Starting phenix.real_space_refine on Mon Aug 5 23:08:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3k_18871/08_2024/8r3k_18871.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3k_18871/08_2024/8r3k_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3k_18871/08_2024/8r3k_18871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3k_18871/08_2024/8r3k_18871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3k_18871/08_2024/8r3k_18871.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3k_18871/08_2024/8r3k_18871.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A GLU 688": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B GLU 697": "OE1" <-> "OE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/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: 14.62, per 1000 atoms: 0.99 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 - 3.50 Amino acid : False - 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: 7.40 Conformation dependent library (CDL) restraints added in 4.5 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: 5.74 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: 6.09 Time building geometry restraints manager: 7.63 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: 89.31 - 98.98: 4 98.98 - 108.65: 1154 108.65 - 118.32: 10758 118.32 - 127.99: 8520 127.99 - 137.66: 202 Bond angle restraints: 20638 Sorted by residual: angle pdb=" CA PRO A 28 " pdb=" N PRO A 28 " pdb=" CD PRO A 28 " ideal model delta sigma weight residual 112.00 97.83 14.17 1.40e+00 5.10e-01 1.02e+02 angle pdb=" N PRO A 28 " pdb=" CD PRO A 28 " pdb=" CG PRO A 28 " ideal model delta sigma weight residual 103.20 89.31 13.89 1.50e+00 4.44e-01 8.58e+01 angle pdb=" P1 POP B 801 " pdb=" O POP B 801 " pdb=" P2 POP B 801 " ideal model delta sigma weight residual 139.66 120.47 19.19 3.00e+00 1.11e-01 4.09e+01 angle pdb=" CA PRO A 28 " pdb=" CB PRO A 28 " pdb=" CG PRO A 28 " ideal model delta sigma weight residual 104.50 95.32 9.18 1.90e+00 2.77e-01 2.34e+01 angle pdb=" N LEU B 753 " pdb=" CA LEU B 753 " pdb=" C LEU B 753 " ideal model delta sigma weight residual 110.97 107.16 3.81 1.09e+00 8.42e-01 1.22e+01 ... (remaining 20633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.46: 8798 33.46 - 66.93: 491 66.93 - 100.39: 31 100.39 - 133.86: 1 133.86 - 167.32: 2 Dihedral angle restraints: 9323 sinusoidal: 4298 harmonic: 5025 Sorted by residual: dihedral pdb=" O4' U V 15 " pdb=" C1' U V 15 " pdb=" N1 U V 15 " pdb=" C2 U V 15 " ideal model delta sinusoidal sigma weight residual 200.00 45.92 154.08 1 1.50e+01 4.44e-03 8.10e+01 dihedral pdb=" O4' U V 31 " pdb=" C1' U V 31 " pdb=" N1 U V 31 " pdb=" C2 U V 31 " ideal model delta sinusoidal sigma weight residual -128.00 39.32 -167.32 1 1.70e+01 3.46e-03 6.56e+01 dihedral pdb=" CA ASP A 286 " pdb=" CB ASP A 286 " pdb=" CG ASP A 286 " pdb=" OD1 ASP A 286 " ideal model delta sinusoidal sigma weight residual -30.00 -87.73 57.73 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 9320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1677 0.034 - 0.068: 443 0.068 - 0.102: 107 0.102 - 0.136: 48 0.136 - 0.170: 6 Chirality restraints: 2281 Sorted by residual: chirality pdb=" CA PRO A 28 " pdb=" N PRO A 28 " pdb=" C PRO A 28 " pdb=" CB PRO A 28 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA LEU B 753 " pdb=" N LEU B 753 " pdb=" C LEU B 753 " pdb=" CB LEU B 753 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE B 667 " pdb=" N ILE B 667 " pdb=" C ILE B 667 " pdb=" CB ILE B 667 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 2278 not shown) Planarity restraints: 2502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 27 " 0.049 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO A 28 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 28 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 28 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A 295 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 199 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO C 200 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 200 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 200 " -0.026 5.00e-02 4.00e+02 ... (remaining 2499 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 102 2.49 - 3.09: 10729 3.09 - 3.70: 23021 3.70 - 4.30: 34185 4.30 - 4.90: 57402 Nonbonded interactions: 125439 Sorted by model distance: nonbonded pdb=" O2 POP B 801 " pdb="MG MG B 802 " model vdw 1.888 2.170 nonbonded pdb=" OD2 ASP B 305 " pdb="MG MG B 803 " model vdw 2.004 2.170 nonbonded pdb=" OD1 ASP B 445 " pdb="MG MG B 803 " model vdw 2.018 2.170 nonbonded pdb=" OD2 ASP B 522 " pdb=" OH TYR B 559 " model vdw 2.040 3.040 nonbonded pdb=" OD1 ASP B 305 " pdb="MG MG B 802 " model vdw 2.053 2.170 ... (remaining 125434 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.240 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: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 57.110 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 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= 0.217 Angle : 0.544 19.191 20638 Z= 0.288 Chirality : 0.036 0.170 2281 Planarity : 0.004 0.068 2502 Dihedral : 18.618 167.320 6069 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.20 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (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 TRP 0.019 0.001 TRP A 706 HIS 0.003 0.001 HIS A 144 PHE 0.012 0.001 PHE B 740 TYR 0.011 0.001 TYR B 217 ARG 0.010 0.000 ARG A 124 *********************** 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 fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.694 Fit side-chains REVERT: B 199 MET cc_start: 0.7630 (mmm) cc_final: 0.7372 (mmm) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2937 time to fit residues: 100.8282 Evaluate side-chains 224 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 134 ASN B 567 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 15152 Z= 0.264 Angle : 0.565 7.128 20638 Z= 0.296 Chirality : 0.041 0.165 2281 Planarity : 0.004 0.043 2502 Dihedral : 13.004 171.203 2516 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.21 % Allowed : 24.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1703 helix: 1.92 (0.18), residues: 817 sheet: -0.21 (0.38), residues: 186 loop : -0.34 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 706 HIS 0.006 0.001 HIS A 713 PHE 0.015 0.001 PHE B 740 TYR 0.019 0.001 TYR A 130 ARG 0.007 0.001 ARG A 124 *********************** 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 fitting. rotamer outliers: 34 poor density : 227 time to evaluate : 1.652 Fit side-chains REVERT: A 52 HIS cc_start: 0.7111 (OUTLIER) cc_final: 0.6344 (m90) REVERT: A 361 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8496 (mmtp) REVERT: A 524 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: B 407 MET cc_start: 0.8203 (tmm) cc_final: 0.8002 (tmm) REVERT: B 449 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8434 (tt) REVERT: B 567 GLN cc_start: 0.6585 (OUTLIER) cc_final: 0.6304 (tm-30) REVERT: B 608 GLU cc_start: 0.8248 (tt0) cc_final: 0.8015 (tt0) REVERT: B 720 SER cc_start: 0.8891 (m) cc_final: 0.8638 (m) REVERT: C 243 MET cc_start: 0.8454 (mmm) cc_final: 0.8243 (mmm) outliers start: 34 outliers final: 16 residues processed: 250 average time/residue: 0.2923 time to fit residues: 104.3979 Evaluate side-chains 231 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 211 time to evaluate : 1.690 ------------------------------------------------------------------------------- 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 304 LEU 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 567 GLN Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 597 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15152 Z= 0.274 Angle : 0.541 6.731 20638 Z= 0.282 Chirality : 0.041 0.153 2281 Planarity : 0.004 0.039 2502 Dihedral : 13.045 170.683 2516 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.86 % Allowed : 23.24 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1703 helix: 1.81 (0.18), residues: 816 sheet: -0.33 (0.37), residues: 186 loop : -0.48 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 706 HIS 0.004 0.001 HIS A 510 PHE 0.015 0.001 PHE B 344 TYR 0.017 0.001 TYR B 217 ARG 0.009 0.001 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 222 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7828 (tm-30) REVERT: A 52 HIS cc_start: 0.7145 (OUTLIER) cc_final: 0.6374 (m90) REVERT: A 130 TYR cc_start: 0.6914 (t80) cc_final: 0.6557 (t80) REVERT: A 187 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.6115 (pp) REVERT: A 202 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6720 (pt0) REVERT: A 361 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8548 (mmtp) REVERT: A 372 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: A 524 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: A 593 GLU cc_start: 0.8602 (tt0) cc_final: 0.8121 (tp30) REVERT: B 387 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: B 407 MET cc_start: 0.8184 (tmm) cc_final: 0.7885 (tmm) REVERT: B 449 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8410 (tt) REVERT: B 720 SER cc_start: 0.8914 (m) cc_final: 0.8642 (m) REVERT: C 187 LYS cc_start: 0.8256 (ptmt) cc_final: 0.7971 (ptmt) outliers start: 44 outliers final: 28 residues processed: 254 average time/residue: 0.2979 time to fit residues: 108.2708 Evaluate side-chains 246 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 211 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 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 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 712 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 182 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 455 ASN 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 46 ARG Chi-restraints excluded: chain C residue 109 VAL 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 156 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 158 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1335 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= 0.220 Angle : 0.513 7.170 20638 Z= 0.268 Chirality : 0.039 0.145 2281 Planarity : 0.004 0.035 2502 Dihedral : 13.027 171.291 2516 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.86 % Allowed : 23.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.20), residues: 1703 helix: 1.79 (0.18), residues: 821 sheet: -0.35 (0.37), residues: 186 loop : -0.50 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 49 HIS 0.005 0.001 HIS A 510 PHE 0.012 0.001 PHE B 344 TYR 0.014 0.001 TYR B 217 ARG 0.009 0.000 ARG A 116 *********************** 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 265 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 221 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7805 (tm-30) REVERT: A 52 HIS cc_start: 0.7149 (OUTLIER) cc_final: 0.6365 (m90) REVERT: A 130 TYR cc_start: 0.6902 (t80) cc_final: 0.6510 (t80) REVERT: A 166 GLU cc_start: 0.7339 (tm-30) cc_final: 0.7110 (tm-30) REVERT: A 187 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5928 (pp) REVERT: A 202 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6750 (pt0) REVERT: A 361 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8585 (mmtp) REVERT: A 372 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: A 388 ASN cc_start: 0.6942 (p0) cc_final: 0.6506 (p0) REVERT: A 431 ASP cc_start: 0.7856 (m-30) cc_final: 0.7319 (p0) REVERT: A 524 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: A 561 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8467 (tmm) REVERT: A 593 GLU cc_start: 0.8583 (tt0) cc_final: 0.8077 (tp30) REVERT: B 449 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8372 (tt) REVERT: B 608 GLU cc_start: 0.8317 (tt0) cc_final: 0.8073 (tt0) REVERT: B 720 SER cc_start: 0.8868 (m) cc_final: 0.8582 (m) REVERT: C 46 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7561 (ttm170) REVERT: C 187 LYS cc_start: 0.8243 (ptmt) cc_final: 0.7964 (ptmt) outliers start: 44 outliers final: 29 residues processed: 253 average time/residue: 0.3293 time to fit residues: 120.3221 Evaluate side-chains 252 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 215 time to evaluate : 2.103 ------------------------------------------------------------------------------- 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 202 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 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 579 LEU Chi-restraints excluded: chain B residue 709 VAL 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 236 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15152 Z= 0.220 Angle : 0.516 7.780 20638 Z= 0.268 Chirality : 0.039 0.145 2281 Planarity : 0.004 0.099 2502 Dihedral : 13.057 171.658 2516 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.06 % Allowed : 23.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1703 helix: 1.80 (0.18), residues: 814 sheet: -0.26 (0.38), residues: 175 loop : -0.50 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 706 HIS 0.004 0.001 HIS A 510 PHE 0.012 0.001 PHE A 46 TYR 0.014 0.001 TYR B 217 ARG 0.008 0.000 ARG B 287 *********************** 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 271 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 224 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7763 (tm-30) REVERT: A 52 HIS cc_start: 0.7138 (OUTLIER) cc_final: 0.6358 (m90) REVERT: A 101 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7255 (mt-10) REVERT: A 130 TYR cc_start: 0.6909 (t80) cc_final: 0.6504 (t80) REVERT: A 187 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5869 (pp) REVERT: A 202 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6771 (pt0) REVERT: A 361 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8611 (mmtp) REVERT: A 372 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: A 431 ASP cc_start: 0.7849 (m-30) cc_final: 0.7343 (p0) REVERT: A 524 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: A 561 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8500 (tmm) REVERT: A 593 GLU cc_start: 0.8575 (tt0) cc_final: 0.8075 (tp30) REVERT: A 629 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7089 (mt-10) REVERT: B 449 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8383 (tt) REVERT: B 720 SER cc_start: 0.8886 (m) cc_final: 0.8606 (m) REVERT: C 187 LYS cc_start: 0.8236 (ptmt) cc_final: 0.7957 (ptmt) outliers start: 47 outliers final: 33 residues processed: 258 average time/residue: 0.2996 time to fit residues: 110.8588 Evaluate side-chains 252 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 211 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 162 THR 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 304 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 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 164 MET 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 151 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 0.0570 chunk 13 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN B 425 ASN B 671 ASN ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1542 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= 0.190 Angle : 0.499 7.210 20638 Z= 0.261 Chirality : 0.039 0.199 2281 Planarity : 0.004 0.036 2502 Dihedral : 13.020 172.339 2516 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.26 % Allowed : 22.98 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.20), residues: 1703 helix: 1.90 (0.18), residues: 808 sheet: -0.32 (0.37), residues: 185 loop : -0.33 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 706 HIS 0.005 0.001 HIS A 510 PHE 0.011 0.001 PHE A 46 TYR 0.013 0.001 TYR B 559 ARG 0.010 0.000 ARG A 185 *********************** 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 270 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 220 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7740 (tm-30) REVERT: A 101 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7220 (mt-10) REVERT: A 187 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.5898 (pp) REVERT: A 202 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6811 (pt0) REVERT: A 372 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: A 388 ASN cc_start: 0.7041 (p0) cc_final: 0.6567 (p0) REVERT: A 431 ASP cc_start: 0.7817 (m-30) cc_final: 0.7337 (p0) REVERT: A 524 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7751 (mt-10) REVERT: A 561 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8475 (tmm) REVERT: A 593 GLU cc_start: 0.8539 (tt0) cc_final: 0.8064 (tp30) REVERT: A 629 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7117 (mt-10) REVERT: B 449 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8321 (tt) REVERT: B 507 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8280 (mtm) REVERT: B 720 SER cc_start: 0.8838 (m) cc_final: 0.8538 (m) REVERT: C 38 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6645 (ttp-170) outliers start: 50 outliers final: 35 residues processed: 256 average time/residue: 0.3275 time to fit residues: 120.7602 Evaluate side-chains 260 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 216 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL 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 304 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 314 ASN 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 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 38 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 18 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 0.0270 chunk 103 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 GLN B 671 ASN ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1594 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= 0.212 Angle : 0.517 7.835 20638 Z= 0.270 Chirality : 0.039 0.168 2281 Planarity : 0.004 0.053 2502 Dihedral : 13.012 172.546 2516 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.52 % Allowed : 23.24 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1703 helix: 1.77 (0.18), residues: 819 sheet: -0.20 (0.38), residues: 175 loop : -0.46 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 706 HIS 0.005 0.001 HIS A 510 PHE 0.012 0.001 PHE B 344 TYR 0.013 0.001 TYR B 217 ARG 0.012 0.000 ARG A 185 *********************** 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 270 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 216 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7715 (tm-30) REVERT: A 52 HIS cc_start: 0.7175 (OUTLIER) cc_final: 0.6423 (m90) REVERT: A 101 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: A 187 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5915 (pp) REVERT: A 372 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: A 431 ASP cc_start: 0.7825 (m-30) cc_final: 0.7346 (p0) REVERT: A 524 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: A 561 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8484 (tmm) REVERT: A 593 GLU cc_start: 0.8543 (tt0) cc_final: 0.8069 (tp30) REVERT: A 629 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7108 (mt-10) REVERT: B 449 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8333 (tt) REVERT: B 507 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8285 (mtm) REVERT: B 567 GLN cc_start: 0.6450 (OUTLIER) cc_final: 0.6149 (tm-30) REVERT: B 720 SER cc_start: 0.8834 (m) cc_final: 0.8536 (m) REVERT: C 38 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.6584 (ttp-170) outliers start: 54 outliers final: 39 residues processed: 254 average time/residue: 0.2905 time to fit residues: 106.8722 Evaluate side-chains 261 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 212 time to evaluate : 1.714 ------------------------------------------------------------------------------- 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 142 LYS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 159 GLU 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 387 GLU Chi-restraints excluded: chain B residue 397 ILE 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 709 VAL Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 152 optimal weight: 0.3980 chunk 160 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1626 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= 0.205 Angle : 0.512 8.569 20638 Z= 0.268 Chirality : 0.039 0.203 2281 Planarity : 0.004 0.048 2502 Dihedral : 13.006 172.879 2516 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.32 % Allowed : 23.24 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.20), residues: 1703 helix: 1.78 (0.18), residues: 819 sheet: -0.18 (0.38), residues: 175 loop : -0.47 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 706 HIS 0.004 0.001 HIS A 510 PHE 0.012 0.001 PHE B 344 TYR 0.013 0.001 TYR B 217 ARG 0.010 0.000 ARG A 185 *********************** 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 266 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 215 time to evaluate : 1.682 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7715 (tm-30) REVERT: A 52 HIS cc_start: 0.7162 (OUTLIER) cc_final: 0.6411 (m90) REVERT: A 101 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: A 130 TYR cc_start: 0.6905 (t80) cc_final: 0.6628 (t80) REVERT: A 187 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5959 (pp) REVERT: A 202 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6838 (pt0) REVERT: A 372 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: A 431 ASP cc_start: 0.7823 (m-30) cc_final: 0.7351 (p0) REVERT: A 524 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: A 561 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8482 (tmm) REVERT: A 593 GLU cc_start: 0.8547 (tt0) cc_final: 0.8055 (tp30) REVERT: A 629 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7119 (mt-10) REVERT: B 449 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8334 (tt) REVERT: B 507 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8280 (mtm) REVERT: B 720 SER cc_start: 0.8826 (m) cc_final: 0.8542 (m) REVERT: C 38 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6537 (ttp-170) outliers start: 51 outliers final: 38 residues processed: 251 average time/residue: 0.2811 time to fit residues: 102.6277 Evaluate side-chains 259 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 211 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 142 LYS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 162 THR 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 304 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 159 GLU 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 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 38 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.7980 chunk 160 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 165 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1677 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= 0.200 Angle : 0.515 7.185 20638 Z= 0.269 Chirality : 0.039 0.220 2281 Planarity : 0.004 0.045 2502 Dihedral : 13.000 173.221 2516 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.32 % Allowed : 23.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1703 helix: 1.83 (0.18), residues: 813 sheet: -0.28 (0.37), residues: 185 loop : -0.35 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 706 HIS 0.004 0.001 HIS A 510 PHE 0.013 0.001 PHE B 344 TYR 0.013 0.001 TYR B 217 ARG 0.009 0.000 ARG A 185 *********************** 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 265 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 214 time to evaluate : 1.688 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7710 (tm-30) REVERT: A 52 HIS cc_start: 0.7179 (OUTLIER) cc_final: 0.6441 (m90) REVERT: A 101 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7265 (mt-10) REVERT: A 130 TYR cc_start: 0.6917 (t80) cc_final: 0.6643 (t80) REVERT: A 187 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5957 (pp) REVERT: A 202 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6844 (pt0) REVERT: A 372 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: A 431 ASP cc_start: 0.7811 (m-30) cc_final: 0.7334 (p0) REVERT: A 524 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: A 561 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8480 (tmm) REVERT: A 593 GLU cc_start: 0.8539 (tt0) cc_final: 0.8062 (tp30) REVERT: A 629 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7122 (mt-10) REVERT: B 449 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8330 (tt) REVERT: B 507 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8271 (mtm) REVERT: B 720 SER cc_start: 0.8830 (m) cc_final: 0.8545 (m) REVERT: C 38 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6509 (ttp-170) outliers start: 51 outliers final: 39 residues processed: 251 average time/residue: 0.2816 time to fit residues: 102.5595 Evaluate side-chains 260 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 211 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 142 LYS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 162 THR 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 304 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 159 GLU 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 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 38 ARG Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 173 optimal weight: 0.0570 chunk 159 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 109 optimal weight: 0.0270 chunk 147 optimal weight: 1.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN B 567 GLN ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15152 Z= 0.161 Angle : 0.492 7.074 20638 Z= 0.259 Chirality : 0.038 0.161 2281 Planarity : 0.003 0.039 2502 Dihedral : 12.957 174.489 2516 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.06 % Allowed : 23.70 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1703 helix: 1.91 (0.18), residues: 812 sheet: -0.19 (0.36), residues: 185 loop : -0.32 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 706 HIS 0.005 0.001 HIS A 510 PHE 0.012 0.001 PHE B 699 TYR 0.010 0.001 TYR B 555 ARG 0.009 0.000 ARG B 287 ********************** 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 271 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 224 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 52 HIS cc_start: 0.7274 (OUTLIER) cc_final: 0.6520 (m90) REVERT: A 101 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7263 (mt-10) REVERT: A 130 TYR cc_start: 0.6899 (t80) cc_final: 0.6599 (t80) REVERT: A 187 LEU cc_start: 0.6126 (OUTLIER) cc_final: 0.5826 (pp) REVERT: A 202 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6816 (pt0) REVERT: A 372 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: A 431 ASP cc_start: 0.7772 (m-30) cc_final: 0.7341 (p0) REVERT: A 524 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: A 561 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8438 (tmm) REVERT: A 593 GLU cc_start: 0.8439 (tt0) cc_final: 0.8017 (tp30) REVERT: A 629 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7102 (mt-10) REVERT: B 449 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8237 (tt) REVERT: B 507 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8240 (mtm) REVERT: B 567 GLN cc_start: 0.6371 (OUTLIER) cc_final: 0.6082 (tm-30) REVERT: B 704 SER cc_start: 0.8791 (m) cc_final: 0.8553 (p) REVERT: B 716 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: B 720 SER cc_start: 0.8702 (m) cc_final: 0.8358 (m) REVERT: C 11 MET cc_start: 0.8440 (mmm) cc_final: 0.8120 (tpt) REVERT: C 38 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6555 (ttp-170) REVERT: C 187 LYS cc_start: 0.8183 (ptmt) cc_final: 0.7974 (ptmt) outliers start: 47 outliers final: 30 residues processed: 257 average time/residue: 0.3058 time to fit residues: 112.9999 Evaluate side-chains 253 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 211 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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 142 LYS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 202 GLU 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 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 159 GLU 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 425 ASN Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 473 VAL 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 716 GLU Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 109 VAL 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 42 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 138 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 141 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 121 optimal weight: 0.2980 chunk 7 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN B 567 GLN B 671 ASN ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.137611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.108478 restraints weight = 45269.067| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.76 r_work: 0.3083 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.261 15152 Z= 0.311 Angle : 0.955 59.200 20638 Z= 0.575 Chirality : 0.042 0.598 2281 Planarity : 0.004 0.037 2502 Dihedral : 12.994 174.490 2516 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.73 % Allowed : 24.02 % Favored : 73.24 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.20), residues: 1703 helix: 1.92 (0.18), residues: 812 sheet: -0.18 (0.36), residues: 185 loop : -0.34 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 706 HIS 0.005 0.001 HIS A 510 PHE 0.010 0.001 PHE B 699 TYR 0.010 0.001 TYR B 555 ARG 0.008 0.000 ARG A 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3488.04 seconds wall clock time: 69 minutes 57.86 seconds (4197.86 seconds total)