Starting phenix.real_space_refine on Fri Jul 3 01:53:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gzr_34402/07_2026/8gzr_34402.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gzr_34402/07_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_34402/07_2026/8gzr_34402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gzr_34402/07_2026/8gzr_34402.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gzr_34402/07_2026/8gzr_34402.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gzr_34402/07_2026/8gzr_34402.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gzr_34402/07_2026/8gzr_34402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gzr_34402/07_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-dev-6108/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: {'RNA': 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: 2.59, 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: 0.89 Conformation dependent library (CDL) restraints added in 517.5 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: 1.19 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: 2.22 Time building geometry restraints manager: 1.17 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: 15789 2.44 - 4.87: 126 4.87 - 7.31: 22 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 - 24.72: 6533 24.72 - 49.45: 374 49.45 - 74.17: 41 74.17 - 98.90: 5 98.90 - 123.62: 1 Dihedral angle restraints: 6954 sinusoidal: 3141 harmonic: 3813 Sorted by residual: dihedral pdb=" CA TYR A 451 " pdb=" C TYR A 451 " pdb=" N ASN A 452 " pdb=" CA ASN A 452 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA HIS A 711 " pdb=" C HIS A 711 " pdb=" N HIS A 712 " pdb=" CA HIS A 712 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA LYS A 357 " pdb=" C LYS A 357 " pdb=" N VAL A 358 " pdb=" CA VAL A 358 " ideal model delta harmonic sigma weight residual 180.00 -163.04 -16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 6951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1557 0.065 - 0.129: 186 0.129 - 0.194: 4 0.194 - 0.259: 0 0.259 - 0.323: 1 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=" CB VAL B 462 " pdb=" CA VAL B 462 " pdb=" CG1 VAL B 462 " pdb=" CG2 VAL B 462 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" C1' SAH A1005 " pdb=" C2' SAH A1005 " pdb=" N9 SAH A1005 " pdb=" O4' SAH A1005 " both_signs ideal model delta sigma weight residual False 2.35 2.52 -0.17 2.00e-01 2.50e+01 7.34e-01 ... (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: 0.940 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.430 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.640 ------------------------------------------------------------------------------- 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= 0.350 Angle : 0.628 12.177 15946 Z= 0.327 Chirality : 0.043 0.323 1748 Planarity : 0.004 0.046 1919 Dihedral : 14.371 123.622 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 0.00726 / 0.35 (11650) covalent geometry : angle 0.62766 / 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 : 0.471 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: 0.7682 time to fit residues: 131.3913 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 : 0.421 ------------------------------------------------------------------------------- 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 = 0.3221 r_free = 0.3221 target = 0.113415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.084081 restraints weight = 13447.425| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 1.64 r_work: 0.2650 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11657 Z= 0.104 Angle : 0.469 5.002 15946 Z= 0.249 Chirality : 0.040 0.139 1748 Planarity : 0.004 0.045 1919 Dihedral : 7.826 122.526 1904 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.89 % Allowed : 6.26 % Favored : 92.84 % 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: 1.10 (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 0.020 0.002 PHE B 289 TRP 0.013 0.001 TRP A 746 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (11650) covalent geometry : angle 0.46913 / 0.25 (15944) hydrogen bonds : bond 0.03724 / 2.52 ( 467) hydrogen bonds : angle 4.60306 / 3.36 ( 1284) metal coordination : bond 0.00488 / 0.34 ( 7) metal coordination : angle 1.68219 / 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 150 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.392 Fit side-chains REVERT: A 141 ASP cc_start: 0.8843 (m-30) cc_final: 0.8495 (m-30) REVERT: A 146 ASP cc_start: 0.8858 (t70) cc_final: 0.8587 (t70) REVERT: A 240 ASN cc_start: 0.8261 (t0) cc_final: 0.7860 (t0) REVERT: A 356 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8067 (mt-10) REVERT: A 435 ASP cc_start: 0.8215 (m-30) cc_final: 0.7943 (m-30) REVERT: B 336 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7709 (mt-10) REVERT: B 378 LYS cc_start: 0.7816 (mtpm) cc_final: 0.7446 (mtpt) REVERT: B 421 ASP cc_start: 0.7888 (m-30) cc_final: 0.7533 (m-30) outliers start: 10 outliers final: 3 residues processed: 144 average time/residue: 0.7596 time to fit residues: 116.5876 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 : 0.444 ------------------------------------------------------------------------------- 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: 2.9990 chunk 33 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 0.0000 chunk 35 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 121 optimal weight: 0.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.113190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.083709 restraints weight = 13484.228| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 1.65 r_work: 0.2654 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.1024 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= 0.111 Angle : 0.455 5.217 15946 Z= 0.241 Chirality : 0.040 0.140 1748 Planarity : 0.004 0.046 1919 Dihedral : 7.386 124.265 1904 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.07 % Allowed : 8.41 % Favored : 90.52 % 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: 0.57 (0.23), residues: 1319 helix: 1.30 (0.23), residues: 538 sheet: -0.62 (0.37), residues: 187 loop : -0.00 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 352 TYR 0.015 0.001 TYR A 482 PHE 0.018 0.001 PHE B 289 TRP 0.013 0.001 TRP A 746 HIS 0.003 0.001 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (11650) covalent geometry : angle 0.45497 / 0.24 (15944) hydrogen bonds : bond 0.03542 / 2.40 ( 467) hydrogen bonds : angle 4.40513 / 3.22 ( 1284) metal coordination : bond 0.00467 / 0.31 ( 7) metal coordination : angle 1.23155 / 0.53 ( 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 148 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.440 Fit side-chains REVERT: A 141 ASP cc_start: 0.8841 (m-30) cc_final: 0.8524 (m-30) REVERT: A 240 ASN cc_start: 0.8331 (t0) cc_final: 0.7982 (t0) REVERT: A 356 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8107 (mt-10) REVERT: A 396 GLU cc_start: 0.8013 (mp0) cc_final: 0.7720 (mm-30) REVERT: A 435 ASP cc_start: 0.8243 (m-30) cc_final: 0.7949 (m-30) REVERT: A 632 ASP cc_start: 0.8210 (m-30) cc_final: 0.7890 (m-30) REVERT: B 378 LYS cc_start: 0.7777 (mtpm) cc_final: 0.7441 (mtpt) REVERT: B 421 ASP cc_start: 0.8014 (m-30) cc_final: 0.7642 (m-30) outliers start: 12 outliers final: 5 residues processed: 142 average time/residue: 0.7727 time to fit residues: 117.1326 Evaluate side-chains 136 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 309 GLU 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: 7.9990 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3170 r_free = 0.3170 target = 0.109515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.079840 restraints weight = 13524.877| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 1.65 r_work: 0.2524 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2390 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11657 Z= 0.242 Angle : 0.561 7.249 15946 Z= 0.294 Chirality : 0.045 0.159 1748 Planarity : 0.005 0.050 1919 Dihedral : 7.854 131.583 1904 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.43 % Allowed : 9.21 % Favored : 89.36 % 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: 0.35 (0.23), residues: 1319 helix: 1.06 (0.23), residues: 536 sheet: -0.81 (0.36), residues: 182 loop : -0.05 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 598 TYR 0.022 0.002 TYR A 482 PHE 0.021 0.002 PHE A 674 TRP 0.015 0.002 TRP A 746 HIS 0.006 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.24 (11650) covalent geometry : angle 0.56114 / 0.29 (15944) hydrogen bonds : bond 0.04731 / 3.19 ( 467) hydrogen bonds : angle 4.62627 / 3.39 ( 1284) metal coordination : bond 0.00958 / 0.64 ( 7) metal coordination : angle 0.79208 / 0.30 ( 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 153 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.453 Fit side-chains REVERT: A 141 ASP cc_start: 0.8928 (m-30) cc_final: 0.8584 (m-30) REVERT: A 146 ASP cc_start: 0.8938 (t70) cc_final: 0.8652 (t70) REVERT: A 240 ASN cc_start: 0.8523 (t0) cc_final: 0.8151 (t0) REVERT: A 356 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8168 (mt-10) REVERT: A 824 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7993 (ttp) REVERT: B 378 LYS cc_start: 0.7727 (mtpm) cc_final: 0.7421 (mtpt) REVERT: B 382 LYS cc_start: 0.7860 (ptpt) cc_final: 0.7500 (pttp) REVERT: B 421 ASP cc_start: 0.8115 (m-30) cc_final: 0.7798 (m-30) outliers start: 16 outliers final: 7 residues processed: 145 average time/residue: 0.8040 time to fit residues: 124.1365 Evaluate side-chains 143 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 244 MET 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 191 ILE 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: 0.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN A 613 ASN A 742 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.081341 restraints weight = 13404.936| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 1.63 r_work: 0.2606 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11657 Z= 0.163 Angle : 0.500 6.680 15946 Z= 0.264 Chirality : 0.042 0.159 1748 Planarity : 0.004 0.048 1919 Dihedral : 7.598 127.086 1904 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.25 % Allowed : 10.11 % Favored : 88.64 % 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: 0.42 (0.23), residues: 1319 helix: 1.16 (0.23), residues: 537 sheet: -0.82 (0.36), residues: 184 loop : -0.05 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.018 0.001 TYR A 482 PHE 0.019 0.002 PHE A 674 TRP 0.015 0.001 TRP A 746 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (11650) covalent geometry : angle 0.50001 / 0.26 (15944) hydrogen bonds : bond 0.04046 / 2.74 ( 467) hydrogen bonds : angle 4.48835 / 3.29 ( 1284) metal coordination : bond 0.00643 / 0.42 ( 7) metal coordination : angle 1.21092 / 0.52 ( 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: 14 poor density : 140 time to evaluate : 0.444 Fit side-chains REVERT: A 141 ASP cc_start: 0.8873 (m-30) cc_final: 0.8551 (m-30) REVERT: A 146 ASP cc_start: 0.8876 (t70) cc_final: 0.8563 (t70) REVERT: A 240 ASN cc_start: 0.8480 (t0) cc_final: 0.8108 (t0) REVERT: A 321 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8723 (m-40) REVERT: A 356 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8156 (mt-10) REVERT: A 396 GLU cc_start: 0.7993 (mp0) cc_final: 0.7653 (mm-30) REVERT: A 632 ASP cc_start: 0.8205 (m-30) cc_final: 0.7875 (m-30) REVERT: A 824 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8054 (ttp) REVERT: B 378 LYS cc_start: 0.7696 (mtpm) cc_final: 0.7396 (mtpt) REVERT: B 382 LYS cc_start: 0.7861 (ptpt) cc_final: 0.7476 (pttp) REVERT: B 421 ASP cc_start: 0.8092 (m-30) cc_final: 0.7775 (m-30) REVERT: B 472 GLN cc_start: 0.8667 (mt0) cc_final: 0.8359 (pt0) outliers start: 14 outliers final: 8 residues processed: 147 average time/residue: 0.6714 time to fit residues: 105.7369 Evaluate side-chains 149 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 244 MET Chi-restraints excluded: chain A residue 321 ASN 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: 2.9990 chunk 95 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.0370 chunk 114 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.113903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.084553 restraints weight = 13425.052| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 1.65 r_work: 0.2653 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11657 Z= 0.088 Angle : 0.435 5.110 15946 Z= 0.231 Chirality : 0.039 0.147 1748 Planarity : 0.004 0.046 1919 Dihedral : 7.177 122.095 1904 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.52 % Allowed : 10.82 % Favored : 87.66 % 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: 0.68 (0.23), residues: 1319 helix: 1.42 (0.23), residues: 538 sheet: -0.60 (0.38), residues: 179 loop : 0.02 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.012 0.001 TYR A 482 PHE 0.014 0.001 PHE B 534 TRP 0.011 0.001 TRP A 859 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 (11650) covalent geometry : angle 0.43494 / 0.23 (15944) hydrogen bonds : bond 0.03175 / 2.16 ( 467) hydrogen bonds : angle 4.29019 / 3.14 ( 1284) metal coordination : bond 0.00304 / 0.20 ( 7) metal coordination : angle 1.58149 / 0.67 ( 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 158 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.446 Fit side-chains REVERT: A 141 ASP cc_start: 0.8851 (m-30) cc_final: 0.8566 (m-30) REVERT: A 146 ASP cc_start: 0.8855 (t70) cc_final: 0.8599 (t70) REVERT: A 240 ASN cc_start: 0.8392 (t0) cc_final: 0.8040 (t0) REVERT: A 352 ARG cc_start: 0.8638 (mtp180) cc_final: 0.8409 (ttp-170) REVERT: A 356 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8090 (mt-10) REVERT: A 396 GLU cc_start: 0.7956 (mp0) cc_final: 0.7591 (mm-30) REVERT: A 632 ASP cc_start: 0.8180 (m-30) cc_final: 0.7838 (m-30) REVERT: B 339 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7877 (t70) REVERT: B 378 LYS cc_start: 0.7752 (mtpm) cc_final: 0.7475 (mtpt) REVERT: B 382 LYS cc_start: 0.7823 (ptpt) cc_final: 0.7461 (pttp) REVERT: B 421 ASP cc_start: 0.8125 (m-30) cc_final: 0.7791 (m-30) outliers start: 17 outliers final: 4 residues processed: 148 average time/residue: 0.7788 time to fit residues: 123.0594 Evaluate side-chains 141 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 322 THR Chi-restraints excluded: chain B residue 339 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 118 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 28 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3193 r_free = 0.3193 target = 0.111145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.081586 restraints weight = 13467.681| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 1.64 r_work: 0.2620 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11657 Z= 0.146 Angle : 0.480 5.874 15946 Z= 0.253 Chirality : 0.041 0.146 1748 Planarity : 0.004 0.048 1919 Dihedral : 7.304 126.332 1904 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.52 % Allowed : 10.73 % Favored : 87.75 % 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: 0.66 (0.23), residues: 1319 helix: 1.38 (0.23), residues: 537 sheet: -0.68 (0.37), residues: 184 loop : 0.06 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 352 TYR 0.018 0.001 TYR A 482 PHE 0.018 0.002 PHE A 674 TRP 0.014 0.001 TRP A 746 HIS 0.004 0.001 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (11650) covalent geometry : angle 0.47982 / 0.25 (15944) hydrogen bonds : bond 0.03769 / 2.54 ( 467) hydrogen bonds : angle 4.36314 / 3.20 ( 1284) metal coordination : bond 0.00539 / 0.35 ( 7) metal coordination : angle 0.86556 / 0.38 ( 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: 17 poor density : 137 time to evaluate : 0.457 Fit side-chains REVERT: A 141 ASP cc_start: 0.8858 (m-30) cc_final: 0.8558 (m-30) REVERT: A 146 ASP cc_start: 0.8862 (t70) cc_final: 0.8613 (t70) REVERT: A 240 ASN cc_start: 0.8488 (t0) cc_final: 0.8118 (t0) REVERT: A 352 ARG cc_start: 0.8657 (mtp180) cc_final: 0.8053 (ttt-90) REVERT: A 356 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8112 (mt-10) REVERT: A 396 GLU cc_start: 0.7990 (mp0) cc_final: 0.7623 (mm-30) REVERT: A 468 LYS cc_start: 0.8485 (mmtp) cc_final: 0.8127 (mptp) REVERT: A 632 ASP cc_start: 0.8167 (m-30) cc_final: 0.7822 (m-30) REVERT: A 824 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8033 (ttp) REVERT: B 378 LYS cc_start: 0.7699 (mtpm) cc_final: 0.7428 (mtpt) REVERT: B 382 LYS cc_start: 0.7818 (ptpt) cc_final: 0.7414 (pttp) REVERT: B 421 ASP cc_start: 0.8164 (m-30) cc_final: 0.7846 (m-30) outliers start: 17 outliers final: 7 residues processed: 145 average time/residue: 0.7480 time to fit residues: 115.7405 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 : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 81 optimal weight: 0.3980 chunk 89 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 = 0.3189 r_free = 0.3189 target = 0.110816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.081419 restraints weight = 13329.755| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 1.62 r_work: 0.2605 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9139 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11657 Z= 0.178 Angle : 0.507 7.337 15946 Z= 0.266 Chirality : 0.042 0.152 1748 Planarity : 0.004 0.048 1919 Dihedral : 7.396 128.258 1904 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.25 % Allowed : 11.54 % 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: 0.58 (0.23), residues: 1319 helix: 1.30 (0.23), residues: 536 sheet: -0.73 (0.37), residues: 184 loop : 0.04 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 598 TYR 0.019 0.002 TYR A 482 PHE 0.020 0.002 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 0.00422 / 0.18 (11650) covalent geometry : angle 0.50698 / 0.27 (15944) hydrogen bonds : bond 0.04079 / 2.75 ( 467) hydrogen bonds : angle 4.43502 / 3.25 ( 1284) metal coordination : bond 0.00651 / 0.43 ( 7) metal coordination : angle 0.89240 / 0.40 ( 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 153 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.437 Fit side-chains REVERT: A 141 ASP cc_start: 0.8858 (m-30) cc_final: 0.8550 (m-30) REVERT: A 146 ASP cc_start: 0.8903 (t70) cc_final: 0.8620 (t70) REVERT: A 240 ASN cc_start: 0.8544 (t0) cc_final: 0.8177 (t0) REVERT: A 356 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8184 (mt-10) REVERT: A 396 GLU cc_start: 0.7979 (mp0) cc_final: 0.7614 (mm-30) REVERT: A 632 ASP cc_start: 0.8203 (m-30) cc_final: 0.7860 (m-30) REVERT: A 824 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8061 (ttp) REVERT: B 378 LYS cc_start: 0.7670 (mtpm) cc_final: 0.7399 (mtpt) REVERT: B 382 LYS cc_start: 0.7858 (ptpt) cc_final: 0.7440 (pttp) REVERT: B 421 ASP cc_start: 0.8166 (m-30) cc_final: 0.7858 (m-30) outliers start: 14 outliers final: 5 residues processed: 145 average time/residue: 0.6269 time to fit residues: 97.0659 Evaluate side-chains 144 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 824 MET Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 574 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 129 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 118 optimal weight: 0.0770 overall best weight: 1.7744 ------------------------------------------------------------------------------- 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 = 0.3198 r_free = 0.3198 target = 0.111472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.082078 restraints weight = 13322.400| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 1.63 r_work: 0.2616 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.1144 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= 0.149 Angle : 0.486 5.245 15946 Z= 0.256 Chirality : 0.041 0.151 1748 Planarity : 0.004 0.047 1919 Dihedral : 7.291 126.901 1904 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.98 % Allowed : 11.99 % Favored : 87.03 % 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: 0.61 (0.23), residues: 1319 helix: 1.32 (0.23), residues: 536 sheet: -0.70 (0.37), residues: 184 loop : 0.06 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 352 TYR 0.018 0.001 TYR A 482 PHE 0.018 0.002 PHE A 674 TRP 0.016 0.001 TRP A 746 HIS 0.004 0.001 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (11650) covalent geometry : angle 0.48552 / 0.26 (15944) hydrogen bonds : bond 0.03816 / 2.58 ( 467) hydrogen bonds : angle 4.38929 / 3.22 ( 1284) metal coordination : bond 0.00570 / 0.37 ( 7) metal coordination : angle 1.06390 / 0.48 ( 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 150 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.440 Fit side-chains REVERT: A 141 ASP cc_start: 0.8843 (m-30) cc_final: 0.8545 (m-30) REVERT: A 146 ASP cc_start: 0.8891 (t70) cc_final: 0.8627 (t70) REVERT: A 240 ASN cc_start: 0.8506 (t0) cc_final: 0.8141 (t0) REVERT: A 356 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8175 (mt-10) REVERT: A 396 GLU cc_start: 0.7967 (mp0) cc_final: 0.7604 (mm-30) REVERT: A 632 ASP cc_start: 0.8176 (m-30) cc_final: 0.7827 (m-30) REVERT: A 824 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8034 (ttp) REVERT: B 378 LYS cc_start: 0.7671 (mtpm) cc_final: 0.7405 (mtpt) REVERT: B 382 LYS cc_start: 0.7853 (ptpt) cc_final: 0.7430 (pttp) REVERT: B 421 ASP cc_start: 0.8174 (m-30) cc_final: 0.7845 (m-30) outliers start: 11 outliers final: 7 residues processed: 144 average time/residue: 0.6602 time to fit residues: 101.5620 Evaluate side-chains 146 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 574 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 75 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3204 r_free = 0.3204 target = 0.111878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.082398 restraints weight = 13447.252| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 1.64 r_work: 0.2631 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11657 Z= 0.122 Angle : 0.464 4.994 15946 Z= 0.245 Chirality : 0.040 0.145 1748 Planarity : 0.004 0.046 1919 Dihedral : 7.130 124.907 1904 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.89 % Allowed : 11.99 % Favored : 87.12 % 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: 0.70 (0.23), residues: 1319 helix: 1.39 (0.23), residues: 537 sheet: -0.65 (0.37), residues: 184 loop : 0.10 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 352 TYR 0.016 0.001 TYR A 482 PHE 0.016 0.001 PHE A 674 TRP 0.016 0.001 TRP A 746 HIS 0.003 0.001 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (11650) covalent geometry : angle 0.46423 / 0.25 (15944) hydrogen bonds : bond 0.03528 / 2.38 ( 467) hydrogen bonds : angle 4.31352 / 3.17 ( 1284) metal coordination : bond 0.00458 / 0.30 ( 7) metal coordination : angle 1.09822 / 0.49 ( 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 148 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.441 Fit side-chains REVERT: A 141 ASP cc_start: 0.8851 (m-30) cc_final: 0.8560 (m-30) REVERT: A 240 ASN cc_start: 0.8510 (t0) cc_final: 0.8147 (t0) REVERT: A 352 ARG cc_start: 0.8651 (mtp180) cc_final: 0.8398 (ttp-170) REVERT: A 356 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8109 (mt-10) REVERT: A 396 GLU cc_start: 0.7974 (mp0) cc_final: 0.7605 (mm-30) REVERT: A 632 ASP cc_start: 0.8170 (m-30) cc_final: 0.7818 (m-30) REVERT: B 378 LYS cc_start: 0.7708 (mtpm) cc_final: 0.7450 (mtpt) REVERT: B 382 LYS cc_start: 0.7830 (ptpt) cc_final: 0.7399 (pttp) REVERT: B 421 ASP cc_start: 0.8164 (m-30) cc_final: 0.7840 (m-30) outliers start: 10 outliers final: 6 residues processed: 142 average time/residue: 0.7394 time to fit residues: 111.8933 Evaluate side-chains 140 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 B residue 322 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 84 optimal weight: 3.9990 chunk 16 optimal weight: 0.0270 chunk 44 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- 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 = 0.3226 r_free = 0.3226 target = 0.113445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.084133 restraints weight = 13395.821| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 1.64 r_work: 0.2634 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11657 Z= 0.103 Angle : 0.445 4.950 15946 Z= 0.235 Chirality : 0.039 0.133 1748 Planarity : 0.004 0.046 1919 Dihedral : 6.956 123.234 1904 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.98 % Allowed : 12.25 % Favored : 86.76 % 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: 540 sheet: -0.53 (0.38), residues: 179 loop : 0.10 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 187 TYR 0.014 0.001 TYR A 482 PHE 0.015 0.001 PHE B 534 TRP 0.016 0.001 TRP A 746 HIS 0.003 0.001 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (11650) covalent geometry : angle 0.44516 / 0.24 (15944) hydrogen bonds : bond 0.03243 / 2.20 ( 467) hydrogen bonds : angle 4.22982 / 3.10 ( 1284) metal coordination : bond 0.00385 / 0.25 ( 7) metal coordination : angle 1.20771 / 0.52 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4042.48 seconds wall clock time: 69 minutes 38.24 seconds (4178.24 seconds total)