Starting phenix.real_space_refine on Sun Apr 7 12:46:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcz_36170/04_2024/8jcz_36170_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcz_36170/04_2024/8jcz_36170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcz_36170/04_2024/8jcz_36170.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcz_36170/04_2024/8jcz_36170.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcz_36170/04_2024/8jcz_36170_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcz_36170/04_2024/8jcz_36170_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.042 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 65 5.16 5 C 6631 2.51 5 N 1843 2.21 5 O 2001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 373": "OE1" <-> "OE2" Residue "2 PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 476": "OE1" <-> "OE2" Residue "3 TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 219": "OE1" <-> "OE2" Residue "3 ASP 221": "OD1" <-> "OD2" Residue "3 TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 385": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10540 Number of models: 1 Model: "" Number of chains: 4 Chain: "2" Number of atoms: 5237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5237 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 184} Link IDs: {'PTRANS': 37, 'TRANS': 723} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 722 Unresolved non-hydrogen angles: 930 Unresolved non-hydrogen dihedrals: 598 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 8, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 13, 'GLU:plan': 16, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 422 Chain: "3" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5223 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 28, 'TRANS': 714} Chain breaks: 4 Unresolved non-hydrogen bonds: 692 Unresolved non-hydrogen angles: 882 Unresolved non-hydrogen dihedrals: 592 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 9, 'PHE:plan': 13, 'GLU:plan': 11, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 401 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: 6.15, per 1000 atoms: 0.58 Number of scatterers: 10540 At special positions: 0 Unit cell: (88.893, 121.023, 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 65 16.00 O 2001 8.00 N 1843 7.00 C 6631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, 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 3 240 " - pdb=" SG CYS 3 527 " 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: 4.35 Conformation dependent library (CDL) restraints added in 2.2 seconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 8 sheets defined 43.4% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain '2' and resid 60 through 73 Processing helix chain '2' and resid 95 through 107 removed outlier: 4.034A pdb=" N ASP 2 104 " --> pdb=" O GLU 2 100 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE 2 105 " --> pdb=" O GLN 2 101 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL 2 106 " --> pdb=" O ALA 2 102 " (cutoff:3.500A) Processing helix chain '2' and resid 145 through 157 removed outlier: 4.170A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) Processing helix chain '2' and resid 170 through 172 No H-bonds generated for 'chain '2' and resid 170 through 172' Processing helix chain '2' and resid 189 through 201 Processing helix chain '2' and resid 215 through 230 removed outlier: 6.625A pdb=" N GLY 2 220 " --> pdb=" O TYR 2 216 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE 2 221 " --> pdb=" O GLY 2 217 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU 2 222 " --> pdb=" O GLU 2 218 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA 2 223 " --> pdb=" O THR 2 219 " (cutoff:3.500A) Processing helix chain '2' and resid 247 through 259 Processing helix chain '2' and resid 272 through 285 Processing helix chain '2' and resid 325 through 332 Processing helix chain '2' and resid 345 through 352 Processing helix chain '2' and resid 378 through 399 Processing helix chain '2' and resid 415 through 421 Processing helix chain '2' and resid 566 through 593 removed outlier: 4.764A pdb=" N GLY 2 570 " --> pdb=" O TRP 2 567 " (cutoff:3.500A) Proline residue: 2 571 - end of helix Processing helix chain '2' and resid 604 through 625 Processing helix chain '2' and resid 633 through 659 removed outlier: 3.535A pdb=" N GLY 2 640 " --> pdb=" O ARG 2 636 " (cutoff:3.500A) Processing helix chain '2' and resid 677 through 700 Processing helix chain '2' and resid 727 through 749 removed outlier: 3.517A pdb=" N SER 2 731 " --> pdb=" O SER 2 727 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS 2 748 " --> pdb=" O LEU 2 744 " (cutoff:3.500A) Processing helix chain '2' and resid 756 through 785 Proline residue: 2 778 - end of helix removed outlier: 4.188A pdb=" N SER 2 785 " --> pdb=" O TYR 2 781 " (cutoff:3.500A) Processing helix chain '2' and resid 787 through 818 removed outlier: 4.178A pdb=" N THR 2 791 " --> pdb=" O TYR 2 787 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N THR 2 792 " --> pdb=" O ARG 2 788 " (cutoff:3.500A) Proline residue: 2 812 - end of helix removed outlier: 3.932A pdb=" N HIS 2 815 " --> pdb=" O ALA 2 811 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 81 Processing helix chain '3' and resid 102 through 111 removed outlier: 4.145A pdb=" N GLU 3 111 " --> pdb=" O GLU 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 164 removed outlier: 4.253A pdb=" N LEU 3 163 " --> pdb=" O ASN 3 159 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE 3 164 " --> pdb=" O LEU 3 160 " (cutoff:3.500A) Processing helix chain '3' and resid 176 through 178 No H-bonds generated for 'chain '3' and resid 176 through 178' Processing helix chain '3' and resid 194 through 207 removed outlier: 3.929A pdb=" N ALA 3 198 " --> pdb=" O ASP 3 194 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA 3 202 " --> pdb=" O ALA 3 198 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU 3 203 " --> pdb=" O LYS 3 199 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE 3 204 " --> pdb=" O ALA 3 200 " (cutoff:3.500A) Processing helix chain '3' and resid 222 through 236 removed outlier: 3.612A pdb=" N GLY 3 226 " --> pdb=" O TYR 3 222 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU 3 228 " --> pdb=" O GLU 3 224 " (cutoff:3.500A) Processing helix chain '3' and resid 253 through 264 Processing helix chain '3' and resid 278 through 291 removed outlier: 3.600A pdb=" N ARG 3 290 " --> pdb=" O ALA 3 286 " (cutoff:3.500A) Processing helix chain '3' and resid 307 through 310 No H-bonds generated for 'chain '3' and resid 307 through 310' Processing helix chain '3' and resid 314 through 317 No H-bonds generated for 'chain '3' and resid 314 through 317' Processing helix chain '3' and resid 331 through 338 removed outlier: 3.528A pdb=" N ARG 3 335 " --> pdb=" O ARG 3 331 " (cutoff:3.500A) Processing helix chain '3' and resid 351 through 358 Processing helix chain '3' and resid 388 through 411 removed outlier: 4.429A pdb=" N MET 3 391 " --> pdb=" O SER 3 388 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE 3 392 " --> pdb=" O LYS 3 389 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL 3 394 " --> pdb=" O MET 3 391 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR 3 398 " --> pdb=" O ASN 3 395 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N HIS 3 402 " --> pdb=" O ALA 3 399 " (cutoff:3.500A) Processing helix chain '3' and resid 420 through 422 No H-bonds generated for 'chain '3' and resid 420 through 422' Processing helix chain '3' and resid 427 through 433 Processing helix chain '3' and resid 494 through 496 No H-bonds generated for 'chain '3' and resid 494 through 496' Processing helix chain '3' and resid 575 through 597 removed outlier: 4.322A pdb=" N GLY 3 579 " --> pdb=" O ALA 3 575 " (cutoff:3.500A) Proline residue: 3 580 - end of helix Processing helix chain '3' and resid 613 through 632 removed outlier: 3.795A pdb=" N THR 3 629 " --> pdb=" O SER 3 625 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE 3 630 " --> pdb=" O TYR 3 626 " (cutoff:3.500A) Processing helix chain '3' and resid 642 through 664 removed outlier: 3.668A pdb=" N LYS 3 662 " --> pdb=" O ALA 3 658 " (cutoff:3.500A) Processing helix chain '3' and resid 685 through 707 removed outlier: 3.654A pdb=" N LEU 3 693 " --> pdb=" O VAL 3 689 " (cutoff:3.500A) Processing helix chain '3' and resid 721 through 723 No H-bonds generated for 'chain '3' and resid 721 through 723' Processing helix chain '3' and resid 738 through 757 Processing helix chain '3' and resid 768 through 791 Proline residue: 3 787 - end of helix removed outlier: 3.985A pdb=" N TYR 3 790 " --> pdb=" O LEU 3 786 " (cutoff:3.500A) Processing helix chain '3' and resid 797 through 824 Proline residue: 3 821 - end of helix Processing sheet with id= A, first strand: chain '2' and resid 25 through 28 removed outlier: 4.185A pdb=" N GLY 2 36 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY 2 35 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL 2 139 " --> pdb=" O GLY 2 35 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU 2 37 " --> pdb=" O VAL 2 139 " (cutoff:3.500A) 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 266 through 268 Processing sheet with id= D, first strand: chain '2' and resid 314 through 319 removed outlier: 4.222A pdb=" N ALA 2 314 " --> pdb=" O TYR 2 458 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY 2 472 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR 2 457 " --> pdb=" O LYS 2 470 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LYS 2 470 " --> pdb=" O THR 2 457 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU 2 459 " --> pdb=" O TYR 2 468 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TYR 2 468 " --> pdb=" O LEU 2 459 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '2' and resid 507 through 512 removed outlier: 3.844A pdb=" N ILE 2 523 " --> pdb=" O GLU 2 508 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS 2 510 " --> pdb=" O LEU 2 521 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU 2 521 " --> pdb=" O LYS 2 510 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 33 through 35 removed outlier: 6.480A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY 3 42 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL 3 145 " --> pdb=" O GLY 3 42 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU 3 44 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY 3 147 " --> pdb=" O LEU 3 44 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLY 3 147 " --> pdb=" O PRO 3 167 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ILE 3 169 " --> pdb=" O GLY 3 147 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 214 through 217 removed outlier: 6.149A pdb=" N THR 3 296 " --> pdb=" O VAL 3 272 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU 3 274 " --> pdb=" O THR 3 296 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL 3 298 " --> pdb=" O LEU 3 274 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '3' and resid 321 through 325 removed outlier: 3.722A pdb=" N GLY 3 484 " --> pdb=" O VAL 3 468 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASN 3 470 " --> pdb=" O LYS 3 482 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LYS 3 482 " --> pdb=" O ASN 3 470 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLN 3 472 " --> pdb=" O TYR 3 480 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N TYR 3 480 " --> pdb=" O GLN 3 472 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL 3 474 " --> pdb=" O TYR 3 478 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TYR 3 478 " --> pdb=" O VAL 3 474 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1290 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: 3.33 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2949 1.33 - 1.46: 2006 1.46 - 1.58: 5720 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 10755 Sorted by residual: bond pdb=" CAT Z99 22002 " pdb=" OAP Z99 22002 " ideal model delta sigma weight residual 1.364 1.455 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" CAT Z99 32002 " pdb=" OAP Z99 32002 " ideal model delta sigma weight residual 1.364 1.453 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" CAS Z99 32002 " pdb=" OAP Z99 32002 " ideal model delta sigma weight residual 1.369 1.452 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" CAS Z99 22002 " pdb=" OAP Z99 22002 " ideal model delta sigma weight residual 1.369 1.451 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" CA PRO 3 192 " pdb=" C PRO 3 192 " ideal model delta sigma weight residual 1.517 1.537 -0.020 6.70e-03 2.23e+04 8.52e+00 ... (remaining 10750 not shown) Histogram of bond angle deviations from ideal: 59.73 - 74.58: 6 74.58 - 89.44: 0 89.44 - 104.30: 157 104.30 - 119.16: 8615 119.16 - 134.02: 5933 Bond angle restraints: 14711 Sorted by residual: angle pdb=" CAX Z99 22002 " pdb=" CAZ Z99 22002 " pdb=" CAY Z99 22002 " ideal model delta sigma weight residual 120.67 111.40 9.27 3.00e+00 1.11e-01 9.55e+00 angle pdb=" O PRO 3 192 " pdb=" C PRO 3 192 " pdb=" N PRO 3 193 " ideal model delta sigma weight residual 121.15 122.60 -1.45 4.70e-01 4.53e+00 9.46e+00 angle pdb=" CAX Z99 32002 " pdb=" CAZ Z99 32002 " pdb=" CAY Z99 32002 " ideal model delta sigma weight residual 120.67 111.88 8.79 3.00e+00 1.11e-01 8.58e+00 angle pdb=" CG1 VAL 3 504 " pdb=" CB VAL 3 504 " pdb=" CG2 VAL 3 504 " ideal model delta sigma weight residual 110.80 104.37 6.43 2.20e+00 2.07e-01 8.53e+00 angle pdb=" N VAL 3 474 " pdb=" CA VAL 3 474 " pdb=" C VAL 3 474 " ideal model delta sigma weight residual 108.86 104.23 4.63 1.63e+00 3.76e-01 8.07e+00 ... (remaining 14706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 6329 35.86 - 71.72: 107 71.72 - 107.57: 12 107.57 - 143.43: 4 143.43 - 179.29: 2 Dihedral angle restraints: 6454 sinusoidal: 2101 harmonic: 4353 Sorted by residual: dihedral pdb=" CB CYS 2 400 " pdb=" SG CYS 2 400 " pdb=" SG CYS 2 407 " pdb=" CB CYS 2 407 " ideal model delta sinusoidal sigma weight residual 93.00 -179.62 -87.38 1 1.00e+01 1.00e-02 9.16e+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 -86.00 -158.80 72.80 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CB CYS 2 525 " pdb=" SG CYS 2 525 " pdb=" SG CYS 2 537 " pdb=" CB CYS 2 537 " ideal model delta sinusoidal sigma weight residual -86.00 -23.84 -62.16 1 1.00e+01 1.00e-02 5.12e+01 ... (remaining 6451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.049: 1723 1.049 - 2.097: 0 2.097 - 3.146: 0 3.146 - 4.194: 0 4.194 - 5.243: 2 Chirality restraints: 1725 Sorted by residual: chirality pdb=" CAW Z99 32002 " pdb=" CAN Z99 32002 " pdb=" CAU Z99 32002 " pdb=" CAV Z99 32002 " both_signs ideal model delta sigma weight residual False 2.61 -2.63 5.24 2.00e-01 2.50e+01 6.87e+02 chirality pdb=" CAW Z99 22002 " pdb=" CAN Z99 22002 " pdb=" CAU Z99 22002 " pdb=" CAV Z99 22002 " both_signs ideal model delta sigma weight residual False 2.61 -2.46 5.07 2.00e-01 2.50e+01 6.43e+02 chirality pdb=" CAZ Z99 22002 " pdb=" CAO Z99 22002 " pdb=" CAX Z99 22002 " pdb=" CAY Z99 22002 " both_signs ideal model delta sigma weight residual True 2.39 -2.72 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 1722 not shown) Planarity restraints: 1932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 2 74 " -0.201 9.50e-02 1.11e+02 8.99e-02 4.98e+00 pdb=" NE ARG 2 74 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG 2 74 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG 2 74 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG 2 74 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU 2 495 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C LEU 2 495 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU 2 495 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO 2 496 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA 2 132 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO 2 133 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO 2 133 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO 2 133 " -0.026 5.00e-02 4.00e+02 ... (remaining 1929 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2147 2.78 - 3.31: 10265 3.31 - 3.84: 17471 3.84 - 4.37: 19476 4.37 - 4.90: 33752 Nonbonded interactions: 83111 Sorted by model distance: nonbonded pdb=" O SER 3 255 " pdb=" OG SER 3 258 " model vdw 2.247 2.440 nonbonded pdb=" OG SER 2 148 " pdb=" OG SER 2 167 " model vdw 2.303 2.440 nonbonded pdb=" O LEU 3 39 " pdb=" N GLY 3 92 " model vdw 2.307 2.520 nonbonded pdb=" OD1 ASP 3 334 " pdb=" NE2 GLN 3 386 " model vdw 2.309 2.520 nonbonded pdb=" O ALA 3 658 " pdb=" OG1 THR 3 661 " model vdw 2.311 2.440 ... (remaining 83106 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 10.310 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 32.890 Find NCS groups from input model: 0.420 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:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 0.091 10755 Z= 0.223 Angle : 0.567 9.272 14711 Z= 0.271 Chirality : 0.181 5.243 1725 Planarity : 0.004 0.090 1930 Dihedral : 14.971 179.291 3582 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.22 % Allowed : 7.03 % Favored : 92.76 % 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: 0.07 (0.22), residues: 1486 helix: 2.13 (0.21), residues: 646 sheet: -0.64 (0.55), residues: 114 loop : -1.92 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 2 297 HIS 0.004 0.001 HIS 2 77 PHE 0.008 0.001 PHE 3 195 TYR 0.023 0.001 TYR 3 256 ARG 0.004 0.000 ARG 2 445 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 1.125 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 96 average time/residue: 0.9212 time to fit residues: 98.5204 Evaluate side-chains 95 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 474 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 0.0670 chunk 71 optimal weight: 30.0000 chunk 87 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 2 374 GLN 3 315 HIS 3 472 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10755 Z= 0.322 Angle : 0.613 11.109 14711 Z= 0.299 Chirality : 0.044 0.234 1725 Planarity : 0.004 0.059 1930 Dihedral : 4.648 47.113 1686 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.41 % Allowed : 7.78 % Favored : 90.81 % 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: -0.10 (0.22), residues: 1486 helix: 2.01 (0.20), residues: 654 sheet: -0.85 (0.46), residues: 145 loop : -2.08 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 3 303 HIS 0.003 0.001 HIS 3 402 PHE 0.013 0.002 PHE 3 195 TYR 0.014 0.002 TYR 2 165 ARG 0.007 0.001 ARG 2 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.182 Fit side-chains REVERT: 2 29 GLU cc_start: 0.6324 (mp0) cc_final: 0.6080 (mp0) REVERT: 2 233 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7531 (pt) REVERT: 2 458 TYR cc_start: 0.8911 (t80) cc_final: 0.8665 (t80) REVERT: 3 201 MET cc_start: 0.8068 (ptt) cc_final: 0.7848 (ptt) REVERT: 3 434 TYR cc_start: 0.8359 (m-80) cc_final: 0.7446 (m-80) outliers start: 13 outliers final: 5 residues processed: 112 average time/residue: 1.1400 time to fit residues: 139.6876 Evaluate side-chains 95 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 233 ILE Chi-restraints excluded: chain 2 residue 259 GLN Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 3 residue 492 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 0.0470 chunk 92 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 136 optimal weight: 0.0170 chunk 147 optimal weight: 20.0000 chunk 121 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 46 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 3 472 GLN 3 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10755 Z= 0.201 Angle : 0.500 7.595 14711 Z= 0.249 Chirality : 0.041 0.148 1725 Planarity : 0.003 0.035 1930 Dihedral : 4.250 53.290 1685 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.05 % Allowed : 10.16 % Favored : 87.78 % 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: -0.13 (0.22), residues: 1486 helix: 1.99 (0.20), residues: 657 sheet: -0.98 (0.48), residues: 131 loop : -2.09 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 291 HIS 0.003 0.001 HIS 3 485 PHE 0.013 0.001 PHE 3 195 TYR 0.011 0.001 TYR 2 473 ARG 0.008 0.000 ARG 2 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.062 Fit side-chains REVERT: 2 29 GLU cc_start: 0.6334 (mp0) cc_final: 0.6053 (mp0) REVERT: 2 227 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: 2 233 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7565 (pt) REVERT: 2 375 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.6914 (tm-30) REVERT: 2 458 TYR cc_start: 0.8868 (t80) cc_final: 0.8626 (t80) REVERT: 3 199 LYS cc_start: 0.8348 (mtpp) cc_final: 0.8060 (mptt) REVERT: 3 434 TYR cc_start: 0.8390 (m-80) cc_final: 0.7521 (m-80) outliers start: 19 outliers final: 6 residues processed: 111 average time/residue: 0.9813 time to fit residues: 120.0854 Evaluate side-chains 101 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 233 ILE Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 3 residue 481 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 chunk 144 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 39 optimal weight: 0.3980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 3 472 GLN 3 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10755 Z= 0.224 Angle : 0.507 7.015 14711 Z= 0.255 Chirality : 0.041 0.154 1725 Planarity : 0.003 0.036 1930 Dihedral : 4.186 56.132 1685 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.05 % Allowed : 12.43 % Favored : 85.51 % 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: 1486 helix: 2.02 (0.20), residues: 657 sheet: -1.26 (0.45), residues: 152 loop : -2.15 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 3 303 HIS 0.003 0.001 HIS 2 390 PHE 0.013 0.001 PHE 3 195 TYR 0.010 0.001 TYR 2 165 ARG 0.007 0.000 ARG 2 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 1.137 Fit side-chains REVERT: 2 29 GLU cc_start: 0.6378 (mp0) cc_final: 0.6100 (mp0) REVERT: 2 227 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6198 (mp0) REVERT: 2 233 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7661 (pt) REVERT: 2 375 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: 2 458 TYR cc_start: 0.8926 (t80) cc_final: 0.8698 (t80) REVERT: 3 199 LYS cc_start: 0.8356 (mtpp) cc_final: 0.8057 (mptt) REVERT: 3 227 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7722 (tp) REVERT: 3 434 TYR cc_start: 0.8414 (m-80) cc_final: 0.7750 (m-80) outliers start: 19 outliers final: 10 residues processed: 114 average time/residue: 0.9784 time to fit residues: 123.0018 Evaluate side-chains 105 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 233 ILE Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 3 residue 41 LEU Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 493 ASP Chi-restraints excluded: chain 3 residue 798 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 107 optimal weight: 0.0060 chunk 59 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 100 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 74 optimal weight: 40.0000 chunk 130 optimal weight: 5.9990 chunk 36 optimal weight: 0.0470 overall best weight: 0.7096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 2 56 HIS 3 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10755 Z= 0.237 Angle : 0.513 8.614 14711 Z= 0.256 Chirality : 0.041 0.148 1725 Planarity : 0.003 0.036 1930 Dihedral : 4.192 58.286 1685 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.38 % Allowed : 14.27 % Favored : 83.35 % 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: -0.23 (0.22), residues: 1486 helix: 1.99 (0.21), residues: 656 sheet: -1.34 (0.46), residues: 142 loop : -2.15 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 291 HIS 0.003 0.001 HIS 3 485 PHE 0.013 0.001 PHE 3 195 TYR 0.022 0.001 TYR 3 318 ARG 0.005 0.000 ARG 2 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: 2 29 GLU cc_start: 0.6435 (mp0) cc_final: 0.6150 (mp0) REVERT: 2 227 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6256 (mp0) REVERT: 2 233 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7685 (pt) REVERT: 2 375 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.6668 (tm-30) REVERT: 2 414 ASN cc_start: 0.7571 (t0) cc_final: 0.7292 (t0) REVERT: 2 458 TYR cc_start: 0.8917 (t80) cc_final: 0.8693 (t80) REVERT: 3 141 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7489 (tp) REVERT: 3 199 LYS cc_start: 0.8386 (mtpp) cc_final: 0.8044 (mptt) REVERT: 3 228 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: 3 434 TYR cc_start: 0.8395 (m-80) cc_final: 0.7783 (m-80) outliers start: 22 outliers final: 10 residues processed: 107 average time/residue: 1.0421 time to fit residues: 122.9050 Evaluate side-chains 107 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 100 GLU Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 233 ILE Chi-restraints excluded: chain 2 residue 259 GLN Chi-restraints excluded: chain 2 residue 290 THR Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 228 GLU Chi-restraints excluded: chain 3 residue 481 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 28 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 2 56 HIS 3 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10755 Z= 0.229 Angle : 0.509 7.050 14711 Z= 0.256 Chirality : 0.041 0.145 1725 Planarity : 0.004 0.062 1930 Dihedral : 4.209 56.988 1685 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.92 % Allowed : 14.27 % Favored : 82.81 % 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: -0.24 (0.22), residues: 1486 helix: 1.99 (0.20), residues: 656 sheet: -1.36 (0.44), residues: 152 loop : -2.17 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 3 297 HIS 0.002 0.001 HIS 2 390 PHE 0.013 0.001 PHE 3 195 TYR 0.023 0.001 TYR 3 318 ARG 0.019 0.000 ARG 3 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: 2 29 GLU cc_start: 0.6476 (mp0) cc_final: 0.6186 (mp0) REVERT: 2 233 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7566 (pt) REVERT: 2 368 ARG cc_start: 0.7063 (mmm160) cc_final: 0.6822 (tpp-160) REVERT: 2 375 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.6602 (tm-30) REVERT: 2 414 ASN cc_start: 0.7669 (t0) cc_final: 0.7406 (t0) REVERT: 2 458 TYR cc_start: 0.8892 (t80) cc_final: 0.8671 (t80) REVERT: 3 199 LYS cc_start: 0.8411 (mtpp) cc_final: 0.8054 (mptt) REVERT: 3 434 TYR cc_start: 0.8400 (m-80) cc_final: 0.7857 (m-80) outliers start: 27 outliers final: 8 residues processed: 117 average time/residue: 1.0081 time to fit residues: 130.1374 Evaluate side-chains 105 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 100 GLU Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 233 ILE Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 798 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 105 optimal weight: 0.0570 chunk 122 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 90 optimal weight: 0.2980 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 30.0000 chunk 89 optimal weight: 0.3980 chunk 57 optimal weight: 30.0000 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 2 56 HIS 3 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10755 Z= 0.194 Angle : 0.507 12.044 14711 Z= 0.252 Chirality : 0.041 0.143 1725 Planarity : 0.003 0.036 1930 Dihedral : 4.126 54.339 1685 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.27 % Allowed : 15.68 % Favored : 82.05 % 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: -0.17 (0.22), residues: 1486 helix: 2.00 (0.20), residues: 659 sheet: -1.22 (0.44), residues: 156 loop : -2.12 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 2 487 HIS 0.002 0.001 HIS 2 390 PHE 0.014 0.001 PHE 3 275 TYR 0.023 0.001 TYR 3 318 ARG 0.006 0.000 ARG 2 229 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: 2 29 GLU cc_start: 0.6434 (mp0) cc_final: 0.6142 (mp0) REVERT: 2 227 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6408 (mp0) REVERT: 2 375 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: 2 414 ASN cc_start: 0.7733 (t0) cc_final: 0.7527 (t0) REVERT: 2 458 TYR cc_start: 0.8883 (t80) cc_final: 0.8667 (t80) REVERT: 3 199 LYS cc_start: 0.8374 (mtpp) cc_final: 0.8025 (mptt) REVERT: 3 434 TYR cc_start: 0.8394 (m-80) cc_final: 0.7792 (m-80) outliers start: 21 outliers final: 9 residues processed: 112 average time/residue: 1.0240 time to fit residues: 126.1532 Evaluate side-chains 107 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 100 GLU Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 3 residue 98 THR Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 798 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 71 optimal weight: 30.0000 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 131 optimal weight: 30.0000 chunk 138 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 2 56 HIS 3 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10755 Z= 0.331 Angle : 0.583 10.502 14711 Z= 0.289 Chirality : 0.043 0.166 1725 Planarity : 0.004 0.037 1930 Dihedral : 4.533 53.726 1685 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.59 % Allowed : 16.43 % Favored : 80.97 % 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: -0.35 (0.22), residues: 1486 helix: 1.89 (0.20), residues: 657 sheet: -1.49 (0.43), residues: 156 loop : -2.21 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 3 303 HIS 0.003 0.001 HIS 3 485 PHE 0.015 0.002 PHE 3 275 TYR 0.024 0.002 TYR 3 318 ARG 0.007 0.000 ARG 2 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: 2 29 GLU cc_start: 0.6593 (mp0) cc_final: 0.6297 (mp0) REVERT: 2 227 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: 2 375 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.6719 (tm-30) REVERT: 2 414 ASN cc_start: 0.7903 (t0) cc_final: 0.7674 (t0) REVERT: 2 458 TYR cc_start: 0.8952 (t80) cc_final: 0.8739 (t80) REVERT: 3 233 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7468 (mm-30) REVERT: 3 434 TYR cc_start: 0.8446 (m-80) cc_final: 0.7997 (m-80) outliers start: 24 outliers final: 11 residues processed: 111 average time/residue: 1.0170 time to fit residues: 124.5296 Evaluate side-chains 107 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 100 GLU Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 3 residue 98 THR Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 798 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 121 optimal weight: 0.0070 chunk 127 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 2 56 HIS 3 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10755 Z= 0.246 Angle : 0.540 10.406 14711 Z= 0.269 Chirality : 0.042 0.149 1725 Planarity : 0.003 0.037 1930 Dihedral : 4.408 53.769 1685 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.05 % Allowed : 17.30 % Favored : 80.65 % 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: -0.36 (0.22), residues: 1486 helix: 1.85 (0.20), residues: 662 sheet: -1.65 (0.42), residues: 163 loop : -2.16 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 3 297 HIS 0.002 0.001 HIS 2 390 PHE 0.014 0.001 PHE 3 195 TYR 0.025 0.001 TYR 3 318 ARG 0.006 0.000 ARG 2 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: 2 29 GLU cc_start: 0.6460 (mp0) cc_final: 0.6147 (mp0) REVERT: 2 227 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6427 (mp0) REVERT: 2 375 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.6528 (tm-30) REVERT: 2 414 ASN cc_start: 0.7963 (t0) cc_final: 0.7761 (t0) REVERT: 2 458 TYR cc_start: 0.8899 (t80) cc_final: 0.8684 (t80) REVERT: 3 199 LYS cc_start: 0.8451 (mtpp) cc_final: 0.8041 (mptt) REVERT: 3 434 TYR cc_start: 0.8432 (m-80) cc_final: 0.8044 (m-80) outliers start: 19 outliers final: 12 residues processed: 113 average time/residue: 1.0325 time to fit residues: 128.7984 Evaluate side-chains 109 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 100 GLU Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 417 ARG Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 3 residue 98 THR Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 798 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 chunk 137 optimal weight: 30.0000 chunk 118 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 2 56 HIS 3 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10755 Z= 0.248 Angle : 0.543 10.229 14711 Z= 0.270 Chirality : 0.042 0.150 1725 Planarity : 0.003 0.037 1930 Dihedral : 4.398 51.991 1685 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.38 % Allowed : 17.41 % 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: -0.35 (0.22), residues: 1486 helix: 1.85 (0.20), residues: 662 sheet: -1.61 (0.42), residues: 163 loop : -2.16 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 3 303 HIS 0.002 0.001 HIS 2 87 PHE 0.013 0.001 PHE 3 195 TYR 0.025 0.002 TYR 3 318 ARG 0.006 0.000 ARG 2 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: 2 29 GLU cc_start: 0.6451 (mp0) cc_final: 0.6148 (mp0) REVERT: 2 227 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6461 (mp0) REVERT: 2 269 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: 2 375 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.6515 (tm-30) REVERT: 2 458 TYR cc_start: 0.8902 (t80) cc_final: 0.8700 (t80) REVERT: 3 72 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7598 (ttt) REVERT: 3 199 LYS cc_start: 0.8481 (mtpp) cc_final: 0.8068 (mptt) REVERT: 3 228 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: 3 434 TYR cc_start: 0.8429 (m-80) cc_final: 0.8101 (m-80) outliers start: 22 outliers final: 13 residues processed: 110 average time/residue: 1.0796 time to fit residues: 130.2226 Evaluate side-chains 116 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 100 GLU Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 226 LEU Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 269 PHE Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 417 ARG Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 98 THR Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 228 GLU Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 798 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.0470 chunk 17 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 122 optimal weight: 0.0170 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 3 472 GLN 3 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.232466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.147447 restraints weight = 11074.290| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.97 r_work: 0.3351 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10755 Z= 0.166 Angle : 0.501 10.054 14711 Z= 0.250 Chirality : 0.040 0.144 1725 Planarity : 0.003 0.037 1930 Dihedral : 4.162 48.489 1685 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.95 % Allowed : 17.41 % Favored : 80.65 % 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: -0.19 (0.23), residues: 1486 helix: 1.98 (0.21), residues: 662 sheet: -1.50 (0.43), residues: 157 loop : -2.08 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 487 HIS 0.002 0.000 HIS 2 390 PHE 0.012 0.001 PHE 3 195 TYR 0.024 0.001 TYR 3 318 ARG 0.006 0.000 ARG 2 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3314.05 seconds wall clock time: 60 minutes 21.86 seconds (3621.86 seconds total)