Starting phenix.real_space_refine on Fri Jan 19 07:15:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/01_2024/8jcv_36166_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/01_2024/8jcv_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_36166/01_2024/8jcv_36166.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/01_2024/8jcv_36166.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/01_2024/8jcv_36166_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcv_36166/01_2024/8jcv_36166_updated.pdb" } resolution = 3.4 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= 0.027 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-1.21-5211/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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.16, per 1000 atoms: 0.58 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: 4.65 Conformation dependent library (CDL) restraints added in 2.4 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: 2.91 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: 3.38 Time building geometry restraints manager: 4.95 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 - 34.55: 6411 34.55 - 69.09: 117 69.09 - 103.64: 20 103.64 - 138.19: 7 138.19 - 172.73: 2 Dihedral angle restraints: 6557 sinusoidal: 2167 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 6554 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: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.220 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 32.970 Find NCS groups from input model: 0.390 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.850 ------------------------------------------------------------------------------- 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 : 14.870 172.733 3664 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 % Allowed : 0.43 % Favored : 99.46 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 3 554 HIS 0.005 0.000 HIS 2 390 PHE 0.010 0.001 PHE 2 250 TYR 0.010 0.001 TYR 3 478 ARG 0.010 0.000 ARG 2 74 *********************** 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 : 1.212 Fit side-chains revert: symmetry clash REVERT: 2 250 PHE cc_start: 0.6027 (m-10) cc_final: 0.5815 (m-10) REVERT: 2 410 MET cc_start: 0.6932 (ppp) cc_final: 0.6662 (ppp) REVERT: 3 422 MET cc_start: 0.5571 (ttp) cc_final: 0.5050 (ttp) REVERT: 3 537 TYR cc_start: 0.6835 (p90) cc_final: 0.6511 (p90) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.2611 time to fit residues: 43.7313 Evaluate side-chains 90 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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: 0.7228 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 10880 Z= 0.394 Angle : 0.619 11.025 14870 Z= 0.320 Chirality : 0.044 0.176 1725 Planarity : 0.005 0.068 1969 Dihedral : 5.145 41.718 1706 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.18 % Allowed : 8.60 % Favored : 90.22 % 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: 0.90 (0.23), residues: 1500 helix: 2.46 (0.20), residues: 658 sheet: -0.43 (0.45), residues: 142 loop : -1.06 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 3 303 HIS 0.004 0.001 HIS 2 87 PHE 0.019 0.002 PHE 2 327 TYR 0.016 0.002 TYR 3 256 ARG 0.005 0.001 ARG 2 74 *********************** 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: 11 poor density : 100 time to evaluate : 1.103 Fit side-chains REVERT: 2 238 SER cc_start: 0.8169 (t) cc_final: 0.7827 (p) REVERT: 2 245 MET cc_start: 0.4907 (OUTLIER) cc_final: 0.4159 (tmm) REVERT: 2 250 PHE cc_start: 0.6050 (m-10) cc_final: 0.5716 (m-10) REVERT: 2 410 MET cc_start: 0.6830 (ppp) cc_final: 0.6289 (ppp) REVERT: 3 49 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7079 (mt-10) outliers start: 11 outliers final: 6 residues processed: 105 average time/residue: 0.2449 time to fit residues: 36.8339 Evaluate side-chains 92 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 195 MET Chi-restraints excluded: chain 2 residue 198 ILE Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 292 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 0.0040 chunk 42 optimal weight: 0.1980 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 137 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 136 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 110 optimal weight: 0.3980 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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** 3 386 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2005 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= 0.162 Angle : 0.490 7.588 14870 Z= 0.248 Chirality : 0.040 0.135 1725 Planarity : 0.004 0.063 1969 Dihedral : 4.569 33.805 1706 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.86 % Allowed : 10.65 % Favored : 88.49 % 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: 0.90 (0.22), residues: 1500 helix: 2.49 (0.20), residues: 662 sheet: -0.69 (0.43), residues: 142 loop : -1.04 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 3 554 HIS 0.003 0.000 HIS 2 390 PHE 0.009 0.001 PHE 2 269 TYR 0.011 0.001 TYR 3 256 ARG 0.005 0.000 ARG 2 445 *********************** 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 98 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 1.228 Fit side-chains REVERT: 2 245 MET cc_start: 0.4930 (OUTLIER) cc_final: 0.4180 (tmm) REVERT: 2 250 PHE cc_start: 0.5989 (m-10) cc_final: 0.5657 (m-10) REVERT: 2 410 MET cc_start: 0.6721 (ppp) cc_final: 0.6305 (ppp) REVERT: 3 239 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6359 (mp) outliers start: 8 outliers final: 5 residues processed: 96 average time/residue: 0.2322 time to fit residues: 32.5481 Evaluate side-chains 89 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 195 MET Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 270 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 0.0030 chunk 92 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 130 optimal weight: 30.0000 chunk 39 optimal weight: 3.9990 overall best weight: 2.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 54 ASN 2 425 ASN ** 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: 0.7361 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 10880 Z= 0.554 Angle : 0.709 12.489 14870 Z= 0.368 Chirality : 0.047 0.187 1725 Planarity : 0.005 0.067 1969 Dihedral : 5.376 33.371 1706 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.47 % Allowed : 12.15 % Favored : 85.38 % 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: 0.47 (0.23), residues: 1500 helix: 2.21 (0.20), residues: 657 sheet: -1.44 (0.39), residues: 150 loop : -1.21 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 3 303 HIS 0.006 0.001 HIS 2 87 PHE 0.024 0.002 PHE 2 327 TYR 0.015 0.002 TYR 3 256 ARG 0.007 0.001 ARG 2 156 *********************** 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 115 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 1.258 Fit side-chains REVERT: 2 245 MET cc_start: 0.5309 (OUTLIER) cc_final: 0.4940 (tmm) REVERT: 2 334 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7441 (mp) REVERT: 3 72 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8069 (ttt) REVERT: 3 432 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7176 (ttmm) outliers start: 23 outliers final: 13 residues processed: 107 average time/residue: 0.2314 time to fit residues: 36.1212 Evaluate side-chains 100 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 90 ASP Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 158 PHE Chi-restraints excluded: chain 2 residue 195 MET Chi-restraints excluded: chain 2 residue 198 ILE Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 279 LEU Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 270 ARG Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 432 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 131 optimal weight: 50.0000 chunk 36 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** 3 402 HIS 3 516 ASN 3 731 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.121 10880 Z= 0.655 Angle : 0.778 14.991 14870 Z= 0.405 Chirality : 0.050 0.203 1725 Planarity : 0.006 0.074 1969 Dihedral : 6.045 50.611 1706 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.98 % Allowed : 13.87 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.16 (0.22), residues: 1500 helix: 1.73 (0.20), residues: 658 sheet: -1.97 (0.38), residues: 153 loop : -1.53 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP 3 297 HIS 0.008 0.001 HIS 2 87 PHE 0.033 0.003 PHE 3 359 TYR 0.018 0.003 TYR 3 256 ARG 0.009 0.001 ARG 2 156 *********************** 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 125 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 88 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: 2 334 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7656 (mp) REVERT: 2 410 MET cc_start: 0.6822 (ppp) cc_final: 0.6236 (ptp) REVERT: 3 432 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7236 (ttmm) outliers start: 37 outliers final: 23 residues processed: 116 average time/residue: 0.2916 time to fit residues: 50.8106 Evaluate side-chains 104 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 79 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 90 ASP Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 2 residue 195 MET Chi-restraints excluded: chain 2 residue 198 ILE Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 279 LEU Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 93 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 270 ARG Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 432 LYS Chi-restraints excluded: chain 3 residue 565 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.9990 chunk 131 optimal weight: 50.0000 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7304 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10880 Z= 0.219 Angle : 0.558 10.485 14870 Z= 0.282 Chirality : 0.041 0.137 1725 Planarity : 0.004 0.073 1969 Dihedral : 5.112 42.194 1706 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.37 % Allowed : 16.77 % Favored : 80.86 % 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: 0.19 (0.22), residues: 1500 helix: 2.06 (0.20), residues: 659 sheet: -1.50 (0.40), residues: 149 loop : -1.49 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 3 529 HIS 0.003 0.001 HIS 2 97 PHE 0.016 0.001 PHE 2 422 TYR 0.013 0.001 TYR 3 256 ARG 0.006 0.000 ARG 2 445 *********************** 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 105 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: 2 334 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7677 (mp) REVERT: 2 410 MET cc_start: 0.6790 (ppp) cc_final: 0.6078 (ptp) REVERT: 2 445 ARG cc_start: 0.7277 (ptp90) cc_final: 0.7033 (ptp90) REVERT: 2 460 ARG cc_start: 0.6911 (tpm170) cc_final: 0.6623 (tpm170) outliers start: 22 outliers final: 15 residues processed: 100 average time/residue: 0.2496 time to fit residues: 36.3010 Evaluate side-chains 93 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 90 ASP Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 158 PHE Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 93 VAL Chi-restraints excluded: chain 3 residue 189 ARG Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 270 ARG Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 492 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 145 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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** 2 469 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: 0.7333 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10880 Z= 0.294 Angle : 0.584 10.396 14870 Z= 0.294 Chirality : 0.042 0.141 1725 Planarity : 0.004 0.073 1969 Dihedral : 5.100 42.853 1706 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.69 % Allowed : 17.10 % Favored : 80.22 % 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: 0.25 (0.23), residues: 1500 helix: 2.15 (0.20), residues: 660 sheet: -1.42 (0.41), residues: 149 loop : -1.51 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 297 HIS 0.003 0.001 HIS 2 87 PHE 0.015 0.002 PHE 3 359 TYR 0.012 0.002 TYR 3 256 ARG 0.005 0.000 ARG 2 445 *********************** 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 105 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 80 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: 2 157 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7557 (mt) REVERT: 2 334 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7747 (mp) REVERT: 2 410 MET cc_start: 0.6888 (ppp) cc_final: 0.6318 (ptp) REVERT: 2 445 ARG cc_start: 0.7230 (ptp90) cc_final: 0.7019 (ptp90) REVERT: 3 72 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8032 (ttt) outliers start: 25 outliers final: 18 residues processed: 100 average time/residue: 0.2201 time to fit residues: 33.4269 Evaluate side-chains 98 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 90 ASP Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 93 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 270 ARG Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 380 ASP Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 492 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 0.0170 chunk 58 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 71 optimal weight: 30.0000 chunk 13 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 162 GLN 2 259 GLN ** 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: 0.7274 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10880 Z= 0.182 Angle : 0.530 8.334 14870 Z= 0.264 Chirality : 0.040 0.134 1725 Planarity : 0.004 0.071 1969 Dihedral : 4.730 41.323 1706 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.58 % Allowed : 17.42 % Favored : 80.00 % 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: 0.41 (0.23), residues: 1500 helix: 2.29 (0.20), residues: 660 sheet: -1.29 (0.42), residues: 149 loop : -1.46 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 2 291 HIS 0.002 0.000 HIS 2 97 PHE 0.011 0.001 PHE 2 158 TYR 0.010 0.001 TYR 2 216 ARG 0.005 0.000 ARG 2 445 *********************** 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 109 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: 2 157 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7478 (mt) REVERT: 2 283 GLN cc_start: 0.6806 (tt0) cc_final: 0.6594 (tt0) REVERT: 2 334 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7712 (mp) REVERT: 2 410 MET cc_start: 0.6692 (ppp) cc_final: 0.6235 (ptp) REVERT: 3 186 TYR cc_start: 0.8200 (m-10) cc_final: 0.7747 (m-10) outliers start: 24 outliers final: 19 residues processed: 104 average time/residue: 0.2237 time to fit residues: 33.8800 Evaluate side-chains 98 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 90 ASP Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 93 VAL Chi-restraints excluded: chain 3 residue 189 ARG Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 270 ARG Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 380 ASP Chi-restraints excluded: chain 3 residue 492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 0.0070 chunk 127 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 128 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- 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: 0.7329 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10880 Z= 0.301 Angle : 0.580 9.514 14870 Z= 0.292 Chirality : 0.042 0.146 1725 Planarity : 0.004 0.071 1969 Dihedral : 4.909 44.345 1706 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.26 % Allowed : 18.39 % Favored : 79.35 % 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: 0.40 (0.23), residues: 1500 helix: 2.29 (0.20), residues: 661 sheet: -1.32 (0.42), residues: 149 loop : -1.46 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 2 297 HIS 0.003 0.001 HIS 2 87 PHE 0.012 0.001 PHE 2 158 TYR 0.011 0.002 TYR 3 256 ARG 0.003 0.000 ARG 2 156 *********************** 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 105 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 334 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7743 (mp) REVERT: 2 410 MET cc_start: 0.6625 (ppp) cc_final: 0.6344 (ptp) outliers start: 21 outliers final: 19 residues processed: 102 average time/residue: 0.2232 time to fit residues: 33.4212 Evaluate side-chains 102 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 90 ASP Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 93 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 270 ARG Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 380 ASP Chi-restraints excluded: chain 3 residue 492 LEU Chi-restraints excluded: chain 3 residue 531 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 150 optimal weight: 30.0000 chunk 138 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 95 optimal weight: 0.8980 chunk 127 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** 3 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10880 Z= 0.229 Angle : 0.554 8.415 14870 Z= 0.278 Chirality : 0.041 0.170 1725 Planarity : 0.004 0.070 1969 Dihedral : 4.770 43.215 1706 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.58 % Allowed : 18.17 % Favored : 79.25 % 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: 0.42 (0.23), residues: 1500 helix: 2.30 (0.20), residues: 661 sheet: -1.36 (0.42), residues: 151 loop : -1.43 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 3 529 HIS 0.002 0.001 HIS 2 87 PHE 0.014 0.001 PHE 2 158 TYR 0.010 0.001 TYR 3 212 ARG 0.004 0.000 ARG 3 270 ********************** 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 108 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 157 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7496 (mt) REVERT: 2 334 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7725 (mp) REVERT: 2 410 MET cc_start: 0.6916 (ppp) cc_final: 0.6406 (ptp) REVERT: 3 72 MET cc_start: 0.8264 (ttt) cc_final: 0.8017 (ttt) outliers start: 24 outliers final: 19 residues processed: 105 average time/residue: 0.2365 time to fit residues: 36.8507 Evaluate side-chains 102 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 90 ASP Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 93 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 380 ASP Chi-restraints excluded: chain 3 residue 492 LEU Chi-restraints excluded: chain 3 residue 531 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 123 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.186091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.127970 restraints weight = 17085.751| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 3.50 r_work: 0.3459 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10880 Z= 0.250 Angle : 0.563 8.540 14870 Z= 0.282 Chirality : 0.042 0.161 1725 Planarity : 0.004 0.069 1969 Dihedral : 4.749 44.577 1706 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.37 % Allowed : 18.60 % Favored : 79.03 % 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: 0.46 (0.23), residues: 1500 helix: 2.29 (0.20), residues: 667 sheet: -1.39 (0.42), residues: 151 loop : -1.38 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 3 529 HIS 0.002 0.001 HIS 2 87 PHE 0.012 0.001 PHE 2 158 TYR 0.010 0.001 TYR 3 256 ARG 0.004 0.000 ARG 2 445 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2321.98 seconds wall clock time: 42 minutes 56.05 seconds (2576.05 seconds total)