Starting phenix.real_space_refine on Fri Jul 3 14:47:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r3k_18871/07_2026/8r3k_18871.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r3k_18871/07_2026/8r3k_18871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r3k_18871/07_2026/8r3k_18871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r3k_18871/07_2026/8r3k_18871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r3k_18871/07_2026/8r3k_18871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r3k_18871/07_2026/8r3k_18871.map" } resolution = 3.43 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= 0.001 sd= 0.018 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: 6 Type Number sf(0) Gaussians P 45 5.49 5 Mg 2 5.21 5 S 104 5.16 5 C 9143 2.51 5 N 2567 2.21 5 O 2906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 14767 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5759 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 708, 5748 Classifications: {'peptide': 708} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 708, 5748 Classifications: {'peptide': 708} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 bond proxies already assigned to first conformer: 5858 Chain: "B" Number of atoms: 5937 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 740, 5925 Classifications: {'peptide': 740} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 709} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 740, 5925 Classifications: {'peptide': 740} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 709} Chain breaks: 1 bond proxies already assigned to first conformer: 6024 Chain: "C" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2024 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain: "V" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 655 Classifications: {'RNA': 31} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna2p': 10, 'rna3p': 20} Chain: "M" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 222 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 1} Link IDs: {'rna3p': 9} Chain: "G" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 159 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 5, 'TRANS': 14} Chain breaks: 1 Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {' MG': 2, 'POP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 559 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 559 " occ=0.50 residue: pdb=" N ATYR B 557 " occ=0.70 ... (22 atoms not shown) pdb=" OH BTYR B 557 " occ=0.30 Time building chain proxies: 4.19, per 1000 atoms: 0.28 Number of scatterers: 14767 At special positions: 0 Unit cell: (113.262, 98.336, 128.188, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 45 15.00 Mg 2 11.99 O 2906 8.00 N 2567 7.00 C 9143 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: 1.16 Conformation dependent library (CDL) restraints added in 849.4 milliseconds 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3254 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 16 sheets defined 51.7% alpha, 13.0% beta 12 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 31 through 50 removed outlier: 3.820A pdb=" N PHE A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 139 removed outlier: 3.727A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.707A pdb=" N ALA A 159 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 195 through 198 removed outlier: 3.564A pdb=" N GLU A 198 " --> pdb=" O GLU A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 198' Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.577A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.555A pdb=" N SER A 409 " --> pdb=" O CYS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 451 Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.790A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 582 through 604 removed outlier: 4.090A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 4.145A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 697 through 716 removed outlier: 4.091A pdb=" N ARG A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.576A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 116 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.521A pdb=" N GLN B 124 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.535A pdb=" N GLU B 159 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.653A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 293 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.561A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN B 313 " --> pdb=" O ASN B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 309 through 313' Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 345 removed outlier: 4.660A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 376 removed outlier: 4.014A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 474 Processing helix chain 'B' and resid 504 through 509 removed outlier: 3.641A pdb=" N MET B 507 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 679 through 700 removed outlier: 4.355A pdb=" N ASP B 685 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU B 686 " --> pdb=" O ILE B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 733 Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.851A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 23 Processing helix chain 'C' and resid 26 through 34 removed outlier: 4.115A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 66 Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.616A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.729A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 236 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 removed outlier: 3.629A pdb=" N LYS A 73 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.556A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.157A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU A 549 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N AARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP A 547 " --> pdb=" O AARG A 559 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 542 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.588A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 380 removed outlier: 5.781A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL A 379 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.211A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 181 Processing sheet with id=AB2, first strand: chain 'B' and resid 184 through 192 removed outlier: 3.570A pdb=" N ILE B 205 " --> pdb=" O SER B 678 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 240 through 244 removed outlier: 3.575A pdb=" N THR B 226 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.477A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.161A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.586A pdb=" N LYS C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 2002 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4621 1.34 - 1.45: 2287 1.45 - 1.57: 7974 1.57 - 1.69: 91 1.69 - 1.81: 179 Bond restraints: 15152 Sorted by residual: bond pdb=" CG PRO A 28 " pdb=" CD PRO A 28 " ideal model delta sigma weight residual 1.503 1.276 0.227 3.40e-02 8.65e+02 4.47e+01 bond pdb=" N PRO A 28 " pdb=" CD PRO A 28 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" CB PRO A 28 " pdb=" CG PRO A 28 " ideal model delta sigma weight residual 1.492 1.654 -0.162 5.00e-02 4.00e+02 1.05e+01 bond pdb=" O POP B 801 " pdb=" P2 POP B 801 " ideal model delta sigma weight residual 1.661 1.608 0.053 2.00e-02 2.50e+03 7.06e+00 bond pdb=" O POP B 801 " pdb=" P1 POP B 801 " ideal model delta sigma weight residual 1.660 1.608 0.052 2.00e-02 2.50e+03 6.71e+00 ... (remaining 15147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 20614 3.84 - 7.68: 19 7.68 - 11.51: 1 11.51 - 15.35: 3 15.35 - 19.19: 1 Bond angle restraints: 20638 Sorted by residual: angle pdb=" CA PRO A 28 " pdb=" N PRO A 28 " pdb=" CD PRO A 28 " ideal model delta sigma weight residual 112.00 97.83 14.17 1.40e+00 5.10e-01 1.02e+02 angle pdb=" N PRO A 28 " pdb=" CD PRO A 28 " pdb=" CG PRO A 28 " ideal model delta sigma weight residual 103.20 89.31 13.89 1.50e+00 4.44e-01 8.58e+01 angle pdb=" P1 POP B 801 " pdb=" O POP B 801 " pdb=" P2 POP B 801 " ideal model delta sigma weight residual 139.66 120.47 19.19 3.00e+00 1.11e-01 4.09e+01 angle pdb=" CA PRO A 28 " pdb=" CB PRO A 28 " pdb=" CG PRO A 28 " ideal model delta sigma weight residual 104.50 95.32 9.18 1.90e+00 2.77e-01 2.34e+01 angle pdb=" N LEU B 753 " pdb=" CA LEU B 753 " pdb=" C LEU B 753 " ideal model delta sigma weight residual 110.97 107.16 3.81 1.09e+00 8.42e-01 1.22e+01 ... (remaining 20633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.46: 8798 33.46 - 66.93: 491 66.93 - 100.39: 31 100.39 - 133.86: 1 133.86 - 167.32: 2 Dihedral angle restraints: 9323 sinusoidal: 4298 harmonic: 5025 Sorted by residual: dihedral pdb=" O4' U V 15 " pdb=" C1' U V 15 " pdb=" N1 U V 15 " pdb=" C2 U V 15 " ideal model delta sinusoidal sigma weight residual 200.00 45.92 154.08 1 1.50e+01 4.44e-03 8.10e+01 dihedral pdb=" O4' U V 31 " pdb=" C1' U V 31 " pdb=" N1 U V 31 " pdb=" C2 U V 31 " ideal model delta sinusoidal sigma weight residual -128.00 39.32 -167.32 1 1.70e+01 3.46e-03 6.56e+01 dihedral pdb=" CA ASP A 286 " pdb=" CB ASP A 286 " pdb=" CG ASP A 286 " pdb=" OD1 ASP A 286 " ideal model delta sinusoidal sigma weight residual -30.00 -87.73 57.73 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 9320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1677 0.034 - 0.068: 443 0.068 - 0.102: 107 0.102 - 0.136: 48 0.136 - 0.170: 6 Chirality restraints: 2281 Sorted by residual: chirality pdb=" CA PRO A 28 " pdb=" N PRO A 28 " pdb=" C PRO A 28 " pdb=" CB PRO A 28 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA LEU B 753 " pdb=" N LEU B 753 " pdb=" C LEU B 753 " pdb=" CB LEU B 753 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE B 667 " pdb=" N ILE B 667 " pdb=" C ILE B 667 " pdb=" CB ILE B 667 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 2278 not shown) Planarity restraints: 2502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 27 " 0.049 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO A 28 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 28 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 28 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A 295 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 199 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO C 200 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 200 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 200 " -0.026 5.00e-02 4.00e+02 ... (remaining 2499 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 102 2.49 - 3.09: 10729 3.09 - 3.70: 23021 3.70 - 4.30: 34185 4.30 - 4.90: 57402 Nonbonded interactions: 125439 Sorted by model distance: nonbonded pdb=" O2 POP B 801 " pdb="MG MG B 802 " model vdw 1.888 2.170 nonbonded pdb=" OD2 ASP B 305 " pdb="MG MG B 803 " model vdw 2.004 2.170 nonbonded pdb=" OD1 ASP B 445 " pdb="MG MG B 803 " model vdw 2.018 2.170 nonbonded pdb=" OD2 ASP B 522 " pdb=" OH TYR B 559 " model vdw 2.040 3.040 nonbonded pdb=" OD1 ASP B 305 " pdb="MG MG B 802 " model vdw 2.053 2.170 ... (remaining 125434 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=0.30 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: 3.130 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.900 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 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 : 0.003 0.227 15152 Z= 0.148 Angle : 0.544 19.191 20638 Z= 0.305 Chirality : 0.036 0.170 2281 Planarity : 0.004 0.068 2502 Dihedral : 18.618 167.320 6069 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 25.85 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.23 (0.21), residues: 1703 helix: 2.00 (0.19), residues: 827 sheet: -0.06 (0.40), residues: 184 loop : -0.36 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 124 TYR 0.011 0.001 TYR B 217 PHE 0.012 0.001 PHE B 740 TRP 0.019 0.001 TRP A 706 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (15152) covalent geometry : angle 0.54447 / 0.31 (20638) hydrogen bonds : bond 0.12650 / 8.66 ( 739) hydrogen bonds : angle 5.33702 / 3.87 ( 2060) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.577 Fit side-chains REVERT: B 199 MET cc_start: 0.7630 (mmm) cc_final: 0.7371 (mmm) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.1176 time to fit residues: 41.1545 Evaluate side-chains 224 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 GLN B 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.105461 restraints weight = 47738.922| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.93 r_work: 0.3038 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 15152 Z= 0.156 Angle : 0.537 7.021 20638 Z= 0.288 Chirality : 0.041 0.165 2281 Planarity : 0.004 0.044 2502 Dihedral : 13.001 172.597 2516 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.82 % Allowed : 24.28 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.22 (0.21), residues: 1703 helix: 2.00 (0.18), residues: 818 sheet: -0.15 (0.39), residues: 186 loop : -0.30 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 124 TYR 0.019 0.001 TYR B 559 PHE 0.014 0.001 PHE B 740 TRP 0.017 0.001 TRP A 706 HIS 0.005 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (15152) covalent geometry : angle 0.53739 / 0.29 (20638) hydrogen bonds : bond 0.04427 / 2.96 ( 739) hydrogen bonds : angle 4.46622 / 3.27 ( 2060) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 524 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: B 449 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8306 (tt) REVERT: B 608 GLU cc_start: 0.8254 (tt0) cc_final: 0.8030 (tt0) REVERT: B 720 SER cc_start: 0.8784 (m) cc_final: 0.8495 (m) outliers start: 28 outliers final: 15 residues processed: 240 average time/residue: 0.1168 time to fit residues: 40.8104 Evaluate side-chains 227 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 142 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 25 optimal weight: 0.0670 chunk 56 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 567 GLN B 597 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.107789 restraints weight = 52387.509| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.00 r_work: 0.3054 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15152 Z= 0.137 Angle : 0.502 6.525 20638 Z= 0.268 Chirality : 0.040 0.149 2281 Planarity : 0.004 0.039 2502 Dihedral : 13.010 173.767 2516 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.60 % Allowed : 23.37 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.09 (0.20), residues: 1703 helix: 1.91 (0.18), residues: 819 sheet: -0.20 (0.38), residues: 186 loop : -0.40 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 287 TYR 0.014 0.001 TYR B 559 PHE 0.012 0.001 PHE B 344 TRP 0.016 0.001 TRP A 706 HIS 0.006 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15152) covalent geometry : angle 0.50195 / 0.27 (20638) hydrogen bonds : bond 0.03936 / 2.63 ( 739) hydrogen bonds : angle 4.28951 / 3.14 ( 2060) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7025 (tmm) cc_final: 0.6818 (tmm) REVERT: A 18 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7887 (tm-30) REVERT: A 52 HIS cc_start: 0.7226 (OUTLIER) cc_final: 0.6400 (m90) REVERT: A 187 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5931 (pp) REVERT: A 361 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8554 (mmtp) REVERT: A 372 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: A 388 ASN cc_start: 0.6839 (p0) cc_final: 0.6425 (p0) REVERT: A 524 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: A 561 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8415 (tmm) REVERT: A 579 MET cc_start: 0.8939 (mtp) cc_final: 0.8739 (mtp) REVERT: A 593 GLU cc_start: 0.8290 (tt0) cc_final: 0.7667 (tp30) REVERT: B 449 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8315 (tt) REVERT: B 567 GLN cc_start: 0.6545 (OUTLIER) cc_final: 0.6274 (tm-30) REVERT: B 720 SER cc_start: 0.8834 (m) cc_final: 0.8556 (m) REVERT: C 11 MET cc_start: 0.8562 (mmm) cc_final: 0.8323 (tpp) REVERT: C 187 LYS cc_start: 0.8271 (ptmt) cc_final: 0.7960 (ptmt) outliers start: 40 outliers final: 23 residues processed: 253 average time/residue: 0.1158 time to fit residues: 42.1279 Evaluate side-chains 242 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 140 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 69 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.108168 restraints weight = 35430.371| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.41 r_work: 0.3080 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15152 Z= 0.122 Angle : 0.489 6.893 20638 Z= 0.260 Chirality : 0.039 0.151 2281 Planarity : 0.004 0.053 2502 Dihedral : 13.001 173.998 2516 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.41 % Allowed : 23.89 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.06 (0.20), residues: 1703 helix: 1.89 (0.18), residues: 818 sheet: -0.23 (0.37), residues: 186 loop : -0.43 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 185 TYR 0.014 0.001 TYR B 559 PHE 0.010 0.001 PHE B 344 TRP 0.018 0.001 TRP A 422 HIS 0.006 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (15152) covalent geometry : angle 0.48935 / 0.26 (20638) hydrogen bonds : bond 0.03656 / 2.44 ( 739) hydrogen bonds : angle 4.20441 / 3.08 ( 2060) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7956 (tm-30) REVERT: A 52 HIS cc_start: 0.7289 (OUTLIER) cc_final: 0.6447 (m90) REVERT: A 130 TYR cc_start: 0.6822 (t80) cc_final: 0.6473 (t80) REVERT: A 166 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7300 (tm-30) REVERT: A 187 LEU cc_start: 0.6293 (OUTLIER) cc_final: 0.5991 (pp) REVERT: A 361 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8573 (mmtp) REVERT: A 372 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: A 388 ASN cc_start: 0.6933 (p0) cc_final: 0.6531 (p0) REVERT: A 431 ASP cc_start: 0.7925 (m-30) cc_final: 0.7272 (p0) REVERT: A 524 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: A 593 GLU cc_start: 0.8477 (tt0) cc_final: 0.7804 (tp30) REVERT: A 625 PRO cc_start: 0.8672 (Cg_exo) cc_final: 0.8459 (Cg_endo) REVERT: B 449 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8311 (tt) REVERT: B 567 GLN cc_start: 0.6276 (OUTLIER) cc_final: 0.6008 (tm-30) REVERT: B 720 SER cc_start: 0.8879 (m) cc_final: 0.8600 (m) REVERT: C 11 MET cc_start: 0.8648 (mmm) cc_final: 0.8342 (tpp) REVERT: C 187 LYS cc_start: 0.8321 (ptmt) cc_final: 0.7989 (ptmt) outliers start: 37 outliers final: 24 residues processed: 246 average time/residue: 0.1247 time to fit residues: 44.7799 Evaluate side-chains 241 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 chunk 153 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 591 GLN ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106813 restraints weight = 35748.861| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.35 r_work: 0.3037 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15152 Z= 0.231 Angle : 0.564 7.331 20638 Z= 0.296 Chirality : 0.042 0.169 2281 Planarity : 0.004 0.041 2502 Dihedral : 13.044 173.162 2516 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.65 % Allowed : 22.85 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 0.81 (0.20), residues: 1703 helix: 1.67 (0.18), residues: 824 sheet: -0.23 (0.37), residues: 175 loop : -0.59 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 116 TYR 0.018 0.002 TYR B 217 PHE 0.017 0.002 PHE B 344 TRP 0.021 0.002 TRP A 706 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 (15152) covalent geometry : angle 0.56383 / 0.30 (20638) hydrogen bonds : bond 0.04143 / 2.74 ( 739) hydrogen bonds : angle 4.31052 / 3.17 ( 2060) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 216 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7943 (tm-30) REVERT: A 52 HIS cc_start: 0.7317 (OUTLIER) cc_final: 0.6479 (m90) REVERT: A 101 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: A 130 TYR cc_start: 0.6853 (t80) cc_final: 0.6418 (t80) REVERT: A 187 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.6067 (pp) REVERT: A 361 LYS cc_start: 0.8916 (mmtt) cc_final: 0.8598 (mmtp) REVERT: A 372 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: A 431 ASP cc_start: 0.8002 (m-30) cc_final: 0.7401 (p0) REVERT: A 524 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8042 (mm-30) REVERT: A 561 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8604 (tmm) REVERT: A 593 GLU cc_start: 0.8564 (tt0) cc_final: 0.8110 (tp30) REVERT: B 449 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8452 (tt) REVERT: B 507 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8381 (mtm) REVERT: B 720 SER cc_start: 0.8923 (m) cc_final: 0.8633 (m) REVERT: B 736 LYS cc_start: 0.7766 (mmmt) cc_final: 0.7100 (pttm) REVERT: C 187 LYS cc_start: 0.8349 (ptmt) cc_final: 0.8022 (ptmt) outliers start: 56 outliers final: 37 residues processed: 253 average time/residue: 0.1118 time to fit residues: 41.3958 Evaluate side-chains 256 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 169 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107514 restraints weight = 32093.269| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.19 r_work: 0.3069 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15152 Z= 0.161 Angle : 0.519 7.253 20638 Z= 0.276 Chirality : 0.040 0.159 2281 Planarity : 0.004 0.038 2502 Dihedral : 13.067 173.972 2516 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.06 % Allowed : 23.76 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 0.85 (0.20), residues: 1703 helix: 1.73 (0.18), residues: 817 sheet: -0.23 (0.37), residues: 175 loop : -0.58 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 287 TYR 0.015 0.001 TYR B 217 PHE 0.014 0.001 PHE B 344 TRP 0.021 0.001 TRP A 706 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (15152) covalent geometry : angle 0.51890 / 0.28 (20638) hydrogen bonds : bond 0.03846 / 2.54 ( 739) hydrogen bonds : angle 4.25948 / 3.13 ( 2060) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 225 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7873 (tm-30) REVERT: A 52 HIS cc_start: 0.7281 (OUTLIER) cc_final: 0.6455 (m90) REVERT: A 130 TYR cc_start: 0.6849 (t80) cc_final: 0.6435 (t80) REVERT: A 187 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.5890 (pp) REVERT: A 361 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8582 (mmtp) REVERT: A 372 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8130 (tm-30) REVERT: A 431 ASP cc_start: 0.7903 (m-30) cc_final: 0.7368 (p0) REVERT: A 524 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: A 561 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8577 (tmm) REVERT: A 593 GLU cc_start: 0.8514 (tt0) cc_final: 0.7891 (tp30) REVERT: A 625 PRO cc_start: 0.8674 (Cg_exo) cc_final: 0.8473 (Cg_endo) REVERT: B 449 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8394 (tt) REVERT: B 507 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8321 (mtm) REVERT: B 720 SER cc_start: 0.8872 (m) cc_final: 0.8581 (m) REVERT: B 736 LYS cc_start: 0.7762 (mmmt) cc_final: 0.7113 (pttm) REVERT: C 28 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8158 (ttp) REVERT: C 187 LYS cc_start: 0.8330 (ptmt) cc_final: 0.8022 (ptmt) outliers start: 47 outliers final: 33 residues processed: 257 average time/residue: 0.1256 time to fit residues: 47.1003 Evaluate side-chains 260 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 132 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 160 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 82 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.105868 restraints weight = 41392.529| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.62 r_work: 0.3046 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15152 Z= 0.135 Angle : 0.509 8.564 20638 Z= 0.271 Chirality : 0.039 0.169 2281 Planarity : 0.004 0.036 2502 Dihedral : 13.057 174.442 2516 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.19 % Allowed : 23.76 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 0.92 (0.20), residues: 1703 helix: 1.78 (0.18), residues: 814 sheet: -0.23 (0.37), residues: 175 loop : -0.51 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 287 TYR 0.014 0.001 TYR B 559 PHE 0.013 0.001 PHE B 344 TRP 0.023 0.001 TRP A 706 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15152) covalent geometry : angle 0.50861 / 0.27 (20638) hydrogen bonds : bond 0.03700 / 2.44 ( 739) hydrogen bonds : angle 4.21173 / 3.10 ( 2060) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 219 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7763 (tm-30) REVERT: A 52 HIS cc_start: 0.7268 (OUTLIER) cc_final: 0.6443 (m90) REVERT: A 101 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: A 130 TYR cc_start: 0.6835 (t80) cc_final: 0.6430 (t80) REVERT: A 187 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5812 (pp) REVERT: A 361 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8547 (mmtp) REVERT: A 372 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: A 431 ASP cc_start: 0.7710 (m-30) cc_final: 0.7268 (p0) REVERT: A 524 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: A 561 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8369 (tmm) REVERT: A 593 GLU cc_start: 0.8343 (tt0) cc_final: 0.7758 (tp30) REVERT: A 629 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7066 (mt-10) REVERT: B 237 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8316 (mtmt) REVERT: B 449 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8284 (tt) REVERT: B 507 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8211 (mtm) REVERT: B 720 SER cc_start: 0.8797 (m) cc_final: 0.8492 (m) REVERT: C 46 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7527 (ttm170) REVERT: C 187 LYS cc_start: 0.8249 (ptmt) cc_final: 0.7963 (ptmt) outliers start: 49 outliers final: 36 residues processed: 253 average time/residue: 0.1190 time to fit residues: 43.6924 Evaluate side-chains 258 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 147 optimal weight: 0.1980 chunk 155 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 chunk 139 optimal weight: 0.0010 chunk 100 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN B 567 GLN ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.133559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.105744 restraints weight = 31374.571| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.21 r_work: 0.3094 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15152 Z= 0.122 Angle : 0.511 8.560 20638 Z= 0.272 Chirality : 0.039 0.188 2281 Planarity : 0.004 0.116 2502 Dihedral : 13.073 174.852 2516 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.32 % Allowed : 24.09 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 0.94 (0.20), residues: 1703 helix: 1.81 (0.18), residues: 815 sheet: -0.22 (0.37), residues: 175 loop : -0.50 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 287 TYR 0.014 0.001 TYR B 559 PHE 0.012 0.001 PHE A 46 TRP 0.026 0.001 TRP A 706 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (15152) covalent geometry : angle 0.51147 / 0.27 (20638) hydrogen bonds : bond 0.03605 / 2.37 ( 739) hydrogen bonds : angle 4.16228 / 3.06 ( 2060) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7897 (tm-30) REVERT: A 52 HIS cc_start: 0.7323 (OUTLIER) cc_final: 0.6489 (m90) REVERT: A 130 TYR cc_start: 0.6821 (t80) cc_final: 0.6399 (t80) REVERT: A 187 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5839 (pp) REVERT: A 202 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7169 (pt0) REVERT: A 361 LYS cc_start: 0.8847 (mmtt) cc_final: 0.8620 (mmtp) REVERT: A 372 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: A 431 ASP cc_start: 0.7864 (m-30) cc_final: 0.7339 (p0) REVERT: A 524 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: A 551 ARG cc_start: 0.8486 (mmp-170) cc_final: 0.8222 (mmp-170) REVERT: A 561 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8568 (tmm) REVERT: A 593 GLU cc_start: 0.8457 (tt0) cc_final: 0.7834 (tp30) REVERT: A 629 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7325 (mt-10) REVERT: B 237 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8340 (mtmt) REVERT: B 449 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8309 (tt) REVERT: B 507 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8306 (mtm) REVERT: B 567 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.5977 (tm-30) REVERT: B 720 SER cc_start: 0.8790 (m) cc_final: 0.8485 (m) REVERT: B 736 LYS cc_start: 0.7458 (mmpt) cc_final: 0.6709 (pttm) REVERT: C 187 LYS cc_start: 0.8305 (ptmt) cc_final: 0.8002 (ptmt) outliers start: 51 outliers final: 31 residues processed: 250 average time/residue: 0.1281 time to fit residues: 46.3551 Evaluate side-chains 254 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 164 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 38 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 108 optimal weight: 0.0980 chunk 127 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN B 567 GLN B 671 ASN ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.136029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.106512 restraints weight = 56170.947| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.32 r_work: 0.3018 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 15152 Z= 0.173 Angle : 0.839 59.197 20638 Z= 0.492 Chirality : 0.043 0.756 2281 Planarity : 0.005 0.143 2502 Dihedral : 13.074 174.864 2516 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.86 % Allowed : 23.50 % Favored : 73.63 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 1.25 % 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: 0.94 (0.20), residues: 1703 helix: 1.80 (0.18), residues: 815 sheet: -0.22 (0.37), residues: 175 loop : -0.51 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 287 TYR 0.014 0.001 TYR B 559 PHE 0.011 0.001 PHE B 344 TRP 0.022 0.001 TRP A 706 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (15152) covalent geometry : angle 0.83934 / 0.49 (20638) hydrogen bonds : bond 0.03608 / 2.38 ( 739) hydrogen bonds : angle 4.16470 / 3.06 ( 2060) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7838 (tm-30) REVERT: A 52 HIS cc_start: 0.7316 (OUTLIER) cc_final: 0.6463 (m90) REVERT: A 101 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: A 130 TYR cc_start: 0.6795 (t80) cc_final: 0.6366 (t80) REVERT: A 187 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5825 (pp) REVERT: A 202 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7111 (pt0) REVERT: A 361 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8589 (mmtp) REVERT: A 372 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8066 (tm-30) REVERT: A 431 ASP cc_start: 0.7744 (m-30) cc_final: 0.7274 (p0) REVERT: A 524 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7633 (mt-10) REVERT: A 551 ARG cc_start: 0.8424 (mmp-170) cc_final: 0.8159 (mmp-170) REVERT: A 561 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8443 (tmm) REVERT: A 593 GLU cc_start: 0.8369 (tt0) cc_final: 0.7769 (tp30) REVERT: A 629 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7242 (mt-10) REVERT: B 237 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8329 (mtmt) REVERT: B 449 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8282 (tt) REVERT: B 507 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8246 (mtm) REVERT: B 720 SER cc_start: 0.8766 (m) cc_final: 0.8454 (m) REVERT: B 736 LYS cc_start: 0.7446 (mmpt) cc_final: 0.6702 (pttm) REVERT: C 187 LYS cc_start: 0.8259 (ptmt) cc_final: 0.7962 (ptmt) outliers start: 44 outliers final: 33 residues processed: 242 average time/residue: 0.1297 time to fit residues: 45.5342 Evaluate side-chains 253 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 164 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 0.0670 chunk 78 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 160 optimal weight: 0.9990 chunk 26 optimal weight: 0.0370 chunk 19 optimal weight: 0.2980 chunk 86 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.108234 restraints weight = 42347.221| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.59 r_work: 0.3062 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 15152 Z= 0.173 Angle : 0.839 59.197 20638 Z= 0.492 Chirality : 0.043 0.756 2281 Planarity : 0.005 0.143 2502 Dihedral : 13.074 174.864 2516 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.86 % Allowed : 23.57 % Favored : 73.57 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 1.25 % 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: 0.94 (0.20), residues: 1703 helix: 1.80 (0.18), residues: 815 sheet: -0.22 (0.37), residues: 175 loop : -0.51 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 287 TYR 0.014 0.001 TYR B 559 PHE 0.011 0.001 PHE B 344 TRP 0.022 0.001 TRP A 706 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (15152) covalent geometry : angle 0.83934 / 0.49 (20638) hydrogen bonds : bond 0.03608 / 2.38 ( 739) hydrogen bonds : angle 4.16470 / 3.06 ( 2060) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7775 (tm-30) REVERT: A 52 HIS cc_start: 0.7262 (OUTLIER) cc_final: 0.6458 (m90) REVERT: A 101 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: A 130 TYR cc_start: 0.6818 (t80) cc_final: 0.6409 (t80) REVERT: A 187 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5808 (pp) REVERT: A 202 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.7014 (pt0) REVERT: A 361 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8574 (mmtp) REVERT: A 372 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: A 431 ASP cc_start: 0.7679 (m-30) cc_final: 0.7252 (p0) REVERT: A 524 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: A 551 ARG cc_start: 0.8372 (mmp-170) cc_final: 0.8125 (mmp-170) REVERT: A 561 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8378 (tmm) REVERT: A 593 GLU cc_start: 0.8309 (tt0) cc_final: 0.7724 (tp30) REVERT: A 629 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7154 (mt-10) REVERT: B 237 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8305 (mtmt) REVERT: B 449 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8262 (tt) REVERT: B 507 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8205 (mtm) REVERT: B 720 SER cc_start: 0.8739 (m) cc_final: 0.8422 (m) REVERT: B 736 LYS cc_start: 0.7453 (mmpt) cc_final: 0.6718 (pttm) REVERT: C 187 LYS cc_start: 0.8239 (ptmt) cc_final: 0.7959 (ptmt) outliers start: 44 outliers final: 33 residues processed: 240 average time/residue: 0.1385 time to fit residues: 48.2279 Evaluate side-chains 253 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 164 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 119 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 150 optimal weight: 0.0270 chunk 5 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.108168 restraints weight = 43131.335| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.62 r_work: 0.3059 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 15152 Z= 0.173 Angle : 0.839 59.197 20638 Z= 0.492 Chirality : 0.043 0.756 2281 Planarity : 0.005 0.143 2502 Dihedral : 13.074 174.864 2516 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.86 % Allowed : 23.57 % Favored : 73.57 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 1.25 % 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: 0.94 (0.20), residues: 1703 helix: 1.80 (0.18), residues: 815 sheet: -0.22 (0.37), residues: 175 loop : -0.51 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 287 TYR 0.014 0.001 TYR B 559 PHE 0.011 0.001 PHE B 344 TRP 0.022 0.001 TRP A 706 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (15152) covalent geometry : angle 0.83934 / 0.49 (20638) hydrogen bonds : bond 0.03608 / 2.38 ( 739) hydrogen bonds : angle 4.16470 / 3.06 ( 2060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3348.66 seconds wall clock time: 58 minutes 33.86 seconds (3513.86 seconds total)