: 4 0.194 - 0.259: 35 0.259 - 0.323: 5 Chirality restraints: 1748 Sorted by residual: chirality pdb=" C2' SAH A1005 " pdb=" C1' SAH A1005 " pdb=" C3' SAH A1005 " pdb=" O2' SAH A1005 " both_signs ideal model delta sigma weight residual False -2.53 -2.85 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" C2' G C 5 " pdb=" C3' G C 5 " pdb=" O2' G C 5 " pdb=" C1' G C 5 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C2' U C 6 " pdb=" C3' U C 6 " pdb=" O2' U C 6 " pdb=" C1' U C 6 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1745 not shown) Planarity restraints: 1919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 289 " -0.017 2.00e-02 2.50e+03 1.59e-02 4.42e+00 pdb=" CG PHE B 289 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 289 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 289 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 289 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 289 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 289 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 474 " -0.000 2.00e-02 2.50e+03 1.27e-02 4.04e+00 pdb=" CG TRP A 474 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 474 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 474 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 474 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 474 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 474 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 474 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 474 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 474 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 729 " -0.031 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO A 730 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 730 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 730 " -0.026 5.00e-02 4.00e+02 ... (remaining 1916 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 22 2.37 - 3.00: 5765 3.00 - 3.63: 16818 3.63 - 4.27: 28655 4.27 - 4.90: 45852 Nonbonded interactions: 97112 Sorted by model distance: nonbonded pdb="MN MN A1001 " pdb=" O2B CDP A1006 " model vdw 1.733 2.320 nonbonded pdb=" OD1 ASP A 533 " pdb="MN MN A1001 " model vdw 1.792 2.320 nonbonded pdb=" OD2 ASP A 533 " pdb="MN MN A1002 " model vdw 1.834 2.320 nonbonded pdb="MN MN B 701 " pdb=" O1B CDP B 702 " model vdw 1.836 2.320 nonbonded pdb=" OD2 ASP A 663 " pdb="MN MN A1001 " model vdw 1.897 2.320 ... (remaining 97107 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.790 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 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 0.232 11657 Z= 0.351 Angle : 0.667 12.177 15946 Z= 0.335 Chirality : 0.055 0.323 1748 Planarity : 0.004 0.046 1919 Dihedral : 14.982 81.427 4496 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.09 % Allowed : 0.27 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.22), residues: 1319 helix: 0.61 (0.22), residues: 535 sheet: -0.87 (0.37), residues: 170 loop : -0.18 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 352 TYR 0.016 0.001 TYR A 482 PHE 0.036 0.002 PHE B 289 TRP 0.027 0.002 TRP A 474 HIS 0.004 0.001 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.35 (11650) covalent geometry : angle 0.66727 / 0.33 (15944) hydrogen bonds : bond 0.13355 / 8.70 ( 467) hydrogen bonds : angle 5.61055 / 4.04 ( 1284) metal coordination : bond 0.00599 / 0.36 ( 7) metal coordination : angle 1.64704 / 0.69 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.441 Fit side-chains REVERT: A 39 THR cc_start: 0.8356 (p) cc_final: 0.8129 (p) REVERT: A 141 ASP cc_start: 0.8450 (m-30) cc_final: 0.8028 (m-30) REVERT: A 240 ASN cc_start: 0.8408 (t0) cc_final: 0.7935 (t0) REVERT: A 356 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7175 (mt-10) REVERT: B 336 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7195 (tt0) REVERT: B 421 ASP cc_start: 0.7627 (m-30) cc_final: 0.7400 (m-30) REVERT: B 619 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7922 (ttmt) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.7134 time to fit residues: 122.4162 Evaluate side-chains 133 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN A 742 GLN ** B 385 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 = 0.3228 r_free = 0.3228 target = 0.113926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.084427 restraints weight = 13387.690| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.64 r_work: 0.2676 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11657 Z= 0.108 Angle : 0.545 9.135 15946 Z= 0.266 Chirality : 0.047 0.504 1748 Planarity : 0.004 0.045 1919 Dihedral : 8.932 90.212 1904 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.89 % Allowed : 6.35 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.23), residues: 1319 helix: 1.09 (0.23), residues: 538 sheet: -0.86 (0.36), residues: 187 loop : 0.00 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 281 TYR 0.013 0.001 TYR A 482 PHE 0.021 0.002 PHE B 289 TRP 0.013 0.001 TRP A 746 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (11650) covalent geometry : angle 0.54455 / 0.27 (15944) hydrogen bonds : bond 0.03697 / 2.50 ( 467) hydrogen bonds : angle 4.59063 / 3.35 ( 1284) metal coordination : bond 0.00453 / 0.32 ( 7) metal coordination : angle 1.68251 / 0.71 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.431 Fit side-chains REVERT: A 141 ASP cc_start: 0.8832 (m-30) cc_final: 0.8488 (m-30) REVERT: A 146 ASP cc_start: 0.8864 (t70) cc_final: 0.8598 (t70) REVERT: A 240 ASN cc_start: 0.8243 (t0) cc_final: 0.7815 (t0) REVERT: A 356 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8049 (mt-10) REVERT: A 396 GLU cc_start: 0.8017 (mp0) cc_final: 0.7712 (mm-30) REVERT: A 435 ASP cc_start: 0.8232 (m-30) cc_final: 0.7961 (m-30) REVERT: B 336 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7699 (mt-10) REVERT: B 378 LYS cc_start: 0.7813 (mtpm) cc_final: 0.7449 (mtpt) REVERT: B 421 ASP cc_start: 0.7887 (m-30) cc_final: 0.7531 (m-30) outliers start: 10 outliers final: 3 residues processed: 145 average time/residue: 0.7182 time to fit residues: 111.3576 Evaluate side-chains 132 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain B residue 322 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 0.0970 chunk 35 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 0.0970 chunk 121 optimal weight: 0.9990 overall best weight: 1.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN A 742 GLN B 486 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.082459 restraints weight = 13424.955| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.64 r_work: 0.2608 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9123 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11657 Z= 0.133 Angle : 0.525 6.751 15946 Z= 0.261 Chirality : 0.045 0.313 1748 Planarity : 0.004 0.047 1919 Dihedral : 8.631 104.230 1904 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.07 % Allowed : 8.32 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.23), residues: 1319 helix: 1.24 (0.23), residues: 537 sheet: -0.71 (0.36), residues: 182 loop : -0.02 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.017 0.001 TYR A 482 PHE 0.018 0.002 PHE B 289 TRP 0.013 0.001 TRP A 746 HIS 0.004 0.001 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (11650) covalent geometry : angle 0.52479 / 0.26 (15944) hydrogen bonds : bond 0.03795 / 2.57 ( 467) hydrogen bonds : angle 4.46206 / 3.26 ( 1284) metal coordination : bond 0.00552 / 0.37 ( 7) metal coordination : angle 1.12156 / 0.51 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.418 Fit side-chains REVERT: A 141 ASP cc_start: 0.8853 (m-30) cc_final: 0.8525 (m-30) REVERT: A 240 ASN cc_start: 0.8359 (t0) cc_final: 0.8110 (t0) REVERT: A 356 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8099 (mt-10) REVERT: A 435 ASP cc_start: 0.8239 (m-30) cc_final: 0.7951 (m-30) REVERT: A 632 ASP cc_start: 0.8214 (m-30) cc_final: 0.7885 (m-30) REVERT: B 378 LYS cc_start: 0.7772 (mtpm) cc_final: 0.7440 (mtpt) REVERT: B 421 ASP cc_start: 0.8057 (m-30) cc_final: 0.7675 (m-30) outliers start: 12 outliers final: 4 residues processed: 141 average time/residue: 0.6945 time to fit residues: 104.5306 Evaluate side-chains 135 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain B residue 322 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 133 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.0370 chunk 63 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN A 742 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.111774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.082023 restraints weight = 13427.119| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 1.64 r_work: 0.2625 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11657 Z= 0.162 Angle : 0.543 6.872 15946 Z= 0.270 Chirality : 0.046 0.289 1748 Planarity : 0.004 0.048 1919 Dihedral : 8.576 103.930 1904 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.16 % Allowed : 9.30 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.23), residues: 1319 helix: 1.24 (0.23), residues: 537 sheet: -0.70 (0.37), residues: 182 loop : -0.03 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 352 TYR 0.018 0.001 TYR A 482 PHE 0.019 0.002 PHE A 674 TRP 0.013 0.001 TRP A 746 HIS 0.005 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (11650) covalent geometry : angle 0.54308 / 0.27 (15944) hydrogen bonds : bond 0.04004 / 2.71 ( 467) hydrogen bonds : angle 4.46660 / 3.27 ( 1284) metal coordination : bond 0.00659 / 0.44 ( 7) metal coordination : angle 0.98527 / 0.44 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.458 Fit side-chains REVERT: A 141 ASP cc_start: 0.8854 (m-30) cc_final: 0.8529 (m-30) REVERT: A 146 ASP cc_start: 0.8864 (t70) cc_final: 0.8577 (t70) REVERT: A 240 ASN cc_start: 0.8443 (t0) cc_final: 0.8088 (t0) REVERT: A 356 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8122 (mt-10) REVERT: A 435 ASP cc_start: 0.8208 (m-30) cc_final: 0.7992 (m-30) REVERT: A 632 ASP cc_start: 0.8197 (m-30) cc_final: 0.7864 (m-30) REVERT: A 824 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7993 (ttp) REVERT: B 378 LYS cc_start: 0.7716 (mtpm) cc_final: 0.7404 (mtpt) REVERT: B 382 LYS cc_start: 0.7823 (ptpt) cc_final: 0.7500 (pttp) REVERT: B 421 ASP cc_start: 0.8115 (m-30) cc_final: 0.7787 (m-30) outliers start: 13 outliers final: 5 residues processed: 148 average time/residue: 0.7899 time to fit residues: 124.7377 Evaluate side-chains 143 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 322 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN A 742 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.110225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.080547 restraints weight = 13346.165| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 1.63 r_work: 0.2601 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11657 Z= 0.228 Angle : 0.599 7.033 15946 Z= 0.298 Chirality : 0.049 0.314 1748 Planarity : 0.005 0.050 1919 Dihedral : 8.663 103.490 1904 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.34 % Allowed : 10.20 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.23), residues: 1319 helix: 1.09 (0.23), residues: 536 sheet: -0.82 (0.36), residues: 184 loop : -0.05 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 352 TYR 0.020 0.002 TYR A 482 PHE 0.022 0.002 PHE A 674 TRP 0.014 0.002 TRP A 746 HIS 0.005 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (11650) covalent geometry : angle 0.59932 / 0.30 (15944) hydrogen bonds : bond 0.04532 / 3.05 ( 467) hydrogen bonds : angle 4.56286 / 3.35 ( 1284) metal coordination : bond 0.00855 / 0.56 ( 7) metal coordination : angle 0.81739 / 0.34 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.448 Fit side-chains REVERT: A 141 ASP cc_start: 0.8885 (m-30) cc_final: 0.8558 (m-30) REVERT: A 240 ASN cc_start: 0.8531 (t0) cc_final: 0.8173 (t0) REVERT: A 356 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8117 (mt-10) REVERT: A 632 ASP cc_start: 0.8210 (m-30) cc_final: 0.7876 (m-30) REVERT: B 378 LYS cc_start: 0.7692 (mtpm) cc_final: 0.7402 (mtpt) REVERT: B 382 LYS cc_start: 0.7863 (ptpt) cc_final: 0.7487 (pttp) REVERT: B 421 ASP cc_start: 0.8115 (m-30) cc_final: 0.7793 (m-30) outliers start: 15 outliers final: 8 residues processed: 147 average time/residue: 0.7971 time to fit residues: 125.1355 Evaluate side-chains 145 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 574 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 130 optimal weight: 0.0870 chunk 95 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 25 optimal weight: 0.0050 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.4972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN A 613 ASN ** A 742 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 = 0.3245 r_free = 0.3245 target = 0.115082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.085542 restraints weight = 13329.263| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.64 r_work: 0.2668 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11657 Z= 0.087 Angle : 0.485 7.239 15946 Z= 0.241 Chirality : 0.043 0.286 1748 Planarity : 0.004 0.045 1919 Dihedral : 8.339 106.475 1904 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.16 % Allowed : 11.27 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.23), residues: 1319 helix: 1.44 (0.23), residues: 539 sheet: -0.56 (0.37), residues: 189 loop : 0.06 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 352 TYR 0.011 0.001 TYR A 482 PHE 0.015 0.001 PHE B 534 TRP 0.013 0.001 TRP A 746 HIS 0.003 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (11650) covalent geometry : angle 0.48450 / 0.24 (15944) hydrogen bonds : bond 0.03109 / 2.12 ( 467) hydrogen bonds : angle 4.26323 / 3.13 ( 1284) metal coordination : bond 0.00237 / 0.16 ( 7) metal coordination : angle 1.65369 / 0.71 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.450 Fit side-chains REVERT: A 141 ASP cc_start: 0.8836 (m-30) cc_final: 0.8547 (m-30) REVERT: A 146 ASP cc_start: 0.8785 (t70) cc_final: 0.8515 (t70) REVERT: A 240 ASN cc_start: 0.8378 (t0) cc_final: 0.8029 (t0) REVERT: A 356 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8083 (mt-10) REVERT: A 396 GLU cc_start: 0.7952 (mp0) cc_final: 0.7592 (mm-30) REVERT: A 435 ASP cc_start: 0.8136 (m-30) cc_final: 0.7910 (m-30) REVERT: A 632 ASP cc_start: 0.8171 (m-30) cc_final: 0.7826 (m-30) REVERT: B 291 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8157 (t0) REVERT: B 378 LYS cc_start: 0.7756 (mtpm) cc_final: 0.7482 (mtpt) REVERT: B 382 LYS cc_start: 0.7824 (ptpt) cc_final: 0.7468 (pttp) REVERT: B 421 ASP cc_start: 0.8116 (m-30) cc_final: 0.7791 (m-30) outliers start: 13 outliers final: 2 residues processed: 148 average time/residue: 0.7742 time to fit residues: 122.5158 Evaluate side-chains 135 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 322 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 118 optimal weight: 0.0870 chunk 107 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.2760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 742 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.113314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.083638 restraints weight = 13337.345| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 1.64 r_work: 0.2619 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11657 Z= 0.122 Angle : 0.510 7.292 15946 Z= 0.253 Chirality : 0.044 0.275 1748 Planarity : 0.004 0.047 1919 Dihedral : 8.215 106.601 1904 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.34 % Allowed : 11.18 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.23), residues: 1319 helix: 1.48 (0.23), residues: 537 sheet: -0.57 (0.38), residues: 179 loop : 0.10 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 352 TYR 0.017 0.001 TYR A 482 PHE 0.016 0.001 PHE A 674 TRP 0.015 0.001 TRP A 746 HIS 0.004 0.001 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (11650) covalent geometry : angle 0.50981 / 0.25 (15944) hydrogen bonds : bond 0.03484 / 2.36 ( 467) hydrogen bonds : angle 4.28996 / 3.14 ( 1284) metal coordination : bond 0.00442 / 0.29 ( 7) metal coordination : angle 1.03618 / 0.47 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.445 Fit side-chains REVERT: A 141 ASP cc_start: 0.8851 (m-30) cc_final: 0.8557 (m-30) REVERT: A 146 ASP cc_start: 0.8848 (t70) cc_final: 0.8627 (t70) REVERT: A 240 ASN cc_start: 0.8483 (t0) cc_final: 0.8128 (t0) REVERT: A 352 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8477 (ttt-90) REVERT: A 356 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8022 (mt-10) REVERT: A 396 GLU cc_start: 0.7977 (mp0) cc_final: 0.7602 (mm-30) REVERT: A 435 ASP cc_start: 0.8124 (m-30) cc_final: 0.7911 (m-30) REVERT: A 632 ASP cc_start: 0.8147 (m-30) cc_final: 0.7797 (m-30) REVERT: A 824 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8030 (ttp) REVERT: B 339 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7872 (t70) REVERT: B 378 LYS cc_start: 0.7695 (mtpm) cc_final: 0.7428 (mtpt) REVERT: B 382 LYS cc_start: 0.7783 (ptpt) cc_final: 0.7407 (pttp) REVERT: B 421 ASP cc_start: 0.8155 (m-30) cc_final: 0.7819 (m-30) outliers start: 15 outliers final: 4 residues processed: 145 average time/residue: 0.7451 time to fit residues: 115.6901 Evaluate side-chains 144 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 339 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 13 optimal weight: 0.3980 chunk 63 optimal weight: 0.4980 chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 0.0270 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 742 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.112700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.082871 restraints weight = 13213.978| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 1.64 r_work: 0.2607 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11657 Z= 0.140 Angle : 0.526 7.277 15946 Z= 0.261 Chirality : 0.045 0.270 1748 Planarity : 0.004 0.046 1919 Dihedral : 8.208 106.591 1904 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.34 % Allowed : 11.45 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.23), residues: 1319 helix: 1.44 (0.23), residues: 536 sheet: -0.66 (0.37), residues: 184 loop : 0.10 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 436 TYR 0.018 0.001 TYR A 482 PHE 0.017 0.002 PHE A 674 TRP 0.017 0.001 TRP A 746 HIS 0.004 0.001 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (11650) covalent geometry : angle 0.52600 / 0.26 (15944) hydrogen bonds : bond 0.03660 / 2.48 ( 467) hydrogen bonds : angle 4.32494 / 3.17 ( 1284) metal coordination : bond 0.00519 / 0.33 ( 7) metal coordination : angle 0.85197 / 0.39 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 141 ASP cc_start: 0.8870 (m-30) cc_final: 0.8572 (m-30) REVERT: A 146 ASP cc_start: 0.8869 (t70) cc_final: 0.8616 (t70) REVERT: A 240 ASN cc_start: 0.8495 (t0) cc_final: 0.8132 (t0) REVERT: A 356 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8070 (mt-10) REVERT: A 396 GLU cc_start: 0.7983 (mp0) cc_final: 0.7597 (mm-30) REVERT: A 435 ASP cc_start: 0.8140 (m-30) cc_final: 0.7939 (m-30) REVERT: A 632 ASP cc_start: 0.8170 (m-30) cc_final: 0.7827 (m-30) REVERT: A 824 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8009 (ttp) REVERT: B 339 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7888 (t70) REVERT: B 378 LYS cc_start: 0.7703 (mtpm) cc_final: 0.7440 (mtpt) REVERT: B 382 LYS cc_start: 0.7808 (ptpt) cc_final: 0.7394 (pttp) REVERT: B 421 ASP cc_start: 0.8156 (m-30) cc_final: 0.7836 (m-30) outliers start: 15 outliers final: 5 residues processed: 144 average time/residue: 0.7578 time to fit residues: 116.2322 Evaluate side-chains 145 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 339 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 129 optimal weight: 5.9990 chunk 43 optimal weight: 0.0770 chunk 67 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 742 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.113582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.083924 restraints weight = 13165.200| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 1.63 r_work: 0.2626 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11657 Z= 0.116 Angle : 0.507 7.405 15946 Z= 0.251 Chirality : 0.044 0.261 1748 Planarity : 0.004 0.046 1919 Dihedral : 8.145 107.077 1904 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.07 % Allowed : 11.54 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.23), residues: 1319 helix: 1.48 (0.23), residues: 537 sheet: -0.54 (0.38), residues: 179 loop : 0.11 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 436 TYR 0.016 0.001 TYR A 482 PHE 0.016 0.001 PHE A 674 TRP 0.017 0.001 TRP A 746 HIS 0.003 0.001 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (11650) covalent geometry : angle 0.50676 / 0.25 (15944) hydrogen bonds : bond 0.03418 / 2.32 ( 467) hydrogen bonds : angle 4.26680 / 3.13 ( 1284) metal coordination : bond 0.00408 / 0.26 ( 7) metal coordination : angle 1.08478 / 0.49 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.415 Fit side-chains REVERT: A 141 ASP cc_start: 0.8856 (m-30) cc_final: 0.8570 (m-30) REVERT: A 240 ASN cc_start: 0.8489 (t0) cc_final: 0.8137 (t0) REVERT: A 356 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8088 (mt-10) REVERT: A 396 GLU cc_start: 0.7977 (mp0) cc_final: 0.7616 (mm-30) REVERT: A 632 ASP cc_start: 0.8148 (m-30) cc_final: 0.7799 (m-30) REVERT: B 339 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7894 (t70) REVERT: B 378 LYS cc_start: 0.7676 (mtpm) cc_final: 0.7417 (mtpt) REVERT: B 382 LYS cc_start: 0.7794 (ptpt) cc_final: 0.7395 (pttp) REVERT: B 421 ASP cc_start: 0.8171 (m-30) cc_final: 0.7832 (m-30) REVERT: B 554 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7791 (mp0) outliers start: 12 outliers final: 5 residues processed: 148 average time/residue: 0.7740 time to fit residues: 122.2394 Evaluate side-chains 145 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 554 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 75 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 742 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.112774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.083025 restraints weight = 13314.647| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 1.63 r_work: 0.2635 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11657 Z= 0.139 Angle : 0.530 7.337 15946 Z= 0.263 Chirality : 0.045 0.255 1748 Planarity : 0.004 0.046 1919 Dihedral : 8.123 107.143 1904 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.16 % Allowed : 11.63 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.23), residues: 1319 helix: 1.43 (0.23), residues: 537 sheet: -0.62 (0.37), residues: 184 loop : 0.13 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 187 TYR 0.018 0.001 TYR A 482 PHE 0.017 0.002 PHE A 674 TRP 0.017 0.001 TRP A 746 HIS 0.004 0.001 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (11650) covalent geometry : angle 0.52955 / 0.26 (15944) hydrogen bonds : bond 0.03646 / 2.47 ( 467) hydrogen bonds : angle 4.31599 / 3.17 ( 1284) metal coordination : bond 0.00515 / 0.33 ( 7) metal coordination : angle 0.79704 / 0.37 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.440 Fit side-chains REVERT: A 141 ASP cc_start: 0.8855 (m-30) cc_final: 0.8565 (m-30) REVERT: A 146 ASP cc_start: 0.8869 (t70) cc_final: 0.8562 (t70) REVERT: A 240 ASN cc_start: 0.8517 (t0) cc_final: 0.8166 (t0) REVERT: A 356 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8076 (mt-10) REVERT: A 396 GLU cc_start: 0.7978 (mp0) cc_final: 0.7616 (mm-30) REVERT: A 632 ASP cc_start: 0.8157 (m-30) cc_final: 0.7793 (m-30) REVERT: A 824 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8031 (ttp) REVERT: B 315 MET cc_start: 0.8788 (mtt) cc_final: 0.8503 (mmt) REVERT: B 339 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7892 (t70) REVERT: B 378 LYS cc_start: 0.7691 (mtpm) cc_final: 0.7434 (mtpt) REVERT: B 382 LYS cc_start: 0.7805 (ptpt) cc_final: 0.7404 (pttp) REVERT: B 421 ASP cc_start: 0.8201 (m-30) cc_final: 0.7832 (m-30) outliers start: 13 outliers final: 7 residues processed: 144 average time/residue: 0.7759 time to fit residues: 119.4429 Evaluate side-chains 146 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 574 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 84 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 742 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.112210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.082329 restraints weight = 13282.510| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 1.65 r_work: 0.2598 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11657 Z= 0.154 Angle : 0.542 7.322 15946 Z= 0.270 Chirality : 0.046 0.255 1748 Planarity : 0.004 0.047 1919 Dihedral : 8.133 107.173 1904 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.98 % Allowed : 12.08 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.23), residues: 1319 helix: 1.39 (0.23), residues: 537 sheet: -0.62 (0.37), residues: 184 loop : 0.12 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 187 TYR 0.018 0.001 TYR A 482 PHE 0.018 0.002 PHE A 674 TRP 0.017 0.001 TRP A 746 HIS 0.004 0.001 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (11650) covalent geometry : angle 0.54229 / 0.27 (15944) hydrogen bonds : bond 0.03808 / 2.57 ( 467) hydrogen bonds : angle 4.36264 / 3.20 ( 1284) metal coordination : bond 0.00545 / 0.36 ( 7) metal coordination : angle 0.80677 / 0.38 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4220.43 seconds wall clock time: 72 minutes 43.40 seconds (4363.40 seconds total)