Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 20:44:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcz_36170/07_2023/8jcz_36170_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcz_36170/07_2023/8jcz_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_36170/07_2023/8jcz_36170.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcz_36170/07_2023/8jcz_36170.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcz_36170/07_2023/8jcz_36170_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcz_36170/07_2023/8jcz_36170_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-1.21rc1-5013/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 chiralities: 1 Chain: "3" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.71, per 1000 atoms: 0.54 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: 4.24 Conformation dependent library (CDL) restraints added in 1.7 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: 1.43 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: 2.95 Time building geometry restraints manager: 4.56 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 - 17.48: 5834 17.48 - 34.95: 425 34.95 - 52.43: 90 52.43 - 69.90: 15 69.90 - 87.38: 6 Dihedral angle restraints: 6370 sinusoidal: 2017 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 6367 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: 2.450 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: 10.740 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 29.360 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.020 ------------------------------------------------------------------------------- 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 : 12.895 83.424 3498 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 % 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 *********************** 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 : 1.154 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 96 average time/residue: 0.9063 time to fit residues: 97.1030 Evaluate side-chains 95 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.4622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7372 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 10755 Z= 0.317 Angle : 0.602 11.911 14711 Z= 0.294 Chirality : 0.043 0.241 1725 Planarity : 0.004 0.055 1930 Dihedral : 4.197 57.534 1601 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 1.51 % 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: -0.07 (0.22), residues: 1486 helix: 2.01 (0.20), residues: 655 sheet: -0.79 (0.47), residues: 145 loop : -2.06 (0.22), residues: 686 *********************** 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 114 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 1.188 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 110 average time/residue: 1.0264 time to fit residues: 124.3711 Evaluate side-chains 94 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.5234 time to fit residues: 3.2196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 46 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 3 345 ASN 3 472 GLN 3 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.071 10755 Z= 0.449 Angle : 0.652 9.336 14711 Z= 0.331 Chirality : 0.046 0.193 1725 Planarity : 0.004 0.040 1930 Dihedral : 4.692 56.556 1601 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer Outliers : 2.59 % 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: -0.54 (0.22), residues: 1486 helix: 1.72 (0.20), residues: 653 sheet: -1.59 (0.45), residues: 138 loop : -2.26 (0.21), residues: 695 *********************** 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 129 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 1.142 Fit side-chains outliers start: 24 outliers final: 7 residues processed: 119 average time/residue: 1.0096 time to fit residues: 132.0820 Evaluate side-chains 98 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.4511 time to fit residues: 3.1764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 136 optimal weight: 0.5980 chunk 144 optimal weight: 0.3980 chunk 71 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 39 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 3 472 GLN 3 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2037 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= 0.210 Angle : 0.518 7.880 14711 Z= 0.262 Chirality : 0.041 0.167 1725 Planarity : 0.004 0.042 1930 Dihedral : 4.315 52.970 1601 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer Outliers : 2.81 % 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: -0.41 (0.22), residues: 1486 helix: 1.78 (0.20), residues: 659 sheet: -1.46 (0.44), residues: 148 loop : -2.20 (0.22), residues: 679 *********************** 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 125 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.158 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 116 average time/residue: 0.9021 time to fit residues: 116.5666 Evaluate side-chains 101 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 1.0065 time to fit residues: 3.8697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 107 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 130 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7451 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 10755 Z= 0.295 Angle : 0.552 7.310 14711 Z= 0.279 Chirality : 0.043 0.154 1725 Planarity : 0.004 0.038 1930 Dihedral : 4.248 41.265 1601 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer Outliers : 3.03 % 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: -0.48 (0.22), residues: 1486 helix: 1.79 (0.20), residues: 655 sheet: -1.80 (0.42), residues: 153 loop : -2.21 (0.22), residues: 678 *********************** 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 130 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.190 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 11 residues processed: 120 average time/residue: 1.0608 time to fit residues: 139.9323 Evaluate side-chains 107 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.9470 time to fit residues: 3.5980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 0.3980 chunk 76 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.7456 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 10755 Z= 0.313 Angle : 0.555 7.805 14711 Z= 0.282 Chirality : 0.043 0.155 1725 Planarity : 0.004 0.038 1930 Dihedral : 4.219 36.523 1601 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer Outliers : 3.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1486 helix: 1.79 (0.21), residues: 654 sheet: -1.83 (0.42), residues: 153 loop : -2.21 (0.22), residues: 679 *********************** 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 133 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 100 time to evaluate : 1.084 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 12 residues processed: 122 average time/residue: 0.9551 time to fit residues: 128.4520 Evaluate side-chains 107 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.9326 time to fit residues: 3.5164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 144 optimal weight: 20.0000 chunk 90 optimal weight: 0.4980 chunk 88 optimal weight: 0.3980 chunk 66 optimal weight: 20.0000 chunk 89 optimal weight: 0.0980 chunk 57 optimal weight: 20.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 3 473 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10755 Z= 0.219 Angle : 0.535 12.546 14711 Z= 0.266 Chirality : 0.041 0.151 1725 Planarity : 0.004 0.079 1930 Dihedral : 4.087 32.679 1601 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 2.16 % 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: -0.44 (0.22), residues: 1486 helix: 1.81 (0.20), residues: 659 sheet: -1.73 (0.42), residues: 153 loop : -2.20 (0.22), residues: 674 *********************** 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 118 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.171 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 113 average time/residue: 1.0257 time to fit residues: 127.7333 Evaluate side-chains 103 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.313 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 1.8563 time to fit residues: 3.6044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 40.0000 chunk 13 optimal weight: 0.0030 chunk 113 optimal weight: 0.0270 chunk 131 optimal weight: 30.0000 chunk 138 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 overall best weight: 0.5048 ------------------------------------------------------------------------------- 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: 0.7424 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10755 Z= 0.196 Angle : 0.523 10.745 14711 Z= 0.262 Chirality : 0.041 0.146 1725 Planarity : 0.003 0.044 1930 Dihedral : 3.940 26.868 1601 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 2.38 % 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: -0.36 (0.22), residues: 1486 helix: 1.87 (0.21), residues: 660 sheet: -1.61 (0.43), residues: 157 loop : -2.19 (0.22), residues: 669 *********************** 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 119 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 1.223 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 112 average time/residue: 1.0156 time to fit residues: 125.6961 Evaluate side-chains 107 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.242 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.8692 time to fit residues: 3.5565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 0.0970 chunk 41 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 0.0270 chunk 88 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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: 0.7424 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10755 Z= 0.205 Angle : 0.527 10.477 14711 Z= 0.264 Chirality : 0.041 0.143 1725 Planarity : 0.003 0.038 1930 Dihedral : 3.892 20.258 1601 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.22), residues: 1486 helix: 1.88 (0.21), residues: 662 sheet: -1.55 (0.43), residues: 157 loop : -2.18 (0.22), residues: 667 *********************** 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 110 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 1.244 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 106 average time/residue: 1.0418 time to fit residues: 122.3438 Evaluate side-chains 102 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 1.7696 time to fit residues: 3.4989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 149 optimal weight: 20.0000 chunk 137 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7440 moved from start: 0.2601 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= 0.245 Angle : 0.556 10.708 14711 Z= 0.279 Chirality : 0.042 0.147 1725 Planarity : 0.003 0.038 1930 Dihedral : 3.942 22.742 1601 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.22), residues: 1486 helix: 1.87 (0.21), residues: 661 sheet: -1.52 (0.42), residues: 163 loop : -2.19 (0.22), residues: 662 ********************** 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 111 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 1.153 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 106 average time/residue: 0.9536 time to fit residues: 112.3217 Evaluate side-chains 103 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.169 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.9101 time to fit residues: 3.6262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.0000 chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 122 optimal weight: 0.0670 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.4322 ------------------------------------------------------------------------------- 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 3 472 GLN 3 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.231665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.166132 restraints weight = 11051.169| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.99 r_work: 0.3539 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10755 Z= 0.186 Angle : 0.529 10.564 14711 Z= 0.264 Chirality : 0.041 0.141 1725 Planarity : 0.003 0.038 1930 Dihedral : 3.864 24.735 1601 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 1.51 % 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: -0.28 (0.22), residues: 1486 helix: 1.93 (0.21), residues: 661 sheet: -1.49 (0.44), residues: 157 loop : -2.16 (0.22), residues: 668 =============================================================================== Job complete usr+sys time: 3207.86 seconds wall clock time: 57 minutes 49.14 seconds (3469.14 seconds total)