Starting phenix.real_space_refine on Wed Feb 14 04:50:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv2_30210/02_2024/7bv2_30210_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv2_30210/02_2024/7bv2_30210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv2_30210/02_2024/7bv2_30210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv2_30210/02_2024/7bv2_30210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv2_30210/02_2024/7bv2_30210_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv2_30210/02_2024/7bv2_30210_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 28 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5407 2.51 5 N 1437 2.21 5 O 1696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 84": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 729": "OE1" <-> "OE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8630 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6712 Classifications: {'peptide': 834} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 805} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 871 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 481 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 234 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "T" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 9} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 13 Unusual residues: {' MG': 2, ' ZN': 2, 'POP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'F86': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1816 SG CYS A 301 49.560 64.092 38.924 1.00 12.33 S ATOM 1857 SG CYS A 306 49.369 63.471 35.242 1.00 10.05 S ATOM 1889 SG CYS A 310 52.744 63.249 37.074 1.00 9.56 S ATOM 3297 SG CYS A 487 31.730 59.229 47.521 1.00 11.38 S ATOM 4550 SG CYS A 645 30.654 59.341 44.075 1.00 12.29 S ATOM 4556 SG CYS A 646 33.652 60.861 45.159 1.00 10.15 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" O POP A1003 " occ=0.50 ... (7 atoms not shown) pdb=" P2 POP A1003 " occ=0.50 residue: pdb="MG MG A1004 " occ=0.50 residue: pdb="MG MG A1005 " occ=0.50 residue: pdb=" C1 F86 P 101 " occ=0.50 ... (22 atoms not shown) pdb=" P1 F86 P 101 " occ=0.50 Time building chain proxies: 5.70, per 1000 atoms: 0.66 Number of scatterers: 8630 At special positions: 0 Unit cell: (95.316, 93.288, 106.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 58 16.00 P 28 15.00 Mg 2 11.99 O 1696 8.00 N 1437 7.00 C 5407 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 6 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 7 sheets defined 48.6% alpha, 10.3% beta 9 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.682A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 199 removed outlier: 4.434A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 4.045A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.327A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.522A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 448 through 458 removed outlier: 4.012A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.853A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.526A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 581 removed outlier: 3.710A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 641 removed outlier: 5.022A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 687 through 708 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 779 through 789 Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 852 through 871 removed outlier: 3.958A pdb=" N GLU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Proline residue: A 868 - end of helix removed outlier: 4.760A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 894 removed outlier: 4.207A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 925 removed outlier: 4.018A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 96 removed outlier: 3.998A pdb=" N LEU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 removed outlier: 4.036A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.560A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 41 removed outlier: 4.043A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 removed outlier: 3.827A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 32 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.546A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.653A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.398A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= F, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.688A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 127 through 132 removed outlier: 3.521A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 855 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1344 1.29 - 1.43: 2552 1.43 - 1.56: 4834 1.56 - 1.70: 49 1.70 - 1.83: 88 Bond restraints: 8867 Sorted by residual: bond pdb=" O4 F86 P 101 " pdb=" P1 F86 P 101 " ideal model delta sigma weight residual 1.601 1.704 -0.103 1.00e-02 1.00e+04 1.06e+02 bond pdb=" C12 F86 P 101 " pdb=" N2 F86 P 101 " ideal model delta sigma weight residual 1.293 1.359 -0.066 1.00e-02 1.00e+04 4.38e+01 bond pdb=" P U P 20 " pdb=" O5' U P 20 " ideal model delta sigma weight residual 1.593 1.676 -0.083 1.50e-02 4.44e+03 3.08e+01 bond pdb=" C11 F86 P 101 " pdb=" N5 F86 P 101 " ideal model delta sigma weight residual 1.337 1.392 -0.055 1.00e-02 1.00e+04 3.07e+01 bond pdb=" O5 F86 P 101 " pdb=" P1 F86 P 101 " ideal model delta sigma weight residual 1.533 1.483 0.050 1.50e-02 4.44e+03 1.11e+01 ... (remaining 8862 not shown) Histogram of bond angle deviations from ideal: 98.53 - 114.78: 5548 114.78 - 131.04: 6564 131.04 - 147.29: 42 147.29 - 163.54: 0 163.54 - 179.79: 1 Bond angle restraints: 12155 Sorted by residual: angle pdb=" C10 F86 P 101 " pdb=" C9 F86 P 101 " pdb=" C11 F86 P 101 " ideal model delta sigma weight residual 136.68 128.29 8.39 1.00e+00 1.00e+00 7.04e+01 angle pdb=" C10 F86 P 101 " pdb=" C9 F86 P 101 " pdb=" N1 F86 P 101 " ideal model delta sigma weight residual 107.41 115.10 -7.69 1.00e+00 1.00e+00 5.91e+01 angle pdb=" C7 F86 P 101 " pdb=" C10 F86 P 101 " pdb=" C9 F86 P 101 " ideal model delta sigma weight residual 107.84 100.22 7.62 1.00e+00 1.00e+00 5.81e+01 angle pdb=" C5 F86 P 101 " pdb=" N1 F86 P 101 " pdb=" C9 F86 P 101 " ideal model delta sigma weight residual 109.66 105.27 4.39 1.00e+00 1.00e+00 1.93e+01 angle pdb=" C3' A P 19 " pdb=" O3' A P 19 " pdb=" P U P 20 " ideal model delta sigma weight residual 120.20 125.93 -5.73 1.50e+00 4.44e-01 1.46e+01 ... (remaining 12150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.93: 4830 21.93 - 43.86: 369 43.86 - 65.79: 47 65.79 - 87.71: 12 87.71 - 109.64: 2 Dihedral angle restraints: 5260 sinusoidal: 2261 harmonic: 2999 Sorted by residual: dihedral pdb=" CA TYR A 606 " pdb=" C TYR A 606 " pdb=" N SER A 607 " pdb=" CA SER A 607 " ideal model delta harmonic sigma weight residual -180.00 -148.17 -31.83 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" O4 POP A1003 " pdb=" O POP A1003 " pdb=" P2 POP A1003 " pdb=" P1 POP A1003 " ideal model delta sinusoidal sigma weight residual -57.41 -167.06 109.64 1 2.00e+01 2.50e-03 3.21e+01 dihedral pdb=" CA PRO A 612 " pdb=" C PRO A 612 " pdb=" N HIS A 613 " pdb=" CA HIS A 613 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 5257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1063 0.052 - 0.103: 258 0.103 - 0.155: 52 0.155 - 0.207: 8 0.207 - 0.258: 6 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA ARG B 111 " pdb=" N ARG B 111 " pdb=" C ARG B 111 " pdb=" CB ARG B 111 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ASP A 258 " pdb=" N ASP A 258 " pdb=" C ASP A 258 " pdb=" CB ASP A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA LYS A 676 " pdb=" N LYS A 676 " pdb=" C LYS A 676 " pdb=" CB LYS A 676 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1384 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U P 20 " 0.066 2.00e-02 2.50e+03 3.19e-02 2.29e+01 pdb=" N1 U P 20 " -0.052 2.00e-02 2.50e+03 pdb=" C2 U P 20 " -0.025 2.00e-02 2.50e+03 pdb=" O2 U P 20 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U P 20 " -0.006 2.00e-02 2.50e+03 pdb=" C4 U P 20 " 0.009 2.00e-02 2.50e+03 pdb=" O4 U P 20 " 0.030 2.00e-02 2.50e+03 pdb=" C5 U P 20 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U P 20 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 36 " 0.017 2.00e-02 2.50e+03 1.80e-02 4.84e+00 pdb=" CG HIS C 36 " -0.039 2.00e-02 2.50e+03 pdb=" ND1 HIS C 36 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS C 36 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS C 36 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS C 36 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 532 " 0.011 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C LYS A 532 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS A 532 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 533 " 0.012 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 31 2.53 - 3.12: 6461 3.12 - 3.72: 13454 3.72 - 4.31: 20316 4.31 - 4.90: 32251 Nonbonded interactions: 72513 Sorted by model distance: nonbonded pdb=" O4 U P 12 " pdb=" N1 A T 19 " model vdw 1.942 2.496 nonbonded pdb=" O ASN A 790 " pdb=" OD1 ASN A 790 " model vdw 2.135 3.040 nonbonded pdb=" O GLU A 144 " pdb=" OG1 THR A 148 " model vdw 2.248 2.440 nonbonded pdb=" O ILE A 494 " pdb=" NE2 GLN A 573 " model vdw 2.281 2.520 nonbonded pdb=" OG SER A 239 " pdb=" OD1 ASP A 465 " model vdw 2.284 2.440 ... (remaining 72508 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: 0.400 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: 2.020 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 30.330 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 0.005 0.103 8867 Z= 0.305 Angle : 0.738 10.282 12155 Z= 0.449 Chirality : 0.050 0.258 1387 Planarity : 0.004 0.044 1452 Dihedral : 15.439 109.643 3324 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.26), residues: 999 helix: -0.10 (0.23), residues: 472 sheet: -0.43 (0.47), residues: 97 loop : 0.56 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 916 HIS 0.019 0.002 HIS C 36 PHE 0.027 0.002 PHE A 652 TYR 0.024 0.002 TYR A 289 ARG 0.009 0.001 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.010 Fit side-chains REVERT: A 160 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7251 (ttpt) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 1.1184 time to fit residues: 181.8432 Evaluate side-chains 130 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.0020 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8867 Z= 0.131 Angle : 0.490 7.945 12155 Z= 0.264 Chirality : 0.039 0.192 1387 Planarity : 0.004 0.042 1452 Dihedral : 10.767 101.622 1470 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.13 % Allowed : 9.72 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.59 (0.26), residues: 999 helix: 0.50 (0.23), residues: 468 sheet: 0.31 (0.53), residues: 86 loop : 0.52 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.013 0.001 HIS C 36 PHE 0.018 0.001 PHE A 652 TYR 0.014 0.001 TYR A 289 ARG 0.005 0.000 ARG A 750 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 0.988 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 143 average time/residue: 1.2081 time to fit residues: 184.8897 Evaluate side-chains 129 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 169 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 77 optimal weight: 0.0370 chunk 63 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 74 optimal weight: 0.3980 chunk 91 optimal weight: 0.7980 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN C 34 GLN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8867 Z= 0.145 Angle : 0.464 6.795 12155 Z= 0.251 Chirality : 0.039 0.178 1387 Planarity : 0.004 0.039 1452 Dihedral : 10.638 90.310 1470 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.92 % Allowed : 10.73 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.61 (0.26), residues: 999 helix: 0.60 (0.24), residues: 477 sheet: 0.26 (0.52), residues: 87 loop : 0.44 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.011 0.001 HIS C 36 PHE 0.018 0.001 PHE A 652 TYR 0.014 0.001 TYR A 788 ARG 0.004 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 0.915 Fit side-chains REVERT: A 796 GLU cc_start: 0.6363 (mm-30) cc_final: 0.6100 (mt-10) REVERT: A 885 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7346 (mp) outliers start: 17 outliers final: 4 residues processed: 136 average time/residue: 1.2026 time to fit residues: 174.7534 Evaluate side-chains 131 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 169 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 4.9990 chunk 48 optimal weight: 0.0010 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 191 GLN A 468 GLN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN C 18 GLN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8867 Z= 0.291 Angle : 0.542 6.895 12155 Z= 0.292 Chirality : 0.043 0.151 1387 Planarity : 0.004 0.040 1452 Dihedral : 10.879 86.100 1470 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.26 % Allowed : 12.66 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.26), residues: 999 helix: 0.50 (0.24), residues: 469 sheet: 0.17 (0.52), residues: 87 loop : 0.27 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 290 HIS 0.010 0.001 HIS C 36 PHE 0.023 0.002 PHE A 652 TYR 0.019 0.002 TYR A 788 ARG 0.004 0.001 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 0.923 Fit side-chains REVERT: A 136 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6490 (pp20) REVERT: A 796 GLU cc_start: 0.6470 (mm-30) cc_final: 0.6193 (mt-10) REVERT: A 885 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7551 (mp) outliers start: 20 outliers final: 7 residues processed: 131 average time/residue: 1.2997 time to fit residues: 181.5197 Evaluate side-chains 126 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 24 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8867 Z= 0.257 Angle : 0.516 6.866 12155 Z= 0.279 Chirality : 0.042 0.160 1387 Planarity : 0.004 0.041 1452 Dihedral : 10.876 77.230 1470 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.94 % Allowed : 13.79 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 999 helix: 0.40 (0.23), residues: 476 sheet: -0.07 (0.54), residues: 77 loop : 0.20 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.009 0.001 HIS C 36 PHE 0.021 0.002 PHE A 652 TYR 0.017 0.002 TYR A 788 ARG 0.004 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 0.954 Fit side-chains REVERT: A 136 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6539 (pp20) REVERT: A 885 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7603 (mp) outliers start: 26 outliers final: 12 residues processed: 129 average time/residue: 1.3101 time to fit residues: 179.4433 Evaluate side-chains 127 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 24 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8867 Z= 0.173 Angle : 0.475 7.176 12155 Z= 0.254 Chirality : 0.039 0.161 1387 Planarity : 0.004 0.039 1452 Dihedral : 10.738 73.353 1470 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.60 % Allowed : 14.24 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.40 (0.26), residues: 999 helix: 0.52 (0.24), residues: 477 sheet: 0.02 (0.55), residues: 77 loop : 0.23 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.009 0.001 HIS C 36 PHE 0.018 0.001 PHE A 652 TYR 0.014 0.001 TYR A 788 ARG 0.005 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.020 Fit side-chains REVERT: A 167 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.5981 (mm-30) REVERT: A 610 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6474 (mt-10) REVERT: A 885 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7578 (mp) outliers start: 23 outliers final: 10 residues processed: 133 average time/residue: 1.2762 time to fit residues: 180.4999 Evaluate side-chains 129 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 24 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8867 Z= 0.215 Angle : 0.492 6.519 12155 Z= 0.265 Chirality : 0.040 0.143 1387 Planarity : 0.004 0.039 1452 Dihedral : 10.768 73.364 1470 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.15 % Allowed : 14.92 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 999 helix: 0.50 (0.23), residues: 475 sheet: 0.02 (0.55), residues: 77 loop : 0.18 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 PHE 0.019 0.001 PHE A 652 TYR 0.016 0.001 TYR A 788 ARG 0.005 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 0.868 Fit side-chains REVERT: A 885 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7579 (mp) outliers start: 19 outliers final: 13 residues processed: 123 average time/residue: 1.4823 time to fit residues: 193.4272 Evaluate side-chains 127 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 24 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8867 Z= 0.210 Angle : 0.495 8.219 12155 Z= 0.264 Chirality : 0.040 0.144 1387 Planarity : 0.004 0.039 1452 Dihedral : 10.734 73.397 1470 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.49 % Allowed : 14.69 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.38 (0.26), residues: 999 helix: 0.52 (0.24), residues: 475 sheet: 0.05 (0.56), residues: 77 loop : 0.18 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.019 0.001 PHE A 652 TYR 0.016 0.001 TYR A 788 ARG 0.005 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 0.925 Fit side-chains REVERT: A 494 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8386 (mm) REVERT: A 885 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7600 (mp) outliers start: 22 outliers final: 14 residues processed: 125 average time/residue: 1.3133 time to fit residues: 174.8147 Evaluate side-chains 129 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 24 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8867 Z= 0.270 Angle : 0.527 6.843 12155 Z= 0.283 Chirality : 0.042 0.140 1387 Planarity : 0.004 0.040 1452 Dihedral : 10.837 74.018 1470 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.15 % Allowed : 15.14 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.30 (0.26), residues: 999 helix: 0.47 (0.24), residues: 467 sheet: 0.02 (0.56), residues: 73 loop : 0.12 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.020 0.002 PHE A 741 TYR 0.018 0.002 TYR A 788 ARG 0.005 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.902 Fit side-chains REVERT: A 494 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8362 (mm) REVERT: A 885 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7623 (mp) REVERT: C 62 MET cc_start: 0.6058 (ptp) cc_final: 0.5853 (ptp) outliers start: 19 outliers final: 13 residues processed: 128 average time/residue: 1.2385 time to fit residues: 168.9032 Evaluate side-chains 131 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 24 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8867 Z= 0.203 Angle : 0.496 9.183 12155 Z= 0.264 Chirality : 0.040 0.144 1387 Planarity : 0.004 0.039 1452 Dihedral : 10.718 73.458 1470 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.15 % Allowed : 15.71 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 999 helix: 0.51 (0.24), residues: 476 sheet: 0.11 (0.57), residues: 73 loop : 0.16 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 PHE 0.018 0.001 PHE A 652 TYR 0.016 0.001 TYR A 788 ARG 0.006 0.000 ARG A 555 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.907 Fit side-chains REVERT: A 136 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6527 (pp20) REVERT: A 542 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7380 (mmm) REVERT: A 885 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7605 (mp) outliers start: 19 outliers final: 12 residues processed: 124 average time/residue: 1.2275 time to fit residues: 162.1347 Evaluate side-chains 131 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 24 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 54 optimal weight: 0.0970 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.161124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114350 restraints weight = 8514.191| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.94 r_work: 0.3205 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8867 Z= 0.219 Angle : 0.511 9.737 12155 Z= 0.271 Chirality : 0.040 0.139 1387 Planarity : 0.004 0.039 1452 Dihedral : 10.719 73.413 1470 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.03 % Allowed : 15.93 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.32 (0.26), residues: 999 helix: 0.46 (0.24), residues: 475 sheet: 0.10 (0.57), residues: 73 loop : 0.14 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.019 0.002 PHE A 652 TYR 0.016 0.001 TYR A 788 ARG 0.006 0.000 ARG A 555 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3503.71 seconds wall clock time: 62 minutes 59.57 seconds (3779.57 seconds total)