Starting phenix.real_space_refine on Sat Dec 9 10:26:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcw_36167/12_2023/8jcw_36167_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcw_36167/12_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_36167/12_2023/8jcw_36167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcw_36167/12_2023/8jcw_36167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcw_36167/12_2023/8jcw_36167_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcw_36167/12_2023/8jcw_36167_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-1.21rc1-5172/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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.18, per 1000 atoms: 0.57 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: 4.22 Conformation dependent library (CDL) restraints added in 2.3 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: 2.61 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: 3.15 Time building geometry restraints manager: 4.60 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 - 34.72: 6571 34.72 - 69.45: 99 69.45 - 104.17: 17 104.17 - 138.89: 2 138.89 - 173.61: 2 Dihedral angle restraints: 6691 sinusoidal: 2260 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 6688 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: 2.950 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: 10.400 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.410 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:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.160 ------------------------------------------------------------------------------- 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 : 13.684 173.613 3771 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 % Allowed : 0.00 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP 3 706 HIS 0.002 0.000 HIS 2 87 PHE 0.012 0.001 PHE 3 544 TYR 0.008 0.001 TYR 3 563 ARG 0.004 0.000 ARG 3 183 *********************** 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 : 1.215 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 136 average time/residue: 1.0311 time to fit residues: 154.0761 Evaluate side-chains 98 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6216 ------------------------------------------------------------------------------- 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: 0.7585 moved from start: 0.1173 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= 0.242 Angle : 0.552 11.516 15054 Z= 0.274 Chirality : 0.042 0.231 1754 Planarity : 0.004 0.057 1972 Dihedral : 4.309 50.608 1845 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.96 % Allowed : 10.01 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.22), residues: 1515 helix: 2.26 (0.20), residues: 680 sheet: -0.87 (0.44), residues: 139 loop : -1.67 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 3 706 HIS 0.002 0.001 HIS 2 87 PHE 0.013 0.001 PHE 3 195 TYR 0.012 0.001 TYR 3 171 ARG 0.008 0.001 ARG 3 253 *********************** 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 : 1.132 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 116 average time/residue: 0.9504 time to fit residues: 121.9142 Evaluate side-chains 99 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.5042 time to fit residues: 3.4587 ------------------------------------------------------------------------------- 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: 2.9990 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 0.0970 chunk 149 optimal weight: 0.0070 chunk 123 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN 2 439 ASN 3 94 HIS 3 251 ASN ** 3 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 470 ASN 3 472 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10992 Z= 0.353 Angle : 0.612 13.514 15054 Z= 0.306 Chirality : 0.044 0.196 1754 Planarity : 0.005 0.047 1972 Dihedral : 4.799 54.969 1845 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.72 % Allowed : 14.04 % Favored : 83.24 % 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: 0.00 (0.22), residues: 1515 helix: 1.90 (0.21), residues: 693 sheet: -0.83 (0.44), residues: 137 loop : -1.93 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 3 706 HIS 0.003 0.001 HIS 2 396 PHE 0.017 0.002 PHE 3 195 TYR 0.014 0.002 TYR 3 171 ARG 0.007 0.001 ARG 3 335 *********************** 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 125 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 1.142 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 117 average time/residue: 0.9382 time to fit residues: 121.6306 Evaluate side-chains 105 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.3493 time to fit residues: 3.2320 ------------------------------------------------------------------------------- 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: 0.8980 chunk 71 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 138 optimal weight: 0.4980 chunk 146 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN 2 259 GLN 3 232 GLN 3 251 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2143 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= 0.239 Angle : 0.541 10.426 15054 Z= 0.271 Chirality : 0.042 0.168 1754 Planarity : 0.004 0.050 1972 Dihedral : 4.672 53.961 1845 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.48 % Allowed : 14.69 % Favored : 81.83 % 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: 0.11 (0.22), residues: 1515 helix: 2.05 (0.21), residues: 683 sheet: -1.05 (0.43), residues: 148 loop : -1.84 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 3 706 HIS 0.001 0.001 HIS 3 94 PHE 0.012 0.001 PHE 3 195 TYR 0.011 0.001 TYR 3 171 ARG 0.012 0.000 ARG 2 229 *********************** 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 133 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 1.171 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 24 residues processed: 122 average time/residue: 0.8865 time to fit residues: 120.6791 Evaluate side-chains 117 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 7 average time/residue: 0.3015 time to fit residues: 4.3023 ------------------------------------------------------------------------------- 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: 1.9990 chunk 2 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 75 optimal weight: 30.0000 chunk 131 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 3 472 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.066 10992 Z= 0.589 Angle : 0.727 14.506 15054 Z= 0.363 Chirality : 0.049 0.232 1754 Planarity : 0.006 0.068 1972 Dihedral : 5.620 57.021 1845 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 5.01 % Allowed : 14.36 % Favored : 80.63 % 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: 1515 helix: 1.61 (0.21), residues: 689 sheet: -1.23 (0.41), residues: 141 loop : -2.08 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 3 303 HIS 0.003 0.001 HIS 2 87 PHE 0.017 0.003 PHE 3 195 TYR 0.019 0.002 TYR 3 171 ARG 0.013 0.001 ARG 2 229 *********************** 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 136 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 90 time to evaluate : 1.131 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 28 residues processed: 124 average time/residue: 0.9515 time to fit residues: 130.9898 Evaluate side-chains 115 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 87 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 23 residues processed: 6 average time/residue: 0.6340 time to fit residues: 6.0495 ------------------------------------------------------------------------------- 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: 9.9990 chunk 132 optimal weight: 0.0770 chunk 29 optimal weight: 0.0670 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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 3 232 GLN 3 251 ASN ** 3 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2585 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= 0.196 Angle : 0.546 13.035 15054 Z= 0.271 Chirality : 0.042 0.187 1754 Planarity : 0.004 0.060 1972 Dihedral : 5.039 58.455 1845 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.74 % Favored : 94.19 % Rotamer: Outliers : 4.46 % Allowed : 15.78 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1515 helix: 1.87 (0.21), residues: 691 sheet: -1.11 (0.42), residues: 148 loop : -1.96 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 3 706 HIS 0.002 0.001 HIS 3 485 PHE 0.011 0.001 PHE 2 67 TYR 0.008 0.001 TYR 3 171 ARG 0.014 0.001 ARG 2 229 *********************** 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 129 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 88 time to evaluate : 1.210 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 33 residues processed: 121 average time/residue: 0.8640 time to fit residues: 117.0140 Evaluate side-chains 117 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 84 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 29 residues processed: 4 average time/residue: 0.4600 time to fit residues: 3.7872 ------------------------------------------------------------------------------- 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: 3.9990 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 89 optimal weight: 0.0770 chunk 67 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 ** 3 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2662 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= 0.234 Angle : 0.556 13.383 15054 Z= 0.277 Chirality : 0.042 0.170 1754 Planarity : 0.005 0.071 1972 Dihedral : 5.009 59.819 1845 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.90 % Allowed : 16.32 % Favored : 78.78 % 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: -0.02 (0.22), residues: 1515 helix: 1.91 (0.21), residues: 691 sheet: -1.01 (0.43), residues: 148 loop : -1.94 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 3 706 HIS 0.001 0.001 HIS 3 485 PHE 0.013 0.001 PHE 3 195 TYR 0.011 0.001 TYR 3 171 ARG 0.017 0.000 ARG 2 229 *********************** 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 130 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 85 time to evaluate : 1.092 Fit side-chains outliers start: 45 outliers final: 32 residues processed: 121 average time/residue: 0.8046 time to fit residues: 109.5891 Evaluate side-chains 116 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 84 time to evaluate : 1.168 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 31 residues processed: 1 average time/residue: 0.1440 time to fit residues: 1.8324 ------------------------------------------------------------------------------- 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: 20.0000 chunk 87 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 133 optimal weight: 0.8980 chunk 140 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 3 232 GLN 3 251 ASN ** 3 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2669 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= 0.222 Angle : 0.555 12.821 15054 Z= 0.274 Chirality : 0.042 0.165 1754 Planarity : 0.004 0.073 1972 Dihedral : 4.969 58.808 1845 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.81 % Allowed : 17.19 % Favored : 79.00 % 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: 0.02 (0.22), residues: 1515 helix: 1.94 (0.21), residues: 691 sheet: -0.94 (0.43), residues: 148 loop : -1.93 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 3 706 HIS 0.002 0.000 HIS 3 485 PHE 0.012 0.001 PHE 3 195 TYR 0.010 0.001 TYR 3 171 ARG 0.018 0.000 ARG 2 229 *********************** 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 122 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 87 time to evaluate : 1.087 Fit side-chains outliers start: 35 outliers final: 32 residues processed: 118 average time/residue: 0.8204 time to fit residues: 109.0384 Evaluate side-chains 115 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 83 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 31 residues processed: 1 average time/residue: 0.0973 time to fit residues: 1.7334 ------------------------------------------------------------------------------- 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: 10.0000 chunk 136 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 chunk 107 optimal weight: 0.0470 chunk 41 optimal weight: 0.0040 chunk 123 optimal weight: 10.0000 chunk 129 optimal weight: 0.0050 chunk 89 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 overall best weight: 0.3704 ------------------------------------------------------------------------------- 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 ** 3 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10992 Z= 0.169 Angle : 0.530 11.188 15054 Z= 0.266 Chirality : 0.041 0.160 1754 Planarity : 0.004 0.075 1972 Dihedral : 4.721 59.903 1845 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.92 % Allowed : 17.63 % Favored : 78.45 % 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: 0.12 (0.22), residues: 1515 helix: 2.02 (0.21), residues: 691 sheet: -0.88 (0.43), residues: 148 loop : -1.87 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 3 706 HIS 0.002 0.000 HIS 3 485 PHE 0.011 0.001 PHE 2 67 TYR 0.007 0.001 TYR 3 563 ARG 0.019 0.000 ARG 2 229 *********************** 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 119 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 83 time to evaluate : 1.184 Fit side-chains outliers start: 36 outliers final: 31 residues processed: 115 average time/residue: 0.8593 time to fit residues: 111.5793 Evaluate side-chains 115 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 84 time to evaluate : 1.073 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 29 residues processed: 2 average time/residue: 0.2424 time to fit residues: 2.3301 ------------------------------------------------------------------------------- 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: 0.7980 chunk 68 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 95 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10992 Z= 0.327 Angle : 0.599 16.707 15054 Z= 0.296 Chirality : 0.043 0.185 1754 Planarity : 0.005 0.078 1972 Dihedral : 5.089 58.797 1845 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.60 % Favored : 93.33 % Rotamer: Outliers : 3.81 % Allowed : 17.85 % Favored : 78.35 % 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: 0.00 (0.22), residues: 1515 helix: 1.92 (0.21), residues: 691 sheet: -0.99 (0.43), residues: 148 loop : -1.91 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 3 706 HIS 0.002 0.001 HIS 2 87 PHE 0.017 0.002 PHE 3 195 TYR 0.025 0.002 TYR 3 318 ARG 0.018 0.001 ARG 2 229 ********************** 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 118 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 83 time to evaluate : 1.290 Fit side-chains outliers start: 35 outliers final: 29 residues processed: 115 average time/residue: 0.9199 time to fit residues: 118.2336 Evaluate side-chains 111 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 82 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 28 residues processed: 1 average time/residue: 0.2625 time to fit residues: 1.9276 ------------------------------------------------------------------------------- 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: 4.9990 chunk 111 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 15 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4400 r_free = 0.4400 target = 0.205756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.124859 restraints weight = 12661.582| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.88 r_work: 0.3152 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2837 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= 0.215 Angle : 0.562 15.478 15054 Z= 0.279 Chirality : 0.042 0.178 1754 Planarity : 0.005 0.076 1972 Dihedral : 4.949 58.064 1845 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.59 % Allowed : 18.39 % Favored : 78.02 % 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: 0.09 (0.22), residues: 1515 helix: 1.98 (0.21), residues: 690 sheet: -0.92 (0.43), residues: 148 loop : -1.87 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 3 706 HIS 0.002 0.000 HIS 3 485 PHE 0.011 0.001 PHE 3 195 TYR 0.010 0.001 TYR 3 171 ARG 0.018 0.000 ARG 2 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3205.06 seconds wall clock time: 57 minutes 53.92 seconds (3473.92 seconds total)