Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 00:20:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/07_2023/8jcy_36169_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/07_2023/8jcy_36169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/07_2023/8jcy_36169.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/07_2023/8jcy_36169.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/07_2023/8jcy_36169_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/07_2023/8jcy_36169_updated.pdb" } resolution = 2.9 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= 0.049 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 60 5.16 5 C 6921 2.51 5 N 1880 2.21 5 O 2013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ASP 429": "OD1" <-> "OD2" Residue "2 PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 83": "OD1" <-> "OD2" Residue "3 GLU 111": "OE1" <-> "OE2" Residue "3 PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 10874 Number of models: 1 Model: "" Number of chains: 4 Chain: "2" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 5258 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 37, 'TRANS': 722} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 693 Unresolved non-hydrogen angles: 891 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 9, 'ASN:plan1': 7, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 12, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 406 Chain: "3" Number of atoms: 5340 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 765, 5330 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 200} Link IDs: {'PTRANS': 30, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 763 Unresolved non-hydrogen angles: 969 Unresolved non-hydrogen dihedrals: 643 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 13, 'TYR:plan': 12, 'ASN:plan1': 10, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 15, 'GLU:plan': 15, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 421 Conformer: "B" Number of residues, atoms: 765, 5330 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 200} Link IDs: {'PTRANS': 30, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 763 Unresolved non-hydrogen angles: 969 Unresolved non-hydrogen dihedrals: 643 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 13, 'TYR:plan': 12, 'ASN:plan1': 10, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 15, 'GLU:plan': 15, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 421 bond proxies already assigned to first conformer: 5422 Chain: "2" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 124 Unusual residues: {'CLR': 3, 'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Unusual residues: {'CLR': 4, 'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS 3 485 " occ=0.68 ... (18 atoms not shown) pdb=" NE2BHIS 3 485 " occ=0.32 Time building chain proxies: 8.90, per 1000 atoms: 0.82 Number of scatterers: 10874 At special positions: 0 Unit cell: (89.964, 122.094, 183.141, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2013 8.00 N 1880 7.00 C 6921 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=2.04 Simple disulfide: pdb=" SG CYS 3 534 " - pdb=" SG CYS 3 546 " distance=2.04 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: 4.77 Conformation dependent library (CDL) restraints added in 3.2 seconds 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 7 sheets defined 43.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain '2' and resid 59 through 73 Processing helix chain '2' and resid 95 through 102 removed outlier: 3.604A pdb=" N GLU 2 100 " --> pdb=" O THR 2 96 " (cutoff:3.500A) Processing helix chain '2' and resid 105 through 109 Processing helix chain '2' and resid 145 through 158 removed outlier: 4.252A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE 2 158 " --> pdb=" O LEU 2 154 " (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 188 through 201 Processing helix chain '2' and resid 215 through 229 removed outlier: 4.695A pdb=" N THR 2 219 " --> pdb=" O ASP 2 215 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY 2 220 " --> pdb=" O TYR 2 216 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU 2 226 " --> pdb=" O GLU 2 222 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU 2 227 " --> pdb=" O ALA 2 223 " (cutoff:3.500A) Processing helix chain '2' and resid 247 through 258 Processing helix chain '2' and resid 272 through 284 Processing helix chain '2' and resid 325 through 332 removed outlier: 3.517A pdb=" N SER 2 329 " --> pdb=" O SER 2 325 " (cutoff:3.500A) Processing helix chain '2' and resid 345 through 352 Processing helix chain '2' and resid 378 through 399 Processing helix chain '2' and resid 408 through 410 No H-bonds generated for 'chain '2' and resid 408 through 410' Processing helix chain '2' and resid 415 through 421 Processing helix chain '2' and resid 486 through 488 No H-bonds generated for 'chain '2' and resid 486 through 488' Processing helix chain '2' and resid 568 through 590 removed outlier: 3.869A pdb=" N VAL 2 590 " --> pdb=" O LEU 2 586 " (cutoff:3.500A) Processing helix chain '2' and resid 596 through 600 Processing helix chain '2' and resid 603 through 624 Processing helix chain '2' and resid 629 through 658 Processing helix chain '2' and resid 676 through 700 Processing helix chain '2' and resid 726 through 748 Processing helix chain '2' and resid 756 through 783 Proline residue: 2 778 - end of helix Processing helix chain '2' and resid 787 through 807 Processing helix chain '2' and resid 809 through 818 Processing helix chain '3' and resid 67 through 81 Processing helix chain '3' and resid 102 through 116 removed outlier: 3.685A pdb=" N LEU 3 110 " --> pdb=" O LEU 3 106 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU 3 111 " --> pdb=" O GLU 3 107 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE 3 112 " --> pdb=" O GLN 3 108 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA 3 115 " --> pdb=" O GLU 3 111 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N SER 3 116 " --> pdb=" O PHE 3 112 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 4.255A pdb=" N LEU 3 163 " --> pdb=" O ASN 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 176 through 179 Processing helix chain '3' and resid 195 through 207 removed outlier: 3.539A pdb=" N LYS 3 199 " --> pdb=" O PHE 3 195 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA 3 202 " --> pdb=" O ALA 3 198 " (cutoff:3.500A) Processing helix chain '3' and resid 222 through 236 Processing helix chain '3' and resid 255 through 264 Processing helix chain '3' and resid 278 through 290 Processing helix chain '3' and resid 331 through 338 Processing helix chain '3' and resid 351 through 359 Processing helix chain '3' and resid 390 through 411 Processing helix chain '3' and resid 421 through 424 No H-bonds generated for 'chain '3' and resid 421 through 424' Processing helix chain '3' and resid 427 through 432 Processing helix chain '3' and resid 435 through 437 No H-bonds generated for 'chain '3' and resid 435 through 437' Processing helix chain '3' and resid 575 through 602 removed outlier: 4.368A 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 611 through 632 Processing helix chain '3' and resid 639 through 664 removed outlier: 3.529A pdb=" N LYS 3 662 " --> pdb=" O LEU 3 659 " (cutoff:3.500A) Processing helix chain '3' and resid 683 through 708 removed outlier: 3.895A pdb=" N LEU 3 707 " --> pdb=" O VAL 3 703 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE 3 708 " --> pdb=" O SER 3 704 " (cutoff:3.500A) Processing helix chain '3' and resid 734 through 757 removed outlier: 3.757A pdb=" N ASP 3 744 " --> pdb=" O SER 3 740 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL 3 745 " --> pdb=" O LEU 3 741 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR 3 754 " --> pdb=" O LEU 3 750 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA 3 755 " --> pdb=" O CYS 3 751 " (cutoff:3.500A) Processing helix chain '3' and resid 765 through 791 removed outlier: 3.528A pdb=" N THR 3 777 " --> pdb=" O PHE 3 773 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU 3 786 " --> pdb=" O TRP 3 782 " (cutoff:3.500A) Proline residue: 3 787 - end of helix removed outlier: 3.785A pdb=" N VAL 3 791 " --> pdb=" O PRO 3 787 " (cutoff:3.500A) Processing helix chain '3' and resid 797 through 825 removed outlier: 5.197A pdb=" N ALA 3 820 " --> pdb=" O GLY 3 816 " (cutoff:3.500A) Proline residue: 3 821 - end of helix Processing sheet with id= A, first strand: chain '2' and resid 26 through 28 removed outlier: 6.562A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU 2 37 " --> pdb=" O ILE 2 140 " (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 208 through 210 removed outlier: 6.181A pdb=" N THR 2 290 " --> pdb=" O ALA 2 266 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU 2 268 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL 2 292 " --> pdb=" O LEU 2 268 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 315 through 319 removed outlier: 3.777A pdb=" N GLY 2 472 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR 2 457 " --> pdb=" O LYS 2 470 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LYS 2 470 " --> pdb=" O THR 2 457 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU 2 459 " --> pdb=" O TYR 2 468 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR 2 468 " --> pdb=" O LEU 2 459 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '3' and resid 33 through 35 removed outlier: 6.234A 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: 6.381A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLY 3 42 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL 3 145 " --> pdb=" O GLY 3 42 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU 3 44 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLY 3 147 " --> pdb=" O LEU 3 44 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY 3 147 " --> pdb=" O PRO 3 167 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE 3 169 " --> pdb=" O GLY 3 147 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 244 through 247 removed outlier: 7.178A pdb=" N THR 3 215 " --> pdb=" O GLU 3 245 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N VAL 3 247 " --> pdb=" O THR 3 215 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA 3 217 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N THR 3 296 " --> pdb=" O VAL 3 272 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU 3 274 " --> pdb=" O THR 3 296 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL 3 298 " --> pdb=" O LEU 3 274 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 321 through 325 removed outlier: 6.470A pdb=" N ASN 3 470 " --> pdb=" O LYS 3 482 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LYS 3 482 " --> pdb=" O ASN 3 470 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN 3 472 " --> pdb=" O TYR 3 480 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N TYR 3 480 " --> pdb=" O GLN 3 472 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER 3 491 " --> pdb=" O AHIS 3 485 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1387 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3627 1.34 - 1.46: 2552 1.46 - 1.58: 4862 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 11118 Sorted by residual: 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 2.00e+01 bond pdb=" CAT Z99 22002 " pdb=" OAP Z99 22002 " ideal model delta sigma weight residual 1.364 1.453 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" CAS Z99 32002 " pdb=" OAP Z99 32002 " ideal model delta sigma weight residual 1.369 1.450 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" CAS Z99 22002 " pdb=" OAP Z99 22002 " ideal model delta sigma weight residual 1.369 1.449 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" CAO Z99 22002 " pdb=" CAZ Z99 22002 " ideal model delta sigma weight residual 1.488 1.533 -0.045 2.00e-02 2.50e+03 5.09e+00 ... (remaining 11113 not shown) Histogram of bond angle deviations from ideal: 59.60 - 74.47: 6 74.47 - 89.35: 0 89.35 - 104.23: 184 104.23 - 119.10: 8988 119.10 - 133.98: 6083 Bond angle restraints: 15261 Sorted by residual: angle pdb=" C VAL 3 701 " pdb=" N MET 3 702 " pdb=" CA MET 3 702 " ideal model delta sigma weight residual 121.58 115.13 6.45 1.95e+00 2.63e-01 1.09e+01 angle pdb=" CAX Z99 32002 " pdb=" CAZ Z99 32002 " pdb=" CAY Z99 32002 " ideal model delta sigma weight residual 120.67 111.08 9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CAX Z99 22002 " pdb=" CAZ Z99 22002 " pdb=" CAY Z99 22002 " ideal model delta sigma weight residual 120.67 111.17 9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" CAW Z99 32002 " pdb=" CAN Z99 32002 " pdb=" CAY Z99 32002 " ideal model delta sigma weight residual 117.71 108.57 9.14 3.00e+00 1.11e-01 9.28e+00 angle pdb=" CA MET 3 702 " pdb=" CB MET 3 702 " pdb=" CG MET 3 702 " ideal model delta sigma weight residual 114.10 120.13 -6.03 2.00e+00 2.50e-01 9.09e+00 ... (remaining 15256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 6131 17.75 - 35.49: 315 35.49 - 53.24: 54 53.24 - 70.99: 9 70.99 - 88.73: 8 Dihedral angle restraints: 6517 sinusoidal: 2093 harmonic: 4424 Sorted by residual: dihedral pdb=" CB CYS 2 234 " pdb=" SG CYS 2 234 " pdb=" SG CYS 2 518 " pdb=" CB CYS 2 518 " ideal model delta sinusoidal sigma weight residual -86.00 -170.72 84.72 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS 3 57 " pdb=" SG CYS 3 57 " pdb=" SG CYS 3 99 " pdb=" CB CYS 3 99 " ideal model delta sinusoidal sigma weight residual 93.00 12.17 80.83 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS 2 504 " pdb=" SG CYS 2 504 " pdb=" SG CYS 2 522 " pdb=" CB CYS 2 522 " ideal model delta sinusoidal sigma weight residual 93.00 16.37 76.63 1 1.00e+01 1.00e-02 7.38e+01 ... (remaining 6514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.034: 1803 1.034 - 2.068: 0 2.068 - 3.101: 0 3.101 - 4.135: 0 4.135 - 5.169: 2 Chirality restraints: 1805 Sorted by residual: 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 -2.56 5.17 2.00e-01 2.50e+01 6.68e+02 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 -2.26 4.87 2.00e-01 2.50e+01 5.93e+02 chirality pdb=" CAZ Z99 32002 " pdb=" CAO Z99 32002 " pdb=" CAX Z99 32002 " pdb=" CAY Z99 32002 " both_signs ideal model delta sigma weight residual True 2.39 -2.70 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1802 not shown) Planarity restraints: 1967 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG 2 411 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.38e+00 pdb=" N PRO 2 412 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO 2 412 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO 2 412 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU 3 224 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C GLU 3 224 " 0.035 2.00e-02 2.50e+03 pdb=" O GLU 3 224 " -0.013 2.00e-02 2.50e+03 pdb=" N THR 3 225 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE 3 532 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO 3 533 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO 3 533 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO 3 533 " 0.022 5.00e-02 4.00e+02 ... (remaining 1964 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 719 2.74 - 3.28: 10851 3.28 - 3.82: 18275 3.82 - 4.36: 19981 4.36 - 4.90: 35317 Nonbonded interactions: 85143 Sorted by model distance: nonbonded pdb=" OG1 THR 2 205 " pdb=" O SER 2 498 " model vdw 2.200 2.440 nonbonded pdb=" O ASP 3 97 " pdb=" NE2 GLN 3 108 " model vdw 2.200 2.520 nonbonded pdb=" O ALA 2 746 " pdb=" OG1 THR 2 749 " model vdw 2.264 2.440 nonbonded pdb=" OG SER 3 154 " pdb=" OG SER 3 173 " model vdw 2.274 2.440 nonbonded pdb=" OG SER 3 327 " pdb=" O SER 3 388 " model vdw 2.304 2.440 ... (remaining 85138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.02 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: 2.550 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: 10.810 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 35.460 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 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 0.089 11118 Z= 0.205 Angle : 0.533 9.588 15261 Z= 0.250 Chirality : 0.172 5.169 1805 Planarity : 0.004 0.072 1965 Dihedral : 11.202 88.734 3599 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.23), residues: 1516 helix: 2.60 (0.20), residues: 693 sheet: -0.75 (0.47), residues: 151 loop : -1.55 (0.23), residues: 672 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.078 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.9042 time to fit residues: 137.3944 Evaluate side-chains 106 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 20.0000 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 11118 Z= 0.249 Angle : 0.561 13.239 15261 Z= 0.276 Chirality : 0.042 0.392 1805 Planarity : 0.004 0.051 1965 Dihedral : 4.597 55.417 1693 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1516 helix: 2.26 (0.20), residues: 694 sheet: -0.96 (0.44), residues: 158 loop : -1.57 (0.23), residues: 664 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.094 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 124 average time/residue: 0.8966 time to fit residues: 123.9845 Evaluate side-chains 113 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.1251 time to fit residues: 2.7079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 138 optimal weight: 0.0870 chunk 149 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 137 optimal weight: 0.0020 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.7570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 11118 Z= 0.239 Angle : 0.538 12.549 15261 Z= 0.268 Chirality : 0.041 0.178 1805 Planarity : 0.004 0.040 1965 Dihedral : 4.637 54.079 1693 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 1.96 % 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: 0.33 (0.22), residues: 1516 helix: 2.11 (0.20), residues: 694 sheet: -1.03 (0.43), residues: 158 loop : -1.61 (0.23), residues: 664 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.133 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 120 average time/residue: 0.9076 time to fit residues: 121.3266 Evaluate side-chains 117 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.1400 time to fit residues: 2.6919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 92 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 332 GLN ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 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 : 0.005 0.043 11118 Z= 0.314 Angle : 0.571 8.174 15261 Z= 0.289 Chirality : 0.042 0.175 1805 Planarity : 0.004 0.037 1965 Dihedral : 4.864 55.612 1693 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 3.05 % 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: 0.13 (0.22), residues: 1516 helix: 1.92 (0.20), residues: 703 sheet: -1.14 (0.42), residues: 151 loop : -1.72 (0.23), residues: 662 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 1.246 Fit side-chains outliers start: 28 outliers final: 14 residues processed: 119 average time/residue: 0.9108 time to fit residues: 121.1072 Evaluate side-chains 113 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 5 average time/residue: 0.1720 time to fit residues: 2.9721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 2 optimal weight: 0.0770 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 131 optimal weight: 30.0000 chunk 37 optimal weight: 0.5980 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11118 Z= 0.229 Angle : 0.526 9.105 15261 Z= 0.264 Chirality : 0.040 0.167 1805 Planarity : 0.004 0.038 1965 Dihedral : 4.741 55.485 1693 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 2.18 % 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: 1516 helix: 2.01 (0.20), residues: 697 sheet: -1.10 (0.42), residues: 157 loop : -1.74 (0.23), residues: 662 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 1.212 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 115 average time/residue: 0.8987 time to fit residues: 115.5290 Evaluate side-chains 109 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.1776 time to fit residues: 2.4671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.3980 chunk 132 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 147 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 11118 Z= 0.247 Angle : 0.535 8.788 15261 Z= 0.269 Chirality : 0.041 0.178 1805 Planarity : 0.004 0.038 1965 Dihedral : 4.740 55.557 1693 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 2.40 % 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: 0.14 (0.22), residues: 1516 helix: 1.93 (0.20), residues: 704 sheet: -1.08 (0.43), residues: 147 loop : -1.74 (0.23), residues: 665 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 1.170 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 111 average time/residue: 0.8618 time to fit residues: 107.5711 Evaluate side-chains 112 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 10 residues processed: 6 average time/residue: 0.1614 time to fit residues: 3.1591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 107 optimal weight: 0.1980 chunk 123 optimal weight: 0.0370 chunk 82 optimal weight: 0.5980 chunk 146 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11118 Z= 0.180 Angle : 0.503 9.209 15261 Z= 0.252 Chirality : 0.040 0.174 1805 Planarity : 0.004 0.038 1965 Dihedral : 4.616 55.527 1693 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 1.85 % 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: 0.26 (0.22), residues: 1516 helix: 2.09 (0.20), residues: 698 sheet: -1.03 (0.43), residues: 147 loop : -1.71 (0.23), residues: 671 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.197 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 106 average time/residue: 0.8158 time to fit residues: 97.9327 Evaluate side-chains 103 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 2 average time/residue: 0.1937 time to fit residues: 2.2293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.0010 chunk 87 optimal weight: 0.4980 chunk 44 optimal weight: 0.0470 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 72 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 115 optimal weight: 0.2980 chunk 133 optimal weight: 10.0000 chunk 140 optimal weight: 0.6980 overall best weight: 0.2684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 11118 Z= 0.144 Angle : 0.485 9.527 15261 Z= 0.243 Chirality : 0.039 0.170 1805 Planarity : 0.003 0.038 1965 Dihedral : 4.502 55.467 1693 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.22), residues: 1516 helix: 2.22 (0.20), residues: 694 sheet: -0.89 (0.43), residues: 152 loop : -1.61 (0.23), residues: 670 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 1.188 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 111 average time/residue: 0.8999 time to fit residues: 112.8703 Evaluate side-chains 107 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 1.326 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 2 average time/residue: 0.2369 time to fit residues: 2.5432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 82 optimal weight: 0.5980 chunk 59 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 0.1980 chunk 129 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 11118 Z= 0.318 Angle : 0.562 10.256 15261 Z= 0.283 Chirality : 0.042 0.179 1805 Planarity : 0.004 0.038 1965 Dihedral : 4.710 56.033 1693 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 1.85 % 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: 0.15 (0.22), residues: 1516 helix: 1.97 (0.20), residues: 703 sheet: -1.14 (0.43), residues: 148 loop : -1.76 (0.23), residues: 665 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 1.160 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 112 average time/residue: 0.8666 time to fit residues: 108.9635 Evaluate side-chains 107 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 1.396 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 1 average time/residue: 0.2607 time to fit residues: 2.0720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.1980 chunk 68 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 0.0980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 11118 Z= 0.240 Angle : 0.538 11.572 15261 Z= 0.270 Chirality : 0.041 0.179 1805 Planarity : 0.004 0.038 1965 Dihedral : 4.692 56.368 1693 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 1.85 % 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: 0.18 (0.22), residues: 1516 helix: 1.99 (0.20), residues: 704 sheet: -1.13 (0.43), residues: 148 loop : -1.74 (0.23), residues: 664 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 1.183 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 108 average time/residue: 0.8898 time to fit residues: 108.2716 Evaluate side-chains 104 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 2 average time/residue: 0.2436 time to fit residues: 2.2982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.0050 chunk 111 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 120 optimal weight: 0.0020 chunk 50 optimal weight: 0.0770 chunk 124 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 106 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 overall best weight: 0.2318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.231749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.190025 restraints weight = 30208.341| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 3.51 r_work: 0.3635 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 11118 Z= 0.141 Angle : 0.503 11.506 15261 Z= 0.253 Chirality : 0.039 0.199 1805 Planarity : 0.004 0.039 1965 Dihedral : 4.524 56.157 1693 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 1.64 % 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: 0.37 (0.22), residues: 1516 helix: 2.25 (0.20), residues: 693 sheet: -1.23 (0.43), residues: 153 loop : -1.64 (0.23), residues: 670 =============================================================================== Job complete usr+sys time: 3018.96 seconds wall clock time: 54 minutes 52.19 seconds (3292.19 seconds total)