Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 23:06:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcw_36167/07_2023/8jcw_36167_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcw_36167/07_2023/8jcw_36167.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/8jcw_36167/07_2023/8jcw_36167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcw_36167/07_2023/8jcw_36167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcw_36167/07_2023/8jcw_36167_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcw_36167/07_2023/8jcw_36167_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= -0.001 sd= 0.070 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 64 5.16 5 C 6806 2.51 5 N 1869 2.21 5 O 2021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 481": "OD1" <-> "OD2" Residue "2 TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 221": "OD1" <-> "OD2" Residue "3 TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 478": "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: 10760 Number of models: 1 Model: "" Number of chains: 4 Chain: "2" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5266 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PTRANS': 37, 'TRANS': 724} Chain breaks: 2 Unresolved non-hydrogen bonds: 696 Unresolved non-hydrogen angles: 890 Unresolved non-hydrogen dihedrals: 580 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 14, 'GLU:plan': 13, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 397 Chain: "3" Number of atoms: 5358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 5358 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PTRANS': 30, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 732 Unresolved non-hydrogen angles: 936 Unresolved non-hydrogen dihedrals: 608 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 14, 'TYR:plan': 9, 'ASN:plan1': 12, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 12, 'GLU:plan': 12, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 385 Chain: "2" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {'CLR': 1, 'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {'CLR': 1, 'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.88, per 1000 atoms: 0.55 Number of scatterers: 10760 At special positions: 0 Unit cell: (88.893, 124.236, 184.212, 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 64 16.00 O 2021 8.00 N 1869 7.00 C 6806 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=2.04 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 21101 " - " ASN 2 203 " " NAG 31001 " - " ASN 3 209 " Time building additional restraints: 4.37 Conformation dependent library (CDL) restraints added in 1.8 seconds 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2866 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 9 sheets defined 42.4% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain '2' and resid 45 through 47 No H-bonds generated for 'chain '2' and resid 45 through 47' Processing helix chain '2' and resid 59 through 73 Processing helix chain '2' and resid 95 through 106 removed outlier: 3.697A pdb=" N ASP 2 104 " --> pdb=" O GLU 2 100 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE 2 105 " --> pdb=" O GLN 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 145 through 156 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 190 through 201 Processing helix chain '2' and resid 215 through 229 removed outlier: 6.384A pdb=" N GLY 2 220 " --> pdb=" O TYR 2 216 " (cutoff:3.500A) Processing helix chain '2' and resid 247 through 258 Processing helix chain '2' and resid 272 through 284 removed outlier: 3.684A pdb=" N GLU 2 277 " --> pdb=" O GLU 2 273 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU 2 278 " --> pdb=" O ASP 2 274 " (cutoff:3.500A) Processing helix chain '2' and resid 325 through 332 Processing helix chain '2' and resid 345 through 353 Processing helix chain '2' and resid 378 through 399 Processing helix chain '2' and resid 408 through 411 No H-bonds generated for 'chain '2' and resid 408 through 411' Processing helix chain '2' and resid 415 through 421 Processing helix chain '2' and resid 570 through 594 removed outlier: 4.051A pdb=" N ASN 2 593 " --> pdb=" O PHE 2 589 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA 2 594 " --> pdb=" O VAL 2 590 " (cutoff:3.500A) Processing helix chain '2' and resid 603 through 623 Processing helix chain '2' and resid 631 through 658 removed outlier: 4.389A pdb=" N LYS 2 653 " --> pdb=" O ALA 2 649 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR 2 654 " --> pdb=" O LEU 2 650 " (cutoff:3.500A) Processing helix chain '2' and resid 676 through 700 removed outlier: 3.620A pdb=" N VAL 2 680 " --> pdb=" O PRO 2 676 " (cutoff:3.500A) Processing helix chain '2' and resid 725 through 747 Processing helix chain '2' and resid 756 through 783 removed outlier: 4.871A pdb=" N PHE 2 761 " --> pdb=" O ASN 2 757 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR 2 767 " --> pdb=" O GLY 2 763 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR 2 768 " --> pdb=" O PHE 2 764 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU 2 777 " --> pdb=" O TRP 2 773 " (cutoff:3.500A) Proline residue: 2 778 - end of helix removed outlier: 3.757A pdb=" N TYR 2 781 " --> pdb=" O LEU 2 777 " (cutoff:3.500A) Processing helix chain '2' and resid 788 through 817 Proline residue: 2 812 - end of helix Processing helix chain '3' and resid 66 through 80 Processing helix chain '3' and resid 102 through 116 removed outlier: 3.710A pdb=" N LEU 3 110 " --> pdb=" O LEU 3 106 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU 3 111 " --> pdb=" O GLU 3 107 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE 3 112 " --> pdb=" O GLN 3 108 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA 3 115 " --> pdb=" O GLU 3 111 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER 3 116 " --> pdb=" O PHE 3 112 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 161 Processing helix chain '3' and resid 176 through 179 Processing helix chain '3' and resid 195 through 207 Processing helix chain '3' and resid 222 through 236 Processing helix chain '3' and resid 255 through 264 Processing helix chain '3' and resid 280 through 290 Processing helix chain '3' and resid 331 through 338 removed outlier: 3.557A 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 390 through 411 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 434 Processing helix chain '3' and resid 579 through 602 removed outlier: 3.594A pdb=" N ASN 3 602 " --> pdb=" O PHE 3 598 " (cutoff:3.500A) Processing helix chain '3' and resid 612 through 631 Processing helix chain '3' and resid 638 through 664 removed outlier: 3.747A pdb=" N LYS 3 662 " --> pdb=" O ALA 3 658 " (cutoff:3.500A) Processing helix chain '3' and resid 683 through 706 Processing helix chain '3' and resid 718 through 720 No H-bonds generated for 'chain '3' and resid 718 through 720' Processing helix chain '3' and resid 732 through 755 removed outlier: 4.047A pdb=" N SER 3 735 " --> pdb=" O VAL 3 732 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER 3 736 " --> pdb=" O LYS 3 733 " (cutoff:3.500A) Processing helix chain '3' and resid 765 through 791 Proline residue: 3 787 - end of helix removed outlier: 4.029A pdb=" N TYR 3 790 " --> pdb=" O LEU 3 786 " (cutoff:3.500A) Processing helix chain '3' and resid 797 through 825 removed outlier: 3.874A pdb=" N CYS 3 817 " --> pdb=" O VAL 3 813 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU 3 818 " --> pdb=" O VAL 3 814 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE 3 819 " --> pdb=" O LEU 3 815 " (cutoff:3.500A) removed outlier: 3.794A 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 84 through 90 removed outlier: 6.578A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY 2 35 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL 2 139 " --> pdb=" O GLY 2 35 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU 2 37 " --> pdb=" O VAL 2 139 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY 2 141 " --> pdb=" O LEU 2 37 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLY 2 141 " --> pdb=" O PRO 2 161 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE 2 163 " --> pdb=" O GLY 2 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 238 through 240 removed outlier: 7.308A pdb=" N THR 2 209 " --> pdb=" O GLU 2 239 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N THR 2 290 " --> pdb=" O ALA 2 266 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU 2 268 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL 2 292 " --> pdb=" O LEU 2 268 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 315 through 319 removed outlier: 3.768A pdb=" N GLY 2 472 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR 2 457 " --> pdb=" O LYS 2 470 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS 2 470 " --> pdb=" O THR 2 457 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU 2 459 " --> pdb=" O TYR 2 468 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N TYR 2 468 " --> pdb=" O LEU 2 459 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR 2 473 " --> pdb=" O THR 2 479 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 508 through 511 Processing sheet with id= E, first strand: chain '2' and resid 529 through 531 Processing sheet with id= F, first strand: chain '3' and resid 91 through 97 removed outlier: 6.394A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY 3 42 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL 3 145 " --> pdb=" O GLY 3 42 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU 3 44 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 244 through 246 removed outlier: 6.702A pdb=" N THR 3 215 " --> pdb=" O GLU 3 245 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR 3 296 " --> pdb=" O VAL 3 272 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU 3 274 " --> pdb=" O THR 3 296 " (cutoff:3.500A) removed outlier: 5.976A 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: 6.291A pdb=" N ASN 3 470 " --> pdb=" O LYS 3 482 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LYS 3 482 " --> pdb=" O ASN 3 470 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN 3 472 " --> pdb=" O TYR 3 480 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N TYR 3 480 " --> pdb=" O GLN 3 472 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 518 through 521 483 hydrogen bonds defined for protein. 1371 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 4.75 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: 3473 1.34 - 1.46: 1630 1.46 - 1.58: 5806 1.58 - 1.70: 1 1.70 - 1.82: 82 Bond restraints: 10992 Sorted by residual: bond pdb=" CAT Z99 31002 " pdb=" OAP Z99 31002 " ideal model delta sigma weight residual 1.364 1.461 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" CAT Z99 21102 " pdb=" OAP Z99 21102 " ideal model delta sigma weight residual 1.364 1.457 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" CAS Z99 31002 " pdb=" OAP Z99 31002 " ideal model delta sigma weight residual 1.369 1.451 -0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" CAS Z99 21102 " pdb=" OAP Z99 21102 " ideal model delta sigma weight residual 1.369 1.449 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C ASN 3 445 " pdb=" N PRO 3 446 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.77e+00 ... (remaining 10987 not shown) Histogram of bond angle deviations from ideal: 59.77 - 74.61: 6 74.61 - 89.46: 0 89.46 - 104.30: 176 104.30 - 119.14: 8791 119.14 - 133.98: 6081 Bond angle restraints: 15054 Sorted by residual: angle pdb=" CA PRO 2 524 " pdb=" N PRO 2 524 " pdb=" CD PRO 2 524 " ideal model delta sigma weight residual 112.00 104.92 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" CB ARG 3 183 " pdb=" CG ARG 3 183 " pdb=" CD ARG 3 183 " ideal model delta sigma weight residual 111.30 100.30 11.00 2.30e+00 1.89e-01 2.29e+01 angle pdb=" N GLU 2 225 " pdb=" CA GLU 2 225 " pdb=" CB GLU 2 225 " ideal model delta sigma weight residual 110.12 116.36 -6.24 1.47e+00 4.63e-01 1.80e+01 angle pdb=" C ARG 3 183 " pdb=" CA ARG 3 183 " pdb=" CB ARG 3 183 " ideal model delta sigma weight residual 109.15 116.45 -7.30 1.78e+00 3.16e-01 1.68e+01 angle pdb=" CAX Z99 21102 " pdb=" CAZ Z99 21102 " pdb=" CAY Z99 21102 " ideal model delta sigma weight residual 120.67 109.36 11.31 3.00e+00 1.11e-01 1.42e+01 ... (remaining 15049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 6043 17.57 - 35.14: 363 35.14 - 52.71: 65 52.71 - 70.28: 15 70.28 - 87.84: 9 Dihedral angle restraints: 6495 sinusoidal: 2064 harmonic: 4431 Sorted by residual: dihedral pdb=" CB CYS 2 632 " pdb=" SG CYS 2 632 " pdb=" SG CYS 2 721 " pdb=" CB CYS 2 721 " ideal model delta sinusoidal sigma weight residual -86.00 1.84 -87.84 1 1.00e+01 1.00e-02 9.24e+01 dihedral pdb=" CB CYS 3 412 " pdb=" SG CYS 3 412 " pdb=" SG CYS 3 419 " pdb=" CB CYS 3 419 " ideal model delta sinusoidal sigma weight residual 93.00 170.52 -77.52 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS 2 50 " pdb=" SG CYS 2 50 " pdb=" SG CYS 2 92 " pdb=" CB CYS 2 92 " ideal model delta sinusoidal sigma weight residual 93.00 29.36 63.64 1 1.00e+01 1.00e-02 5.34e+01 ... (remaining 6492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.973: 1752 0.973 - 1.947: 0 1.947 - 2.920: 0 2.920 - 3.893: 0 3.893 - 4.866: 2 Chirality restraints: 1754 Sorted by residual: chirality pdb=" CAW Z99 21102 " pdb=" CAN Z99 21102 " pdb=" CAU Z99 21102 " pdb=" CAV Z99 21102 " both_signs ideal model delta sigma weight residual False 2.61 -2.26 4.87 2.00e-01 2.50e+01 5.92e+02 chirality pdb=" CAW Z99 31002 " pdb=" CAN Z99 31002 " pdb=" CAU Z99 31002 " pdb=" CAV Z99 31002 " both_signs ideal model delta sigma weight residual False 2.61 -2.15 4.76 2.00e-01 2.50e+01 5.67e+02 chirality pdb=" CAY Z99 31002 " pdb=" CAN Z99 31002 " pdb=" CAR Z99 31002 " pdb=" CAZ Z99 31002 " both_signs ideal model delta sigma weight residual False -2.97 -2.58 -0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 1751 not shown) Planarity restraints: 1974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 2 523 " -0.079 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO 2 524 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO 2 524 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO 2 524 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP 3 706 " 0.014 2.00e-02 2.50e+03 1.14e-02 3.27e+00 pdb=" CG TRP 3 706 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP 3 706 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP 3 706 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP 3 706 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP 3 706 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP 3 706 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP 3 706 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP 3 706 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP 3 706 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR 3 431 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C TYR 3 431 " -0.030 2.00e-02 2.50e+03 pdb=" O TYR 3 431 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS 3 432 " 0.010 2.00e-02 2.50e+03 ... (remaining 1971 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1409 2.75 - 3.29: 10514 3.29 - 3.83: 18139 3.83 - 4.36: 19823 4.36 - 4.90: 34820 Nonbonded interactions: 84705 Sorted by model distance: nonbonded pdb=" OG SER 2 262 " pdb=" O SER 2 498 " model vdw 2.218 2.440 nonbonded pdb=" OE1 GLN 3 232 " pdb=" NH2 ARG 3 235 " model vdw 2.243 2.520 nonbonded pdb=" O TYR 3 212 " pdb=" OG SER 3 507 " model vdw 2.244 2.440 nonbonded pdb=" OE2 GLU 3 224 " pdb=" NZ LYS 3 246 " model vdw 2.295 2.520 nonbonded pdb=" O SER 2 169 " pdb=" NH1 ARG 2 183 " model vdw 2.312 2.520 ... (remaining 84700 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=0.50 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: 2.340 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: 10.940 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 29.940 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:11.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 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 0.109 10992 Z= 0.223 Angle : 0.610 11.306 15054 Z= 0.295 Chirality : 0.168 4.866 1754 Planarity : 0.004 0.116 1972 Dihedral : 11.924 81.906 3575 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % 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: 0.47 (0.22), residues: 1515 helix: 2.39 (0.20), residues: 681 sheet: -0.86 (0.44), residues: 149 loop : -1.68 (0.22), residues: 685 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 1.138 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 136 average time/residue: 1.0087 time to fit residues: 150.1786 Evaluate side-chains 98 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4566 ------------------------------------------------------------------------------- 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: 0.6980 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 88 optimal weight: 0.3980 chunk 138 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 232 GLN 3 251 ASN 3 341 ASN 3 470 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 10992 Z= 0.237 Angle : 0.564 11.549 15054 Z= 0.278 Chirality : 0.042 0.197 1754 Planarity : 0.004 0.058 1972 Dihedral : 4.358 55.265 1649 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % 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: 0.35 (0.22), residues: 1515 helix: 2.25 (0.20), residues: 682 sheet: -0.89 (0.44), residues: 139 loop : -1.70 (0.22), residues: 694 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.185 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 116 average time/residue: 0.9953 time to fit residues: 127.7377 Evaluate side-chains 101 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 1.212 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.4791 time to fit residues: 3.2704 ------------------------------------------------------------------------------- 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: 3.9990 chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 0.0570 chunk 149 optimal weight: 0.3980 chunk 123 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN 3 94 HIS ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 251 ASN 3 470 ASN 3 472 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 10992 Z= 0.377 Angle : 0.635 14.060 15054 Z= 0.316 Chirality : 0.045 0.186 1754 Planarity : 0.005 0.050 1972 Dihedral : 4.863 58.515 1649 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 3.16 % 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: -0.03 (0.22), residues: 1515 helix: 1.88 (0.21), residues: 691 sheet: -0.76 (0.44), residues: 131 loop : -1.95 (0.21), residues: 693 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 1.212 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 120 average time/residue: 1.0165 time to fit residues: 134.2631 Evaluate side-chains 108 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.3821 time to fit residues: 3.4693 ------------------------------------------------------------------------------- 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: 20.0000 chunk 103 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 0.0030 chunk 146 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN 2 259 GLN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN 3 251 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 10992 Z= 0.364 Angle : 0.604 13.671 15054 Z= 0.302 Chirality : 0.044 0.180 1754 Planarity : 0.005 0.056 1972 Dihedral : 4.737 55.016 1649 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 4.57 % 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: -0.16 (0.22), residues: 1515 helix: 1.80 (0.21), residues: 691 sheet: -1.19 (0.42), residues: 147 loop : -1.98 (0.22), residues: 677 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 94 time to evaluate : 1.193 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 28 residues processed: 125 average time/residue: 0.9512 time to fit residues: 131.8797 Evaluate side-chains 117 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 22 residues processed: 7 average time/residue: 0.6473 time to fit residues: 7.0121 ------------------------------------------------------------------------------- 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: 7.9990 chunk 83 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 109 optimal weight: 0.2980 chunk 60 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN ** 2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN 3 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 10992 Z= 0.374 Angle : 0.612 13.852 15054 Z= 0.308 Chirality : 0.044 0.187 1754 Planarity : 0.005 0.065 1972 Dihedral : 4.750 55.202 1649 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.80 % Favored : 93.14 % Rotamer Outliers : 4.90 % 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: -0.21 (0.22), residues: 1515 helix: 1.77 (0.21), residues: 688 sheet: -1.29 (0.41), residues: 148 loop : -1.99 (0.22), residues: 679 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 90 time to evaluate : 1.211 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 30 residues processed: 124 average time/residue: 0.9658 time to fit residues: 133.1206 Evaluate side-chains 114 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 84 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 25 residues processed: 5 average time/residue: 0.5619 time to fit residues: 4.8846 ------------------------------------------------------------------------------- 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: 2.9990 chunk 132 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 147 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 259 GLN 2 414 ASN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN 3 251 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 10992 Z= 0.232 Angle : 0.536 11.232 15054 Z= 0.271 Chirality : 0.042 0.158 1754 Planarity : 0.004 0.059 1972 Dihedral : 4.571 53.704 1649 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer Outliers : 4.90 % 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: -0.06 (0.22), residues: 1515 helix: 1.87 (0.21), residues: 691 sheet: -1.12 (0.42), residues: 148 loop : -1.92 (0.22), residues: 676 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 88 time to evaluate : 1.140 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 32 residues processed: 125 average time/residue: 0.8910 time to fit residues: 124.2804 Evaluate side-chains 113 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 81 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 31 residues processed: 1 average time/residue: 0.1471 time to fit residues: 1.7908 ------------------------------------------------------------------------------- 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: 20.0000 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN 3 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 10992 Z= 0.241 Angle : 0.551 14.500 15054 Z= 0.276 Chirality : 0.042 0.163 1754 Planarity : 0.005 0.072 1972 Dihedral : 4.574 53.786 1649 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.34 % Favored : 93.60 % Rotamer Outliers : 4.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1515 helix: 1.91 (0.21), residues: 691 sheet: -1.05 (0.42), residues: 148 loop : -1.93 (0.22), residues: 676 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 83 time to evaluate : 1.089 Fit side-chains outliers start: 40 outliers final: 33 residues processed: 117 average time/residue: 0.9086 time to fit residues: 118.5493 Evaluate side-chains 114 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 81 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 32 residues processed: 1 average time/residue: 0.1554 time to fit residues: 1.9191 ------------------------------------------------------------------------------- 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: 7.9990 chunk 87 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 72 optimal weight: 0.0060 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN 2 259 GLN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN 3 251 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 10992 Z= 0.198 Angle : 0.535 13.749 15054 Z= 0.267 Chirality : 0.041 0.178 1754 Planarity : 0.004 0.072 1972 Dihedral : 4.500 53.237 1649 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer Outliers : 4.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.22), residues: 1515 helix: 1.95 (0.21), residues: 691 sheet: -0.92 (0.43), residues: 148 loop : -1.89 (0.22), residues: 676 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 87 time to evaluate : 1.222 Fit side-chains outliers start: 38 outliers final: 33 residues processed: 121 average time/residue: 0.9199 time to fit residues: 123.9546 Evaluate side-chains 118 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 85 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 32 residues processed: 1 average time/residue: 0.2596 time to fit residues: 2.0053 ------------------------------------------------------------------------------- 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: 8.9990 chunk 136 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 41 optimal weight: 0.0020 chunk 123 optimal weight: 9.9990 chunk 129 optimal weight: 0.3980 chunk 89 optimal weight: 0.0170 chunk 144 optimal weight: 0.8980 overall best weight: 0.4426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN ** 2 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN 3 251 ASN 3 341 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 10992 Z= 0.181 Angle : 0.537 12.740 15054 Z= 0.269 Chirality : 0.041 0.163 1754 Planarity : 0.005 0.074 1972 Dihedral : 4.411 52.815 1649 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 4.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1515 helix: 2.01 (0.21), residues: 692 sheet: -0.83 (0.43), residues: 148 loop : -1.86 (0.22), residues: 675 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 85 time to evaluate : 1.177 Fit side-chains outliers start: 37 outliers final: 30 residues processed: 118 average time/residue: 0.8883 time to fit residues: 117.2940 Evaluate side-chains 115 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 29 residues processed: 1 average time/residue: 0.2650 time to fit residues: 1.9441 ------------------------------------------------------------------------------- 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: 0.9980 chunk 68 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN 2 259 GLN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN 3 251 ASN ** 3 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 10992 Z= 0.383 Angle : 0.605 15.228 15054 Z= 0.304 Chirality : 0.044 0.151 1754 Planarity : 0.005 0.079 1972 Dihedral : 4.714 54.069 1649 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.73 % Favored : 93.20 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1515 helix: 1.87 (0.21), residues: 691 sheet: -1.03 (0.43), residues: 148 loop : -1.91 (0.22), residues: 676 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 86 time to evaluate : 1.109 Fit side-chains outliers start: 33 outliers final: 29 residues processed: 115 average time/residue: 1.0183 time to fit residues: 129.5888 Evaluate side-chains 113 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 84 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 2 average time/residue: 0.1775 time to fit residues: 2.1632 ------------------------------------------------------------------------------- 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: 2.9990 chunk 111 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 120 optimal weight: 0.6980 chunk 50 optimal weight: 0.0020 chunk 124 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN 3 251 ASN ** 3 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.205602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.125090 restraints weight = 12658.919| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.82 r_work: 0.3136 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 10992 Z= 0.202 Angle : 0.549 13.073 15054 Z= 0.277 Chirality : 0.041 0.163 1754 Planarity : 0.005 0.081 1972 Dihedral : 4.561 53.143 1649 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.07 % Favored : 93.86 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1515 helix: 1.98 (0.21), residues: 688 sheet: -0.95 (0.43), residues: 148 loop : -1.85 (0.22), residues: 679 =============================================================================== Job complete usr+sys time: 3205.81 seconds wall clock time: 57 minutes 59.78 seconds (3479.78 seconds total)