Starting phenix.real_space_refine on Thu Aug 6 09:44:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r3k_18871/08_2026/8r3k_18871.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r3k_18871/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8r3k_18871/08_2026/8r3k_18871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r3k_18871/08_2026/8r3k_18871.map" model { file = "/net/cci-nas-00/data/ceres_data/8r3k_18871/08_2026/8r3k_18871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r3k_18871/08_2026/8r3k_18871.cif" } 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-2.2rc3-6140/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: 5.19, per 1000 atoms: 0.35 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: 1.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.90 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: 3.00 Time building geometry restraints manager: 1.81 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: 1647 0.034 - 0.068: 429 0.068 - 0.102: 135 0.102 - 0.136: 64 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: 4.260 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: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.030 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.280 ------------------------------------------------------------------------------- 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= 0.151 Angle : 0.564 19.191 20638 Z= 0.334 Chirality : 0.039 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 0.00347 / 0.15 (15152) covalent geometry : angle 0.56443 / 0.33 (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 : 0.575 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: 0.1407 time to fit residues: 49.2107 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 : 0.575 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.136804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.107330 restraints weight = 47439.421| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.84 r_work: 0.3039 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 15152 Z= 0.151 Angle : 0.545 7.303 20638 Z= 0.291 Chirality : 0.041 0.158 2281 Planarity : 0.004 0.044 2502 Dihedral : 12.970 172.751 2516 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.02 % Allowed : 24.02 % Favored : 73.96 % 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: 1.20 (0.20), residues: 1703 helix: 1.98 (0.18), residues: 816 sheet: -0.16 (0.38), residues: 186 loop : -0.31 (0.23), residues: 701 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 0.013 0.001 PHE B 740 TRP 0.018 0.001 TRP A 706 HIS 0.006 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (15152) covalent geometry : angle 0.54487 / 0.29 (20638) hydrogen bonds : bond 0.04327 / 2.89 ( 739) hydrogen bonds : angle 4.46802 / 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 261 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 52 HIS cc_start: 0.7178 (OUTLIER) cc_final: 0.6364 (m90) REVERT: A 524 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: B 449 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8328 (tt) REVERT: B 608 GLU cc_start: 0.8255 (tt0) cc_final: 0.8027 (tt0) REVERT: B 720 SER cc_start: 0.8793 (m) cc_final: 0.8503 (m) outliers start: 31 outliers final: 15 residues processed: 249 average time/residue: 0.1154 time to fit residues: 41.5754 Evaluate side-chains 232 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 156 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 25 optimal weight: 0.0010 chunk 56 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 567 GLN B 597 ASN ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.107226 restraints weight = 52554.399| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.11 r_work: 0.3044 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15152 Z= 0.145 Angle : 0.509 6.537 20638 Z= 0.271 Chirality : 0.040 0.149 2281 Planarity : 0.004 0.038 2502 Dihedral : 12.980 174.355 2516 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.54 % Allowed : 23.24 % Favored : 74.22 % 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: 1.08 (0.20), residues: 1703 helix: 1.90 (0.18), residues: 818 sheet: -0.24 (0.37), residues: 186 loop : -0.39 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 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 0.00340 / 0.15 (15152) covalent geometry : angle 0.50922 / 0.27 (20638) hydrogen bonds : bond 0.03926 / 2.61 ( 739) hydrogen bonds : angle 4.29605 / 3.15 ( 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 263 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7904 (tm-30) REVERT: A 52 HIS cc_start: 0.7233 (OUTLIER) cc_final: 0.6400 (m90) REVERT: A 187 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5974 (pp) REVERT: A 361 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8557 (mmtp) REVERT: A 372 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8028 (tm-30) REVERT: A 388 ASN cc_start: 0.6835 (p0) cc_final: 0.6423 (p0) REVERT: A 524 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: A 561 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8433 (tmm) REVERT: A 579 MET cc_start: 0.8953 (mtp) cc_final: 0.8749 (mtp) REVERT: A 593 GLU cc_start: 0.8308 (tt0) cc_final: 0.7686 (tp30) REVERT: A 625 PRO cc_start: 0.8628 (Cg_exo) cc_final: 0.8416 (Cg_endo) REVERT: B 449 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8250 (tt) REVERT: B 507 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8236 (mtm) REVERT: B 567 GLN cc_start: 0.6557 (OUTLIER) cc_final: 0.6289 (tm-30) REVERT: B 720 SER cc_start: 0.8847 (m) cc_final: 0.8561 (m) REVERT: B 736 LYS cc_start: 0.7746 (mmtt) cc_final: 0.7133 (pttm) REVERT: C 11 MET cc_start: 0.8568 (mmm) cc_final: 0.8304 (tpp) REVERT: C 187 LYS cc_start: 0.8277 (ptmt) cc_final: 0.7964 (ptmt) outliers start: 39 outliers final: 22 residues processed: 248 average time/residue: 0.1221 time to fit residues: 43.6888 Evaluate side-chains 238 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 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 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 507 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 150 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 69 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.138223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110351 restraints weight = 35310.831| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.38 r_work: 0.3087 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 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: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15152 Z= 0.129 Angle : 0.492 6.811 20638 Z= 0.261 Chirality : 0.039 0.143 2281 Planarity : 0.004 0.037 2502 Dihedral : 12.971 174.707 2516 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.93 % Allowed : 23.37 % 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: 1.05 (0.20), residues: 1703 helix: 1.89 (0.18), residues: 818 sheet: -0.22 (0.37), residues: 186 loop : -0.44 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 287 TYR 0.013 0.001 TYR B 559 PHE 0.013 0.001 PHE A 46 TRP 0.018 0.001 TRP A 706 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (15152) covalent geometry : angle 0.49157 / 0.26 (20638) hydrogen bonds : bond 0.03698 / 2.46 ( 739) hydrogen bonds : angle 4.19014 / 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 264 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7965 (tm-30) REVERT: A 52 HIS cc_start: 0.7266 (OUTLIER) cc_final: 0.6435 (m90) REVERT: A 130 TYR cc_start: 0.6836 (t80) cc_final: 0.6487 (t80) REVERT: A 166 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7300 (tm-30) REVERT: A 187 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.5964 (pp) REVERT: A 361 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8590 (mmtp) REVERT: A 372 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8102 (tm-30) REVERT: A 388 ASN cc_start: 0.6937 (p0) cc_final: 0.6540 (p0) REVERT: A 431 ASP cc_start: 0.7918 (m-30) cc_final: 0.7265 (p0) REVERT: A 524 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: A 593 GLU cc_start: 0.8478 (tt0) cc_final: 0.7810 (tp30) REVERT: A 625 PRO cc_start: 0.8679 (Cg_exo) cc_final: 0.8469 (Cg_endo) REVERT: B 449 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8341 (tt) REVERT: B 567 GLN cc_start: 0.6202 (OUTLIER) cc_final: 0.5705 (tm130) REVERT: B 720 SER cc_start: 0.8881 (m) cc_final: 0.8594 (m) REVERT: B 736 LYS cc_start: 0.7723 (mmtt) cc_final: 0.7142 (pttt) REVERT: C 11 MET cc_start: 0.8643 (mmm) cc_final: 0.8331 (tpp) REVERT: C 187 LYS cc_start: 0.8342 (ptmt) cc_final: 0.8004 (ptmt) outliers start: 45 outliers final: 33 residues processed: 249 average time/residue: 0.1191 time to fit residues: 43.0771 Evaluate side-chains 252 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 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 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 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 425 ASN Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 455 ASN 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 36 SER Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 90 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 41 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 161 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN B 567 GLN B 687 GLN 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 = 0.136000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.107535 restraints weight = 36197.958| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.44 r_work: 0.3082 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 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 = 0.2938 r_free = 0.2938 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: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15152 Z= 0.131 Angle : 0.493 6.846 20638 Z= 0.261 Chirality : 0.039 0.144 2281 Planarity : 0.004 0.040 2502 Dihedral : 12.974 174.853 2516 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.12 % Allowed : 23.18 % 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: 0.98 (0.20), residues: 1703 helix: 1.85 (0.18), residues: 820 sheet: -0.20 (0.37), residues: 175 loop : -0.52 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 185 TYR 0.013 0.001 TYR B 217 PHE 0.012 0.001 PHE A 46 TRP 0.018 0.001 TRP A 706 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (15152) covalent geometry : angle 0.49268 / 0.26 (20638) hydrogen bonds : bond 0.03637 / 2.40 ( 739) hydrogen bonds : angle 4.16979 / 3.07 ( 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 265 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 217 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7900 (tm-30) REVERT: A 52 HIS cc_start: 0.7315 (OUTLIER) cc_final: 0.6486 (m90) REVERT: A 130 TYR cc_start: 0.6830 (t80) cc_final: 0.6441 (t80) REVERT: A 187 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.5976 (pp) REVERT: A 361 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8568 (mmtp) REVERT: A 372 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: A 388 ASN cc_start: 0.6983 (p0) cc_final: 0.6617 (p0) REVERT: A 431 ASP cc_start: 0.7949 (m-30) cc_final: 0.7338 (p0) REVERT: A 524 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: A 561 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8547 (tmm) REVERT: A 593 GLU cc_start: 0.8510 (tt0) cc_final: 0.7844 (tp30) REVERT: A 625 PRO cc_start: 0.8667 (Cg_exo) cc_final: 0.8461 (Cg_endo) REVERT: B 449 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8281 (tt) REVERT: B 507 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8321 (mtm) REVERT: B 567 GLN cc_start: 0.5965 (OUTLIER) cc_final: 0.5684 (tm-30) REVERT: B 720 SER cc_start: 0.8871 (m) cc_final: 0.8571 (m) REVERT: B 736 LYS cc_start: 0.7720 (mmtt) cc_final: 0.7174 (pttt) REVERT: C 187 LYS cc_start: 0.8331 (ptmt) cc_final: 0.8003 (ptmt) outliers start: 48 outliers final: 36 residues processed: 249 average time/residue: 0.1307 time to fit residues: 47.7178 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 : 0.590 ------------------------------------------------------------------------------- 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 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 440 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 130 ASP 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 38 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 0.0370 chunk 36 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 32 optimal weight: 0.0770 chunk 157 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 169 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN B 567 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.111259 restraints weight = 32073.163| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.25 r_work: 0.3104 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15152 Z= 0.119 Angle : 0.481 6.786 20638 Z= 0.256 Chirality : 0.038 0.144 2281 Planarity : 0.004 0.034 2502 Dihedral : 12.974 175.113 2516 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.32 % Allowed : 23.05 % Favored : 73.63 % 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: 1.00 (0.20), residues: 1703 helix: 1.87 (0.18), residues: 821 sheet: -0.19 (0.37), residues: 175 loop : -0.52 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 187 TYR 0.012 0.001 TYR B 217 PHE 0.012 0.001 PHE A 46 TRP 0.020 0.001 TRP A 706 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (15152) covalent geometry : angle 0.48118 / 0.26 (20638) hydrogen bonds : bond 0.03534 / 2.33 ( 739) hydrogen bonds : angle 4.12671 / 3.04 ( 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 269 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 218 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 52 HIS cc_start: 0.7320 (OUTLIER) cc_final: 0.6490 (m90) REVERT: A 130 TYR cc_start: 0.6809 (t80) cc_final: 0.6403 (t80) REVERT: A 187 LEU cc_start: 0.6243 (OUTLIER) cc_final: 0.5920 (pp) REVERT: A 361 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8627 (mmtp) REVERT: A 388 ASN cc_start: 0.7047 (p0) cc_final: 0.6696 (p0) REVERT: A 431 ASP cc_start: 0.7920 (m-30) cc_final: 0.7329 (p0) REVERT: A 524 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7816 (mt-10) REVERT: A 561 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8476 (tmm) REVERT: A 593 GLU cc_start: 0.8460 (tt0) cc_final: 0.8009 (tp30) REVERT: A 625 PRO cc_start: 0.8682 (Cg_exo) cc_final: 0.8481 (Cg_endo) REVERT: B 449 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8251 (tt) REVERT: B 507 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8299 (mtm) REVERT: B 567 GLN cc_start: 0.5646 (OUTLIER) cc_final: 0.5332 (tm-30) REVERT: B 720 SER cc_start: 0.8871 (m) cc_final: 0.8584 (m) REVERT: C 11 MET cc_start: 0.8614 (mmm) cc_final: 0.8295 (tpt) REVERT: C 46 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7598 (ttm170) REVERT: C 187 LYS cc_start: 0.8301 (ptmt) cc_final: 0.7991 (ptmt) outliers start: 51 outliers final: 34 residues processed: 253 average time/residue: 0.1317 time to fit residues: 48.5820 Evaluate side-chains 255 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 402 SER Chi-restraints excluded: chain A residue 440 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 130 ASP 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 473 VAL Chi-restraints excluded: chain B residue 491 GLU 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 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: 1.9990 chunk 63 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 160 optimal weight: 0.9980 chunk 27 optimal weight: 0.0980 chunk 82 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN B 567 GLN C 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.106810 restraints weight = 41483.489| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.64 r_work: 0.3065 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 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 = 0.3072 r_free = 0.3072 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: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15152 Z= 0.143 Angle : 0.509 8.237 20638 Z= 0.270 Chirality : 0.039 0.177 2281 Planarity : 0.004 0.116 2502 Dihedral : 13.013 175.123 2516 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.19 % Allowed : 23.50 % Favored : 73.31 % 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: 1.03 (0.20), residues: 1703 helix: 1.86 (0.18), residues: 820 sheet: -0.18 (0.37), residues: 175 loop : -0.46 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 287 TYR 0.013 0.001 TYR B 217 PHE 0.012 0.001 PHE A 46 TRP 0.025 0.001 TRP A 706 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (15152) covalent geometry : angle 0.50868 / 0.27 (20638) hydrogen bonds : bond 0.03609 / 2.37 ( 739) hydrogen bonds : angle 4.13766 / 3.04 ( 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 : 0.581 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7777 (tm-30) REVERT: A 52 HIS cc_start: 0.7266 (OUTLIER) cc_final: 0.6460 (m90) REVERT: A 101 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: A 130 TYR cc_start: 0.6811 (t80) cc_final: 0.6414 (t80) REVERT: A 187 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5937 (pp) REVERT: A 361 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8557 (mmtp) REVERT: A 372 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: A 431 ASP cc_start: 0.7722 (m-30) cc_final: 0.7258 (p0) REVERT: A 524 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: A 561 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8395 (tmm) REVERT: A 593 GLU cc_start: 0.8319 (tt0) cc_final: 0.7888 (tp30) REVERT: A 625 PRO cc_start: 0.8588 (Cg_exo) cc_final: 0.8384 (Cg_endo) REVERT: B 449 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8211 (tt) REVERT: B 720 SER cc_start: 0.8813 (m) cc_final: 0.8508 (m) REVERT: B 736 LYS cc_start: 0.7565 (mmpt) cc_final: 0.6785 (pttt) REVERT: C 11 MET cc_start: 0.8472 (mmm) cc_final: 0.8147 (tpt) REVERT: C 187 LYS cc_start: 0.8248 (ptmt) cc_final: 0.7960 (ptmt) outliers start: 49 outliers final: 34 residues processed: 253 average time/residue: 0.1391 time to fit residues: 51.6497 Evaluate side-chains 257 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 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 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 130 ASP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 182 THR 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 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 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 164 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 147 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 169 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 153 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 92 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.138405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.110941 restraints weight = 31451.092| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.24 r_work: 0.3101 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1464 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= 0.127 Angle : 0.499 8.201 20638 Z= 0.265 Chirality : 0.039 0.166 2281 Planarity : 0.004 0.034 2502 Dihedral : 13.011 175.333 2516 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.86 % Allowed : 23.96 % 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: 1.06 (0.20), residues: 1703 helix: 1.89 (0.18), residues: 820 sheet: -0.17 (0.37), residues: 175 loop : -0.45 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 187 TYR 0.013 0.001 TYR B 217 PHE 0.012 0.001 PHE A 46 TRP 0.025 0.001 TRP A 706 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (15152) covalent geometry : angle 0.49944 / 0.27 (20638) hydrogen bonds : bond 0.03580 / 2.34 ( 739) hydrogen bonds : angle 4.13961 / 3.04 ( 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 263 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7851 (tm-30) REVERT: A 52 HIS cc_start: 0.7321 (OUTLIER) cc_final: 0.6509 (m90) REVERT: A 101 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: A 130 TYR cc_start: 0.6802 (t80) cc_final: 0.6384 (t80) REVERT: A 187 LEU cc_start: 0.6293 (OUTLIER) cc_final: 0.5963 (pp) REVERT: A 202 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7134 (pt0) REVERT: A 361 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8608 (mmtp) REVERT: A 372 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: A 388 ASN cc_start: 0.7200 (p0) cc_final: 0.6717 (p0) REVERT: A 431 ASP cc_start: 0.7920 (m-30) cc_final: 0.7354 (p0) REVERT: A 524 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: A 561 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8574 (tmm) REVERT: A 593 GLU cc_start: 0.8452 (tt0) cc_final: 0.7992 (tp30) REVERT: A 629 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7245 (mt-10) REVERT: B 449 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8258 (tt) REVERT: B 507 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8339 (mtm) REVERT: B 720 SER cc_start: 0.8869 (m) cc_final: 0.8575 (m) REVERT: B 736 LYS cc_start: 0.7733 (mmpt) cc_final: 0.6865 (pttt) REVERT: C 11 MET cc_start: 0.8601 (mmm) cc_final: 0.8270 (tpt) REVERT: C 187 LYS cc_start: 0.8285 (ptmt) cc_final: 0.7982 (ptmt) outliers start: 44 outliers final: 32 residues processed: 248 average time/residue: 0.1275 time to fit residues: 46.6226 Evaluate side-chains 256 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 440 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 130 ASP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 182 THR 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 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 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: 0.8980 chunk 67 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN ** 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 = 0.3588 r_free = 0.3588 target = 0.137735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.108703 restraints weight = 56691.857| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.22 r_work: 0.3009 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15152 Z= 0.144 Angle : 0.507 7.292 20638 Z= 0.269 Chirality : 0.039 0.187 2281 Planarity : 0.004 0.033 2502 Dihedral : 13.006 175.410 2516 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.06 % Allowed : 23.37 % Favored : 73.57 % 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: 1.11 (0.20), residues: 1703 helix: 1.92 (0.18), residues: 808 sheet: -0.28 (0.36), residues: 185 loop : -0.32 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 287 TYR 0.014 0.001 TYR B 217 PHE 0.012 0.001 PHE B 344 TRP 0.030 0.001 TRP A 706 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (15152) covalent geometry : angle 0.50701 / 0.27 (20638) hydrogen bonds : bond 0.03634 / 2.39 ( 739) hydrogen bonds : angle 4.14246 / 3.04 ( 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 267 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7821 (tm-30) REVERT: A 52 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.6462 (m90) REVERT: A 101 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: A 130 TYR cc_start: 0.6796 (t80) cc_final: 0.6408 (t80) REVERT: A 187 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.5887 (pp) REVERT: A 202 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7046 (pt0) REVERT: A 361 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8601 (mmtp) REVERT: A 372 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: A 431 ASP cc_start: 0.7789 (m-30) cc_final: 0.7304 (p0) REVERT: A 524 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: A 561 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8483 (tmm) REVERT: A 593 GLU cc_start: 0.8370 (tt0) cc_final: 0.7922 (tp30) REVERT: A 629 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7289 (mt-10) REVERT: B 237 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8337 (mtmt) REVERT: B 449 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8258 (tt) REVERT: B 507 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8264 (mtm) REVERT: B 720 SER cc_start: 0.8835 (m) cc_final: 0.8534 (m) REVERT: C 187 LYS cc_start: 0.8266 (ptmt) cc_final: 0.7968 (ptmt) outliers start: 47 outliers final: 36 residues processed: 253 average time/residue: 0.1306 time to fit residues: 48.4814 Evaluate side-chains 260 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 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 440 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 130 ASP 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 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 36 SER 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: 0.9980 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 160 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 19 optimal weight: 0.1980 chunk 86 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 268 GLN B 671 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.107791 restraints weight = 42838.828| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.67 r_work: 0.3061 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 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 = 0.3062 r_free = 0.3062 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: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.228 15152 Z= 0.227 Angle : 0.734 59.187 20638 Z= 0.435 Chirality : 0.040 0.431 2281 Planarity : 0.004 0.033 2502 Dihedral : 13.016 175.413 2516 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.06 % Allowed : 23.37 % Favored : 73.57 % Cbeta Deviations : 0.06 % 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: 1.12 (0.20), residues: 1703 helix: 1.94 (0.18), residues: 808 sheet: -0.28 (0.36), residues: 185 loop : -0.32 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 287 TYR 0.013 0.001 TYR B 217 PHE 0.011 0.001 PHE B 344 TRP 0.027 0.001 TRP A 706 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.23 (15152) covalent geometry : angle 0.73359 / 0.44 (20638) hydrogen bonds : bond 0.03660 / 2.39 ( 739) hydrogen bonds : angle 4.15264 / 3.04 ( 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 261 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7756 (tm-30) REVERT: A 52 HIS cc_start: 0.7260 (OUTLIER) cc_final: 0.6455 (m90) REVERT: A 101 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: A 130 TYR cc_start: 0.6802 (t80) cc_final: 0.6417 (t80) REVERT: A 187 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5886 (pp) REVERT: A 202 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6995 (pt0) REVERT: A 361 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8578 (mmtp) REVERT: A 372 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: A 431 ASP cc_start: 0.7720 (m-30) cc_final: 0.7275 (p0) REVERT: A 524 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: A 561 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8421 (tmm) REVERT: A 593 GLU cc_start: 0.8314 (tt0) cc_final: 0.7883 (tp30) REVERT: A 629 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7208 (mt-10) REVERT: B 237 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8315 (mtmt) REVERT: B 425 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.7375 (p0) REVERT: B 449 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8238 (tt) REVERT: B 507 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8216 (mtm) REVERT: B 720 SER cc_start: 0.8815 (m) cc_final: 0.8511 (m) REVERT: C 187 LYS cc_start: 0.8245 (ptmt) cc_final: 0.7960 (ptmt) outliers start: 47 outliers final: 35 residues processed: 248 average time/residue: 0.1287 time to fit residues: 46.5877 Evaluate side-chains 260 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 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 440 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 130 ASP 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 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 36 SER 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: 0.5980 chunk 58 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 112 optimal weight: 50.0000 chunk 132 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 chunk 150 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.107741 restraints weight = 43493.446| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.69 r_work: 0.3048 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.228 15152 Z= 0.227 Angle : 0.734 59.200 20638 Z= 0.435 Chirality : 0.040 0.431 2281 Planarity : 0.004 0.033 2502 Dihedral : 13.016 175.413 2516 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.99 % Allowed : 23.44 % Favored : 73.57 % Cbeta Deviations : 0.06 % 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: 1.12 (0.20), residues: 1703 helix: 1.94 (0.18), residues: 808 sheet: -0.28 (0.36), residues: 185 loop : -0.32 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 287 TYR 0.013 0.001 TYR B 217 PHE 0.011 0.001 PHE B 344 TRP 0.027 0.001 TRP A 706 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.23 (15152) covalent geometry : angle 0.73361 / 0.44 (20638) hydrogen bonds : bond 0.03660 / 2.39 ( 739) hydrogen bonds : angle 4.15264 / 3.04 ( 2060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3569.81 seconds wall clock time: 62 minutes 10.30 seconds (3730.30 seconds total)