Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 21:54:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/07_2023/8jcv_36166_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/07_2023/8jcv_36166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/07_2023/8jcv_36166.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/07_2023/8jcv_36166.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/07_2023/8jcv_36166_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/07_2023/8jcv_36166_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.027 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 6682 2.51 5 N 1891 2.21 5 O 2032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 239": "OE1" <-> "OE2" Residue "3 GLU 32": "OE1" <-> "OE2" Residue "3 GLU 49": "OE1" <-> "OE2" Residue "3 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 10667 Number of models: 1 Model: "" Number of chains: 4 Chain: "2" Number of atoms: 5283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 5283 Classifications: {'peptide': 763} Incomplete info: {'truncation_to_alanine': 179} Link IDs: {'PTRANS': 37, 'TRANS': 725} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 885 Unresolved non-hydrogen dihedrals: 575 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 10, 'ASN:plan1': 5, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 12, 'GLU:plan': 12, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 369 Chain: "3" Number of atoms: 5304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5304 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PTRANS': 29, 'TRANS': 721} Chain breaks: 3 Unresolved non-hydrogen bonds: 682 Unresolved non-hydrogen angles: 874 Unresolved non-hydrogen dihedrals: 583 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 16, 'GLU:plan': 8, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 355 Chain: "2" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.53, per 1000 atoms: 0.52 Number of scatterers: 10667 At special positions: 0 Unit cell: (84.609, 122.094, 183.141, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2032 8.00 N 1891 7.00 C 6682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS 2 50 " - pdb=" SG CYS 2 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 234 " - pdb=" SG CYS 2 518 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 355 " - pdb=" SG CYS 2 362 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 400 " - pdb=" SG CYS 2 407 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 500 " - pdb=" SG CYS 2 519 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 504 " - pdb=" SG CYS 2 522 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 525 " - pdb=" SG CYS 2 537 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 540 " - pdb=" SG CYS 2 553 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 632 " - pdb=" SG CYS 2 721 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 57 " - pdb=" SG CYS 3 99 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 361 " - pdb=" SG CYS 3 373 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 412 " - pdb=" SG CYS 3 419 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 509 " - pdb=" SG CYS 3 528 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 513 " - pdb=" SG CYS 3 531 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 534 " - pdb=" SG CYS 3 546 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 549 " - pdb=" SG CYS 3 562 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 641 " - pdb=" SG CYS 3 730 " distance=2.03 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 Links applied NAG-ASN " NAG 22001 " - " ASN 2 203 " " NAG 32001 " - " ASN 3 209 " Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 1.6 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2842 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 10 sheets defined 43.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain '2' and resid 59 through 74 Processing helix chain '2' and resid 95 through 105 removed outlier: 4.189A pdb=" N ASP 2 104 " --> pdb=" O GLU 2 100 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE 2 105 " --> pdb=" O GLN 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 146 through 158 removed outlier: 4.296A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE 2 158 " --> pdb=" O LEU 2 154 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 173 No H-bonds generated for 'chain '2' and resid 171 through 173' Processing helix chain '2' and resid 190 through 201 Processing helix chain '2' and resid 219 through 230 removed outlier: 3.993A pdb=" N ALA 2 230 " --> pdb=" O LEU 2 226 " (cutoff:3.500A) Processing helix chain '2' and resid 247 through 259 Processing helix chain '2' and resid 272 through 284 Processing helix chain '2' and resid 301 through 304 No H-bonds generated for 'chain '2' and resid 301 through 304' Processing helix chain '2' and resid 325 through 331 Processing helix chain '2' and resid 345 through 352 Processing helix chain '2' and resid 361 through 363 No H-bonds generated for 'chain '2' and resid 361 through 363' Processing helix chain '2' and resid 376 through 399 removed outlier: 4.370A pdb=" N MET 2 379 " --> pdb=" O SER 2 376 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE 2 380 " --> pdb=" O LYS 2 377 " (cutoff:3.500A) Processing helix chain '2' and resid 408 through 410 No H-bonds generated for 'chain '2' and resid 408 through 410' Processing helix chain '2' and resid 415 through 421 Processing helix chain '2' and resid 423 through 425 No H-bonds generated for 'chain '2' and resid 423 through 425' Processing helix chain '2' and resid 482 through 484 No H-bonds generated for 'chain '2' and resid 482 through 484' Processing helix chain '2' and resid 569 through 591 removed outlier: 3.848A pdb=" N THR 2 573 " --> pdb=" O VAL 2 569 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL 2 588 " --> pdb=" O PHE 2 584 " (cutoff:3.500A) Processing helix chain '2' and resid 596 through 600 removed outlier: 3.502A pdb=" N ALA 2 600 " --> pdb=" O PRO 2 596 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 596 through 600' Processing helix chain '2' and resid 603 through 623 Processing helix chain '2' and resid 632 through 659 removed outlier: 4.333A pdb=" N ARG 2 656 " --> pdb=" O THR 2 652 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE 2 657 " --> pdb=" O LYS 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 676 through 701 removed outlier: 3.974A pdb=" N VAL 2 699 " --> pdb=" O VAL 2 695 " (cutoff:3.500A) Processing helix chain '2' and resid 724 through 748 removed outlier: 4.177A pdb=" N GLY 2 730 " --> pdb=" O ALA 2 726 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER 2 731 " --> pdb=" O SER 2 727 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS 2 748 " --> pdb=" O LEU 2 744 " (cutoff:3.500A) Processing helix chain '2' and resid 758 through 785 removed outlier: 3.957A pdb=" N ILE 2 771 " --> pdb=" O TYR 2 767 " (cutoff:3.500A) Proline residue: 2 778 - end of helix removed outlier: 4.330A pdb=" N SER 2 785 " --> pdb=" O TYR 2 781 " (cutoff:3.500A) Processing helix chain '2' and resid 787 through 817 removed outlier: 4.017A pdb=" N ALA 2 811 " --> pdb=" O GLY 2 807 " (cutoff:3.500A) Proline residue: 2 812 - end of helix Processing helix chain '3' and resid 66 through 81 Processing helix chain '3' and resid 102 through 116 removed outlier: 4.146A pdb=" N LEU 3 110 " --> pdb=" O LEU 3 106 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLU 3 111 " --> pdb=" O GLU 3 107 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE 3 112 " --> pdb=" O GLN 3 108 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA 3 115 " --> pdb=" O GLU 3 111 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER 3 116 " --> pdb=" O PHE 3 112 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 164 removed outlier: 3.996A pdb=" N LEU 3 163 " --> pdb=" O ASN 3 159 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE 3 164 " --> pdb=" O LEU 3 160 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 179 No H-bonds generated for 'chain '3' and resid 177 through 179' Processing helix chain '3' and resid 195 through 207 Processing helix chain '3' and resid 221 through 237 removed outlier: 3.715A pdb=" N LEU 3 236 " --> pdb=" O GLN 3 232 " (cutoff:3.500A) Processing helix chain '3' and resid 253 through 264 Processing helix chain '3' and resid 278 through 289 removed outlier: 4.057A pdb=" N ARG 3 282 " --> pdb=" O SER 3 278 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU 3 283 " --> pdb=" O ASP 3 279 " (cutoff:3.500A) Processing helix chain '3' and resid 331 through 339 removed outlier: 3.650A pdb=" N ARG 3 335 " --> pdb=" O ARG 3 331 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER 3 339 " --> pdb=" O ARG 3 335 " (cutoff:3.500A) Processing helix chain '3' and resid 350 through 359 Processing helix chain '3' and resid 381 through 383 No H-bonds generated for 'chain '3' and resid 381 through 383' Processing helix chain '3' and resid 390 through 411 removed outlier: 3.712A pdb=" N MET 3 400 " --> pdb=" O ALA 3 396 " (cutoff:3.500A) Processing helix chain '3' and resid 427 through 432 Processing helix chain '3' and resid 577 through 600 Processing helix chain '3' and resid 614 through 631 removed outlier: 3.501A pdb=" N CYS 3 627 " --> pdb=" O GLY 3 623 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR 3 629 " --> pdb=" O SER 3 625 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE 3 630 " --> pdb=" O TYR 3 626 " (cutoff:3.500A) Processing helix chain '3' and resid 640 through 664 removed outlier: 4.100A pdb=" N LEU 3 659 " --> pdb=" O CYS 3 655 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU 3 660 " --> pdb=" O TYR 3 656 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR 3 661 " --> pdb=" O SER 3 657 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS 3 662 " --> pdb=" O ALA 3 658 " (cutoff:3.500A) Processing helix chain '3' and resid 685 through 705 removed outlier: 3.757A pdb=" N VAL 3 703 " --> pdb=" O GLN 3 699 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER 3 704 " --> pdb=" O ILE 3 700 " (cutoff:3.500A) Processing helix chain '3' and resid 733 through 758 removed outlier: 4.285A pdb=" N ILE 3 739 " --> pdb=" O SER 3 735 " (cutoff:3.500A) Processing helix chain '3' and resid 765 through 790 Proline residue: 3 787 - end of helix removed outlier: 3.526A pdb=" N TYR 3 790 " --> pdb=" O LEU 3 786 " (cutoff:3.500A) Processing helix chain '3' and resid 798 through 824 removed outlier: 3.598A pdb=" N ALA 3 820 " --> pdb=" O GLY 3 816 " (cutoff:3.500A) Proline residue: 3 821 - end of helix Processing sheet with id= A, first strand: chain '2' and resid 32 through 37 Processing sheet with id= B, first strand: chain '2' and resid 162 through 164 Processing sheet with id= C, first strand: chain '2' and resid 208 through 210 removed outlier: 6.233A pdb=" N THR 2 290 " --> pdb=" O ALA 2 266 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU 2 268 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL 2 292 " --> pdb=" O LEU 2 268 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 315 through 319 removed outlier: 3.988A pdb=" N GLY 2 472 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR 2 457 " --> pdb=" O LYS 2 470 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LYS 2 470 " --> pdb=" O THR 2 457 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR 2 479 " --> pdb=" O TYR 2 473 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '3' and resid 32 through 35 removed outlier: 3.610A pdb=" N ILE 3 33 " --> pdb=" O ILE 3 95 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL 3 93 " --> pdb=" O ILE 3 35 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY 3 144 " --> pdb=" O GLY 3 42 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU 3 44 " --> pdb=" O GLY 3 144 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE 3 146 " --> pdb=" O LEU 3 44 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 240 through 242 removed outlier: 3.722A pdb=" N THR 3 215 " --> pdb=" O ALA 3 242 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL 3 271 " --> pdb=" O TYR 3 212 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR 3 296 " --> pdb=" O VAL 3 272 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU 3 274 " --> pdb=" O THR 3 296 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL 3 298 " --> pdb=" O LEU 3 274 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 216 through 218 removed outlier: 6.920A pdb=" N GLU 3 245 " --> pdb=" O ALA 3 217 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain '3' and resid 321 through 325 Processing sheet with id= I, first strand: chain '3' and resid 484 through 486 Processing sheet with id= J, first strand: chain '3' and resid 518 through 522 removed outlier: 3.785A pdb=" N ILE 3 530 " --> pdb=" O MET 3 521 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3431 1.34 - 1.46: 1997 1.46 - 1.58: 5374 1.58 - 1.70: 0 1.70 - 1.83: 78 Bond restraints: 10880 Sorted by residual: bond pdb=" CAT Z99 22101 " pdb=" OAP Z99 22101 " ideal model delta sigma weight residual 1.364 1.451 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CAT Z99 32101 " pdb=" OAP Z99 32101 " ideal model delta sigma weight residual 1.364 1.450 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" CAS Z99 22101 " pdb=" OAP Z99 22101 " ideal model delta sigma weight residual 1.369 1.452 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" CAS Z99 32101 " pdb=" OAP Z99 32101 " ideal model delta sigma weight residual 1.369 1.449 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" CA ALA 3 172 " pdb=" CB ALA 3 172 " ideal model delta sigma weight residual 1.535 1.498 0.037 1.64e-02 3.72e+03 5.06e+00 ... (remaining 10875 not shown) Histogram of bond angle deviations from ideal: 59.90 - 74.76: 6 74.76 - 89.62: 0 89.62 - 104.48: 158 104.48 - 119.33: 8857 119.33 - 134.19: 5849 Bond angle restraints: 14870 Sorted by residual: angle pdb=" C ARG 2 358 " pdb=" N GLN 2 359 " pdb=" CA GLN 2 359 " ideal model delta sigma weight residual 121.40 126.72 -5.32 1.52e+00 4.33e-01 1.23e+01 angle pdb=" N ARG 2 360 " pdb=" CA ARG 2 360 " pdb=" C ARG 2 360 " ideal model delta sigma weight residual 107.73 112.25 -4.52 1.34e+00 5.57e-01 1.14e+01 angle pdb=" C SER 2 340 " pdb=" N ARG 2 341 " pdb=" CA ARG 2 341 " ideal model delta sigma weight residual 120.38 124.95 -4.57 1.37e+00 5.33e-01 1.11e+01 angle pdb=" C ASP 2 215 " pdb=" N TYR 2 216 " pdb=" CA TYR 2 216 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.95e+00 angle pdb=" CA PRO 2 76 " pdb=" C PRO 2 76 " pdb=" N HIS 2 77 " ideal model delta sigma weight residual 116.45 118.78 -2.33 8.50e-01 1.38e+00 7.49e+00 ... (remaining 14865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 5929 16.76 - 33.52: 412 33.52 - 50.28: 96 50.28 - 67.04: 19 67.04 - 83.81: 17 Dihedral angle restraints: 6473 sinusoidal: 2083 harmonic: 4390 Sorted by residual: dihedral pdb=" CB CYS 2 234 " pdb=" SG CYS 2 234 " pdb=" SG CYS 2 518 " pdb=" CB CYS 2 518 " ideal model delta sinusoidal sigma weight residual -86.00 -161.06 75.06 1 1.00e+01 1.00e-02 7.13e+01 dihedral pdb=" CB CYS 3 57 " pdb=" SG CYS 3 57 " pdb=" SG CYS 3 99 " pdb=" CB CYS 3 99 " ideal model delta sinusoidal sigma weight residual 93.00 26.23 66.77 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CB CYS 2 500 " pdb=" SG CYS 2 500 " pdb=" SG CYS 2 519 " pdb=" CB CYS 2 519 " ideal model delta sinusoidal sigma weight residual 93.00 29.54 63.46 1 1.00e+01 1.00e-02 5.31e+01 ... (remaining 6470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.071: 1723 1.071 - 2.143: 0 2.143 - 3.214: 0 3.214 - 4.286: 0 4.286 - 5.357: 2 Chirality restraints: 1725 Sorted by residual: chirality pdb=" CAW Z99 32101 " pdb=" CAN Z99 32101 " pdb=" CAU Z99 32101 " pdb=" CAV Z99 32101 " both_signs ideal model delta sigma weight residual False 2.61 -2.75 5.36 2.00e-01 2.50e+01 7.18e+02 chirality pdb=" CAW Z99 22101 " pdb=" CAN Z99 22101 " pdb=" CAU Z99 22101 " pdb=" CAV Z99 22101 " both_signs ideal model delta sigma weight residual False 2.61 -2.64 5.25 2.00e-01 2.50e+01 6.89e+02 chirality pdb=" CAZ Z99 22101 " pdb=" CAO Z99 22101 " pdb=" CAX Z99 22101 " pdb=" CAY Z99 22101 " both_signs ideal model delta sigma weight residual True 2.39 -2.74 -0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 1722 not shown) Planarity restraints: 1971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP 2 75 " 0.063 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO 2 76 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO 2 76 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO 2 76 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL 2 370 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO 2 371 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO 2 371 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO 2 371 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG 2 74 " -0.110 9.50e-02 1.11e+02 4.94e-02 1.81e+00 pdb=" NE ARG 2 74 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG 2 74 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG 2 74 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG 2 74 " -0.001 2.00e-02 2.50e+03 ... (remaining 1968 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3240 2.82 - 3.34: 10379 3.34 - 3.86: 17012 3.86 - 4.38: 18455 4.38 - 4.90: 32269 Nonbonded interactions: 81355 Sorted by model distance: nonbonded pdb=" NE2 GLN 3 508 " pdb=" O CYS 3 509 " model vdw 2.300 2.520 nonbonded pdb=" NH1 ARG 2 460 " pdb=" O ALA 2 461 " model vdw 2.307 2.520 nonbonded pdb=" O LEU 3 39 " pdb=" N GLY 3 92 " model vdw 2.314 2.520 nonbonded pdb=" NH2 ARG 2 200 " pdb=" O ARG 2 231 " model vdw 2.328 2.520 nonbonded pdb=" O SER 3 255 " pdb=" OG SER 3 258 " model vdw 2.350 2.440 ... (remaining 81350 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=0.08 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.640 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 28.650 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 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 0.087 10880 Z= 0.212 Angle : 0.561 7.501 14870 Z= 0.276 Chirality : 0.186 5.357 1725 Planarity : 0.004 0.098 1969 Dihedral : 12.997 83.805 3580 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.15 (0.22), residues: 1500 helix: 2.85 (0.20), residues: 635 sheet: 0.13 (0.49), residues: 132 loop : -1.09 (0.23), residues: 733 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.287 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.2625 time to fit residues: 43.9617 Evaluate side-chains 90 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 118 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 88 optimal weight: 0.0970 chunk 137 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 162 GLN 2 425 ASN 2 655 ASN 3 67 GLN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 405 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 10880 Z= 0.395 Angle : 0.629 13.736 14870 Z= 0.325 Chirality : 0.045 0.256 1725 Planarity : 0.005 0.066 1969 Dihedral : 4.074 39.530 1622 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.23), residues: 1500 helix: 2.36 (0.20), residues: 660 sheet: -0.54 (0.44), residues: 142 loop : -1.08 (0.24), residues: 698 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 1.237 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 105 average time/residue: 0.2455 time to fit residues: 36.6702 Evaluate side-chains 93 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1115 time to fit residues: 2.8991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 122 optimal weight: 0.0670 chunk 136 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 110 optimal weight: 0.5980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 10880 Z= 0.242 Angle : 0.507 6.585 14870 Z= 0.262 Chirality : 0.041 0.151 1725 Planarity : 0.004 0.064 1969 Dihedral : 4.023 49.330 1622 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.22), residues: 1500 helix: 2.43 (0.20), residues: 662 sheet: -1.03 (0.41), residues: 144 loop : -1.10 (0.24), residues: 694 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.267 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 97 average time/residue: 0.2468 time to fit residues: 34.6660 Evaluate side-chains 92 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 1.203 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1887 time to fit residues: 3.5195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 71 optimal weight: 30.0000 chunk 15 optimal weight: 0.5980 chunk 65 optimal weight: 0.0040 chunk 92 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 72 optimal weight: 0.0980 chunk 130 optimal weight: 9.9990 chunk 39 optimal weight: 0.2980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 162 GLN 2 425 ASN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 386 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 10880 Z= 0.154 Angle : 0.472 6.106 14870 Z= 0.244 Chirality : 0.040 0.132 1725 Planarity : 0.004 0.067 1969 Dihedral : 3.872 48.397 1622 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.23), residues: 1500 helix: 2.53 (0.20), residues: 661 sheet: -0.96 (0.42), residues: 144 loop : -1.07 (0.24), residues: 695 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 1.173 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 95 average time/residue: 0.2322 time to fit residues: 32.1200 Evaluate side-chains 86 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1031 time to fit residues: 2.5458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 131 optimal weight: 50.0000 chunk 36 optimal weight: 0.0870 overall best weight: 2.6964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 54 ASN ** 2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 425 ASN ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.099 10880 Z= 0.609 Angle : 0.719 11.609 14870 Z= 0.379 Chirality : 0.048 0.217 1725 Planarity : 0.005 0.068 1969 Dihedral : 4.917 56.305 1622 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.23), residues: 1500 helix: 2.15 (0.20), residues: 657 sheet: -1.69 (0.38), residues: 150 loop : -1.27 (0.24), residues: 693 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 1.309 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 98 average time/residue: 0.2386 time to fit residues: 34.2331 Evaluate side-chains 91 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1291 time to fit residues: 3.8119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 10.0000 chunk 131 optimal weight: 40.0000 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 146 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10880 Z= 0.221 Angle : 0.535 7.666 14870 Z= 0.276 Chirality : 0.041 0.139 1725 Planarity : 0.004 0.073 1969 Dihedral : 4.410 53.442 1622 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.22), residues: 1500 helix: 2.27 (0.20), residues: 657 sheet: -1.43 (0.39), residues: 146 loop : -1.23 (0.24), residues: 697 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 103 average time/residue: 0.2358 time to fit residues: 35.3267 Evaluate side-chains 88 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1066 time to fit residues: 2.6247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 145 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 259 GLN 2 425 ASN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 10880 Z= 0.319 Angle : 0.576 8.182 14870 Z= 0.295 Chirality : 0.042 0.147 1725 Planarity : 0.004 0.072 1969 Dihedral : 4.444 45.891 1622 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.22), residues: 1500 helix: 2.19 (0.20), residues: 661 sheet: -1.34 (0.40), residues: 139 loop : -1.31 (0.24), residues: 700 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 1.289 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 0.2356 time to fit residues: 31.3836 Evaluate side-chains 84 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1047 time to fit residues: 2.5192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 0.5980 chunk 58 optimal weight: 20.0000 chunk 86 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 71 optimal weight: 30.0000 chunk 13 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10880 Z= 0.204 Angle : 0.538 9.424 14870 Z= 0.270 Chirality : 0.041 0.166 1725 Planarity : 0.004 0.073 1969 Dihedral : 4.210 44.017 1622 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.23), residues: 1500 helix: 2.32 (0.20), residues: 659 sheet: -1.24 (0.41), residues: 139 loop : -1.26 (0.24), residues: 702 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 1.180 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 87 average time/residue: 0.2511 time to fit residues: 32.0971 Evaluate side-chains 82 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1096 time to fit residues: 1.8866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 135 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 259 GLN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 10880 Z= 0.423 Angle : 0.640 13.649 14870 Z= 0.325 Chirality : 0.044 0.163 1725 Planarity : 0.004 0.070 1969 Dihedral : 4.592 38.774 1622 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.23), residues: 1500 helix: 2.14 (0.20), residues: 662 sheet: -1.28 (0.42), residues: 139 loop : -1.33 (0.24), residues: 699 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 87 average time/residue: 0.2435 time to fit residues: 31.3220 Evaluate side-chains 83 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 1.240 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1174 time to fit residues: 2.2996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 0.9980 chunk 68 optimal weight: 20.0000 chunk 99 optimal weight: 0.4980 chunk 150 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 95 optimal weight: 0.9980 chunk 127 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 10880 Z= 0.237 Angle : 0.566 12.978 14870 Z= 0.285 Chirality : 0.042 0.138 1725 Planarity : 0.004 0.071 1969 Dihedral : 4.348 37.350 1622 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.23), residues: 1500 helix: 2.23 (0.20), residues: 661 sheet: -1.46 (0.40), residues: 151 loop : -1.28 (0.25), residues: 688 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 1.197 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 85 average time/residue: 0.2393 time to fit residues: 30.1486 Evaluate side-chains 83 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0961 time to fit residues: 1.9343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.0870 chunk 119 optimal weight: 0.4980 chunk 50 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 22 optimal weight: 0.0570 chunk 105 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 259 GLN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.188637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.128050 restraints weight = 16992.273| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.79 r_work: 0.3491 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 10880 Z= 0.163 Angle : 0.533 13.027 14870 Z= 0.266 Chirality : 0.041 0.138 1725 Planarity : 0.004 0.068 1969 Dihedral : 4.113 35.311 1622 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.23), residues: 1500 helix: 2.34 (0.20), residues: 666 sheet: -1.42 (0.41), residues: 151 loop : -1.27 (0.25), residues: 683 =============================================================================== Job complete usr+sys time: 2143.81 seconds wall clock time: 39 minutes 37.36 seconds (2377.36 seconds total)