Starting phenix.real_space_refine on Thu Feb 22 22:30:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf5_16013/02_2024/8bf5_16013_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf5_16013/02_2024/8bf5_16013.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf5_16013/02_2024/8bf5_16013_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf5_16013/02_2024/8bf5_16013_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf5_16013/02_2024/8bf5_16013_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf5_16013/02_2024/8bf5_16013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf5_16013/02_2024/8bf5_16013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf5_16013/02_2024/8bf5_16013_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf5_16013/02_2024/8bf5_16013_updated.pdb" } resolution = 2.96 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 43 5.49 5 Mg 3 5.21 5 S 131 5.16 5 C 11254 2.51 5 N 3105 2.21 5 O 3472 1.98 5 H 17699 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 240": "OE1" <-> "OE2" Residue "A ARG 575": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A GLU 680": "OE1" <-> "OE2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B ARG 722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 216": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 280": "OE1" <-> "OE2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C GLU 394": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35707 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 11187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 11187 Classifications: {'peptide': 697} Link IDs: {'PTRANS': 26, 'TRANS': 670} Chain breaks: 1 Chain: "B" Number of atoms: 11418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 11418 Classifications: {'peptide': 726} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 692} Chain breaks: 2 Chain: "C" Number of atoms: 11827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 11827 Classifications: {'peptide': 729} Link IDs: {'PTRANS': 28, 'TRANS': 700} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 392 Classifications: {'RNA': 12} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain: "R" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 392 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "M" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 405 Classifications: {'RNA': 13} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 11} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'GTA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.36, per 1000 atoms: 0.43 Number of scatterers: 35707 At special positions: 0 Unit cell: (121.929, 125.015, 115.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 131 16.00 P 43 15.00 Mg 3 11.99 O 3472 8.00 N 3105 7.00 C 11254 6.00 H 17699 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 31.07 Conformation dependent library (CDL) restraints added in 3.6 seconds 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4010 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 20 sheets defined 44.4% alpha, 11.2% beta 11 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 19.93 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 32 through 48 Processing helix chain 'A' and resid 85 through 99 Processing helix chain 'A' and resid 128 through 138 removed outlier: 3.788A pdb=" N LYS A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 183 Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 267 through 270 Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 314 through 317 No H-bonds generated for 'chain 'A' and resid 314 through 317' Processing helix chain 'A' and resid 333 through 348 Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 430 through 447 removed outlier: 3.570A pdb=" N TYR A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 471 Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.900A pdb=" N SER A 530 " --> pdb=" O ARG A 527 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY A 531 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 573 through 595 removed outlier: 3.965A pdb=" N GLN A 579 " --> pdb=" O CYS A 576 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 582 " --> pdb=" O GLN A 579 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 583 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 586 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 629 through 645 Processing helix chain 'A' and resid 649 through 669 removed outlier: 3.581A pdb=" N LEU A 664 " --> pdb=" O ARG A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 4.178A pdb=" N CYS A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 717 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 15 through 21 removed outlier: 5.478A pdb=" N SER B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 102 through 115 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 139 through 152 Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.700A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 246 through 265 removed outlier: 4.433A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 291 Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 315 through 325 Processing helix chain 'B' and resid 331 through 345 removed outlier: 4.253A pdb=" N ALA B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 383 through 395 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 414 through 425 Processing helix chain 'B' and resid 455 through 471 Processing helix chain 'B' and resid 506 through 510 Proline residue: B 509 - end of helix No H-bonds generated for 'chain 'B' and resid 506 through 510' Processing helix chain 'B' and resid 518 through 535 Processing helix chain 'B' and resid 540 through 558 Processing helix chain 'B' and resid 570 through 581 removed outlier: 4.302A pdb=" N ILE B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 587 No H-bonds generated for 'chain 'B' and resid 585 through 587' Processing helix chain 'B' and resid 590 through 592 No H-bonds generated for 'chain 'B' and resid 590 through 592' Processing helix chain 'B' and resid 600 through 602 No H-bonds generated for 'chain 'B' and resid 600 through 602' Processing helix chain 'B' and resid 607 through 611 Processing helix chain 'B' and resid 617 through 623 Processing helix chain 'B' and resid 679 through 698 Processing helix chain 'B' and resid 713 through 731 Processing helix chain 'B' and resid 736 through 748 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 16 through 24 Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.969A pdb=" N ARG C 34 " --> pdb=" O ASN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 65 through 68 No H-bonds generated for 'chain 'C' and resid 65 through 68' Processing helix chain 'C' and resid 95 through 104 Processing helix chain 'C' and resid 111 through 116 Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 158 through 169 Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 185 through 194 Processing helix chain 'C' and resid 202 through 213 Processing helix chain 'C' and resid 228 through 237 removed outlier: 4.213A pdb=" N MET C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N HIS C 235 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N CYS C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 272 Processing helix chain 'C' and resid 278 through 288 removed outlier: 3.578A pdb=" N LYS C 288 " --> pdb=" O GLU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'C' and resid 308 through 317 Processing helix chain 'C' and resid 393 through 407 Processing helix chain 'C' and resid 410 through 414 Processing helix chain 'C' and resid 432 through 442 removed outlier: 3.687A pdb=" N ASN C 442 " --> pdb=" O ARG C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 451 Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 538 through 540 No H-bonds generated for 'chain 'C' and resid 538 through 540' Processing helix chain 'C' and resid 543 through 556 Processing helix chain 'C' and resid 558 through 567 Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 576 through 584 removed outlier: 3.668A pdb=" N SER C 583 " --> pdb=" O GLU C 579 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE C 584 " --> pdb=" O ALA C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 606 removed outlier: 4.251A pdb=" N GLY C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 619 Processing helix chain 'C' and resid 690 through 693 Processing helix chain 'C' and resid 714 through 719 removed outlier: 3.571A pdb=" N LYS C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 77 through 79 removed outlier: 7.270A pdb=" N GLU A 144 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLY A 122 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N MET A 146 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR A 124 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE A 148 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.362A pdb=" N ILE A 481 " --> pdb=" O TYR A 497 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 498 through 502 removed outlier: 3.589A pdb=" N GLY A 542 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A 555 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG A 540 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N CYS A 557 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL A 538 " --> pdb=" O CYS A 557 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 614 through 619 removed outlier: 6.864A pdb=" N VAL A 625 " --> pdb=" O ILE A 617 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= F, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= G, first strand: chain 'B' and resid 178 through 191 Processing sheet with id= H, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.512A pdb=" N ILE B 348 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR B 226 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG B 350 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N THR B 228 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 482 through 485 Processing sheet with id= J, first strand: chain 'B' and resid 355 through 359 Processing sheet with id= K, first strand: chain 'B' and resid 488 through 491 Processing sheet with id= L, first strand: chain 'C' and resid 135 through 137 Processing sheet with id= M, first strand: chain 'C' and resid 143 through 148 Processing sheet with id= N, first strand: chain 'C' and resid 289 through 291 Processing sheet with id= O, first strand: chain 'C' and resid 324 through 326 removed outlier: 6.881A pdb=" N GLU C 364 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ARG C 373 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER C 379 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 342 through 347 Processing sheet with id= Q, first strand: chain 'C' and resid 453 through 455 Processing sheet with id= R, first strand: chain 'C' and resid 639 through 641 Processing sheet with id= S, first strand: chain 'C' and resid 660 through 662 Processing sheet with id= T, first strand: chain 'C' and resid 699 through 702 removed outlier: 7.119A pdb=" N LYS C 737 " --> pdb=" O SER C 701 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR C 731 " --> pdb=" O LYS C 734 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C 736 " --> pdb=" O LEU C 729 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU C 729 " --> pdb=" O VAL C 736 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL C 738 " --> pdb=" O ASN C 727 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ASN C 727 " --> pdb=" O VAL C 738 " (cutoff:3.500A) 721 hydrogen bonds defined for protein. 1989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 14.19 Time building geometry restraints manager: 31.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 17659 1.04 - 1.24: 2405 1.24 - 1.44: 5458 1.44 - 1.65: 10378 1.65 - 1.85: 226 Bond restraints: 36126 Sorted by residual: bond pdb=" C3B GTA M 101 " pdb=" C4B GTA M 101 " ideal model delta sigma weight residual 1.275 1.505 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C1B GTA M 101 " pdb=" C2B GTA M 101 " ideal model delta sigma weight residual 1.277 1.506 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C5 GTA M 101 " pdb=" C6 GTA M 101 " ideal model delta sigma weight residual 1.541 1.331 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C1A GTA M 101 " pdb=" C2A GTA M 101 " ideal model delta sigma weight residual 1.325 1.504 -0.179 2.00e-02 2.50e+03 7.99e+01 bond pdb=" C2B GTA M 101 " pdb=" C3B GTA M 101 " ideal model delta sigma weight residual 1.652 1.488 0.164 2.00e-02 2.50e+03 6.69e+01 ... (remaining 36121 not shown) Histogram of bond angle deviations from ideal: 95.67 - 103.34: 288 103.34 - 111.01: 39285 111.01 - 118.68: 10454 118.68 - 126.35: 14931 126.35 - 134.02: 413 Bond angle restraints: 65371 Sorted by residual: angle pdb=" C5C GTA M 101 " pdb=" C6C GTA M 101 " pdb=" N6C GTA M 101 " ideal model delta sigma weight residual 130.29 116.17 14.12 3.00e+00 1.11e-01 2.21e+01 angle pdb=" N1C GTA M 101 " pdb=" C6C GTA M 101 " pdb=" N6C GTA M 101 " ideal model delta sigma weight residual 109.68 121.86 -12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" C1A GTA M 101 " pdb=" N9 GTA M 101 " pdb=" C4 GTA M 101 " ideal model delta sigma weight residual 114.98 126.45 -11.47 3.00e+00 1.11e-01 1.46e+01 angle pdb=" O31 GTA M 101 " pdb=" P3 GTA M 101 " pdb=" O32 GTA M 101 " ideal model delta sigma weight residual 109.47 119.86 -10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C2B GTA M 101 " pdb=" C3B GTA M 101 " pdb=" C4B GTA M 101 " ideal model delta sigma weight residual 105.72 95.67 10.05 3.00e+00 1.11e-01 1.12e+01 ... (remaining 65366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 16475 35.40 - 70.80: 389 70.80 - 106.21: 26 106.21 - 141.61: 0 141.61 - 177.01: 5 Dihedral angle restraints: 16895 sinusoidal: 9690 harmonic: 7205 Sorted by residual: dihedral pdb=" N3 G R 14 " pdb=" C2 G R 14 " pdb=" N2 G R 14 " pdb=" H22 G R 14 " ideal model delta sinusoidal sigma weight residual 0.00 -177.01 177.01 1 4.00e+01 6.25e-04 1.20e+01 dihedral pdb=" N3 G R 18 " pdb=" C2 G R 18 " pdb=" N2 G R 18 " pdb=" H22 G R 18 " ideal model delta sinusoidal sigma weight residual 0.00 176.35 -176.35 1 4.00e+01 6.25e-04 1.20e+01 dihedral pdb=" N3 G V 12 " pdb=" C2 G V 12 " pdb=" N2 G V 12 " pdb=" H22 G V 12 " ideal model delta sinusoidal sigma weight residual 0.00 173.76 -173.76 1 4.00e+01 6.25e-04 1.20e+01 ... (remaining 16892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2612 0.077 - 0.154: 163 0.154 - 0.230: 0 0.230 - 0.307: 5 0.307 - 0.384: 1 Chirality restraints: 2781 Sorted by residual: chirality pdb=" C4B GTA M 101 " pdb=" C3B GTA M 101 " pdb=" C5B GTA M 101 " pdb=" O4B GTA M 101 " both_signs ideal model delta sigma weight residual False -2.46 -2.85 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C3A GTA M 101 " pdb=" C2A GTA M 101 " pdb=" C4A GTA M 101 " pdb=" O3A GTA M 101 " both_signs ideal model delta sigma weight residual False -2.48 -2.78 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C3B GTA M 101 " pdb=" C2B GTA M 101 " pdb=" C4B GTA M 101 " pdb=" O3B GTA M 101 " both_signs ideal model delta sigma weight residual False -2.47 -2.78 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 2778 not shown) Planarity restraints: 5144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.022 2.00e-02 2.50e+03 8.71e-03 2.47e+00 pdb=" N9 A V 4 " 0.021 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.005 2.00e-02 2.50e+03 pdb=" H8 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" H2 A V 4 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.019 2.00e-02 2.50e+03 7.65e-03 1.90e+00 pdb=" N9 A V 7 " 0.019 2.00e-02 2.50e+03 pdb=" C8 A V 7 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" H8 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" H2 A V 7 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A R 17 " 0.018 2.00e-02 2.50e+03 7.28e-03 1.72e+00 pdb=" N9 A R 17 " -0.017 2.00e-02 2.50e+03 pdb=" C8 A R 17 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A R 17 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A R 17 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A R 17 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A R 17 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A R 17 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A R 17 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A R 17 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A R 17 " -0.002 2.00e-02 2.50e+03 pdb=" H8 A R 17 " -0.000 2.00e-02 2.50e+03 pdb=" H2 A R 17 " -0.002 2.00e-02 2.50e+03 ... (remaining 5141 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1373 2.16 - 2.77: 71399 2.77 - 3.38: 106541 3.38 - 3.99: 139685 3.99 - 4.60: 219928 Nonbonded interactions: 538926 Sorted by model distance: nonbonded pdb=" O GLY C 357 " pdb="HE22 GLN C 408 " model vdw 1.546 1.850 nonbonded pdb=" H GLY B 157 " pdb=" OD2 ASP B 169 " model vdw 1.558 1.850 nonbonded pdb=" OE1 GLU A 333 " pdb=" H GLU A 333 " model vdw 1.588 1.850 nonbonded pdb=" OE2 GLU C 155 " pdb="HH12 ARG C 217 " model vdw 1.590 1.850 nonbonded pdb=" O ALA C 580 " pdb=" HG SER C 583 " model vdw 1.592 1.850 ... (remaining 538921 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.760 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: 0.000 Extract box with map and model: 19.550 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 128.890 Find NCS groups from input model: 0.830 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:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 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 : 0.005 0.230 18427 Z= 0.302 Angle : 0.490 14.119 25015 Z= 0.243 Chirality : 0.039 0.384 2781 Planarity : 0.003 0.037 3058 Dihedral : 12.571 88.434 7264 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.25 % Favored : 97.71 % Rotamer: Outliers : 1.12 % Allowed : 4.25 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 1.06 (0.19), residues: 2138 helix: 2.05 (0.17), residues: 979 sheet: -0.94 (0.33), residues: 243 loop : -0.25 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 PHE 0.010 0.001 PHE B 550 TYR 0.014 0.001 TYR B 554 ARG 0.004 0.000 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 321 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 300 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 655 ASP cc_start: 0.7739 (p0) cc_final: 0.7370 (p0) REVERT: C 66 MET cc_start: 0.8689 (mmt) cc_final: 0.8377 (mmt) REVERT: C 92 MET cc_start: 0.8071 (mmt) cc_final: 0.7870 (mmt) outliers start: 21 outliers final: 4 residues processed: 318 average time/residue: 3.3201 time to fit residues: 1167.6078 Evaluate side-chains 196 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain C residue 332 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 3.9990 chunk 163 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18427 Z= 0.240 Angle : 0.497 6.494 25015 Z= 0.250 Chirality : 0.038 0.152 2781 Planarity : 0.003 0.046 3058 Dihedral : 10.974 85.704 2922 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.52 % Rotamer: Outliers : 1.22 % Allowed : 11.16 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 1.05 (0.18), residues: 2138 helix: 2.01 (0.17), residues: 981 sheet: -0.71 (0.35), residues: 221 loop : -0.32 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 PHE 0.017 0.001 PHE A 118 TYR 0.013 0.001 TYR A 644 ARG 0.006 0.000 ARG B 726 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 197 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 654 MET cc_start: 0.5546 (tmm) cc_final: 0.5332 (tmm) REVERT: B 655 ASP cc_start: 0.7725 (p0) cc_final: 0.7431 (p0) outliers start: 23 outliers final: 11 residues processed: 215 average time/residue: 3.0574 time to fit residues: 735.9037 Evaluate side-chains 193 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 182 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 693 ASN Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 163 optimal weight: 0.2980 chunk 133 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 212 optimal weight: 0.3980 chunk 175 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 157 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 178 GLN C 470 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18427 Z= 0.167 Angle : 0.466 4.912 25015 Z= 0.235 Chirality : 0.037 0.162 2781 Planarity : 0.003 0.045 3058 Dihedral : 10.659 86.355 2922 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.57 % Rotamer: Outliers : 0.85 % Allowed : 11.42 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 1.09 (0.19), residues: 2138 helix: 2.02 (0.17), residues: 983 sheet: -0.78 (0.34), residues: 232 loop : -0.24 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 PHE 0.011 0.001 PHE A 461 TYR 0.013 0.001 TYR B 554 ARG 0.009 0.000 ARG C 417 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8302 (mt) cc_final: 0.8067 (mt) REVERT: B 655 ASP cc_start: 0.7685 (p0) cc_final: 0.7377 (p0) outliers start: 16 outliers final: 10 residues processed: 203 average time/residue: 2.9723 time to fit residues: 675.8649 Evaluate side-chains 190 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 180 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 693 ASN Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 564 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 208 optimal weight: 0.0970 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18427 Z= 0.276 Angle : 0.491 6.920 25015 Z= 0.250 Chirality : 0.038 0.153 2781 Planarity : 0.003 0.038 3058 Dihedral : 10.516 88.810 2922 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 1.28 % Allowed : 11.48 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 1.00 (0.18), residues: 2138 helix: 1.92 (0.17), residues: 983 sheet: -0.66 (0.36), residues: 212 loop : -0.32 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 PHE 0.012 0.001 PHE A 461 TYR 0.015 0.001 TYR A 131 ARG 0.003 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 186 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8358 (mt) cc_final: 0.8151 (mt) REVERT: B 655 ASP cc_start: 0.7643 (p0) cc_final: 0.7334 (p0) REVERT: B 724 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7753 (m-30) outliers start: 24 outliers final: 15 residues processed: 202 average time/residue: 2.9936 time to fit residues: 678.8694 Evaluate side-chains 194 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 724 ASP Chi-restraints excluded: chain B residue 741 LYS Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 564 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 0.0670 chunk 178 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18427 Z= 0.260 Angle : 0.487 6.805 25015 Z= 0.249 Chirality : 0.038 0.153 2781 Planarity : 0.003 0.035 3058 Dihedral : 10.505 91.150 2919 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 1.12 % Allowed : 11.80 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.97 (0.18), residues: 2138 helix: 1.86 (0.16), residues: 983 sheet: -0.60 (0.34), residues: 225 loop : -0.31 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 PHE 0.012 0.001 PHE B 550 TYR 0.013 0.001 TYR A 644 ARG 0.003 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 180 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8334 (mt) cc_final: 0.8112 (mt) REVERT: B 655 ASP cc_start: 0.7683 (p0) cc_final: 0.7382 (p0) REVERT: B 666 ARG cc_start: 0.7187 (ttt180) cc_final: 0.6984 (ttt180) outliers start: 21 outliers final: 13 residues processed: 196 average time/residue: 2.9121 time to fit residues: 646.9007 Evaluate side-chains 186 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 173 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 741 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 208 optimal weight: 0.0670 chunk 173 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 69 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18427 Z= 0.154 Angle : 0.465 6.027 25015 Z= 0.234 Chirality : 0.037 0.153 2781 Planarity : 0.003 0.035 3058 Dihedral : 10.479 90.749 2919 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.62 % Favored : 97.33 % Rotamer: Outliers : 1.22 % Allowed : 11.90 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 1.14 (0.19), residues: 2138 helix: 2.02 (0.17), residues: 983 sheet: -0.62 (0.34), residues: 231 loop : -0.20 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 182 HIS 0.003 0.001 HIS B 47 PHE 0.011 0.001 PHE A 461 TYR 0.013 0.001 TYR B 554 ARG 0.004 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8335 (mt) cc_final: 0.8100 (mt) outliers start: 23 outliers final: 12 residues processed: 201 average time/residue: 2.9588 time to fit residues: 666.1064 Evaluate side-chains 187 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 175 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain B residue 741 LYS Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18427 Z= 0.298 Angle : 0.504 7.866 25015 Z= 0.257 Chirality : 0.038 0.153 2781 Planarity : 0.003 0.035 3058 Dihedral : 10.476 93.457 2919 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 1.12 % Allowed : 12.43 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 1.04 (0.18), residues: 2138 helix: 1.91 (0.17), residues: 983 sheet: -0.57 (0.34), residues: 229 loop : -0.26 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 182 HIS 0.004 0.001 HIS B 47 PHE 0.012 0.001 PHE B 550 TYR 0.014 0.001 TYR A 644 ARG 0.004 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8366 (mt) cc_final: 0.8159 (mt) REVERT: B 655 ASP cc_start: 0.7595 (p0) cc_final: 0.7306 (p0) REVERT: B 669 ARG cc_start: 0.5626 (OUTLIER) cc_final: 0.5357 (mtt180) outliers start: 21 outliers final: 14 residues processed: 191 average time/residue: 2.9646 time to fit residues: 641.1177 Evaluate side-chains 187 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 172 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 669 ARG Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 675 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 189 optimal weight: 0.0070 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18427 Z= 0.217 Angle : 0.495 8.483 25015 Z= 0.248 Chirality : 0.037 0.154 2781 Planarity : 0.003 0.035 3058 Dihedral : 10.501 94.513 2919 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 1.17 % Allowed : 12.65 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 1.07 (0.18), residues: 2138 helix: 1.95 (0.17), residues: 983 sheet: -0.61 (0.34), residues: 231 loop : -0.24 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 182 HIS 0.003 0.001 HIS B 47 PHE 0.011 0.001 PHE A 461 TYR 0.013 0.001 TYR A 644 ARG 0.003 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8353 (mt) cc_final: 0.8138 (mt) REVERT: B 655 ASP cc_start: 0.7552 (p0) cc_final: 0.7258 (p0) REVERT: B 669 ARG cc_start: 0.5644 (OUTLIER) cc_final: 0.5295 (mtt180) outliers start: 22 outliers final: 16 residues processed: 188 average time/residue: 2.8336 time to fit residues: 601.3523 Evaluate side-chains 187 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 669 ARG Chi-restraints excluded: chain B residue 741 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 675 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18427 Z= 0.253 Angle : 0.503 8.469 25015 Z= 0.254 Chirality : 0.038 0.153 2781 Planarity : 0.003 0.035 3058 Dihedral : 10.505 95.837 2919 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.09 % Favored : 96.87 % Rotamer: Outliers : 1.01 % Allowed : 12.91 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 (0.18), residues: 2138 helix: 1.92 (0.17), residues: 983 sheet: -0.59 (0.34), residues: 226 loop : -0.28 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 182 HIS 0.003 0.001 HIS B 47 PHE 0.011 0.001 PHE B 550 TYR 0.014 0.001 TYR A 644 ARG 0.003 0.000 ARG C 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: A 181 LEU cc_start: 0.8383 (mt) cc_final: 0.8137 (mt) REVERT: B 655 ASP cc_start: 0.7570 (p0) cc_final: 0.7280 (p0) REVERT: B 669 ARG cc_start: 0.5615 (OUTLIER) cc_final: 0.5330 (mtt180) REVERT: B 724 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7688 (m-30) outliers start: 19 outliers final: 17 residues processed: 182 average time/residue: 2.8238 time to fit residues: 581.6617 Evaluate side-chains 189 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 669 ARG Chi-restraints excluded: chain B residue 724 ASP Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 741 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 675 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 142 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18427 Z= 0.187 Angle : 0.497 9.049 25015 Z= 0.248 Chirality : 0.037 0.154 2781 Planarity : 0.003 0.035 3058 Dihedral : 10.509 95.767 2919 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.15 % Rotamer: Outliers : 0.80 % Allowed : 13.23 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 1.09 (0.18), residues: 2138 helix: 1.98 (0.17), residues: 983 sheet: -0.62 (0.34), residues: 231 loop : -0.24 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 182 HIS 0.003 0.001 HIS B 47 PHE 0.012 0.001 PHE A 461 TYR 0.015 0.001 TYR B 729 ARG 0.002 0.000 ARG C 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4276 Ramachandran restraints generated. 2138 Oldfield, 0 Emsley, 2138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 169 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8392 (mt) cc_final: 0.8138 (mt) REVERT: B 655 ASP cc_start: 0.7548 (p0) cc_final: 0.7238 (p0) REVERT: B 669 ARG cc_start: 0.5561 (OUTLIER) cc_final: 0.5253 (mtt180) REVERT: B 724 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7674 (m-30) outliers start: 15 outliers final: 14 residues processed: 181 average time/residue: 2.9160 time to fit residues: 593.6542 Evaluate side-chains 184 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 669 ARG Chi-restraints excluded: chain B residue 724 ASP Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 675 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 158 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 176 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.071434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.056081 restraints weight = 134078.066| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.04 r_work: 0.2819 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18427 Z= 0.161 Angle : 0.488 9.216 25015 Z= 0.242 Chirality : 0.037 0.152 2781 Planarity : 0.003 0.065 3058 Dihedral : 10.473 94.883 2919 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 0.64 % Allowed : 13.50 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 1.18 (0.19), residues: 2138 helix: 2.05 (0.17), residues: 982 sheet: -0.56 (0.34), residues: 231 loop : -0.20 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 182 HIS 0.003 0.001 HIS B 47 PHE 0.011 0.001 PHE A 461 TYR 0.015 0.001 TYR A 77 ARG 0.011 0.000 ARG C 443 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12231.75 seconds wall clock time: 216 minutes 18.37 seconds (12978.37 seconds total)