Starting phenix.real_space_refine on Thu Mar 14 22:15:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzf_30252/03_2024/7bzf_30252.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzf_30252/03_2024/7bzf_30252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzf_30252/03_2024/7bzf_30252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzf_30252/03_2024/7bzf_30252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzf_30252/03_2024/7bzf_30252.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzf_30252/03_2024/7bzf_30252.pdb" } resolution = 3.26 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= 0.059 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 19 5.49 5 S 70 5.16 5 C 6245 2.51 5 N 1669 2.21 5 O 1927 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A ASP 258": "OD1" <-> "OD2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A ASP 304": "OD1" <-> "OD2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A ASP 523": "OD1" <-> "OD2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A ASP 711": "OD1" <-> "OD2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 802": "OE1" <-> "OE2" Residue "A ASP 824": "OD1" <-> "OD2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ASP 851": "OD1" <-> "OD2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A ARG 914": "NH1" <-> "NH2" Residue "A GLU 919": "OE1" <-> "OE2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "B ASP 101": "OD1" <-> "OD2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "C GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9932 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7333 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 883} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 519 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "D" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 802 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "G" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 194 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2450 SG CYS A 301 79.275 41.008 52.381 1.00 28.24 S ATOM 2523 SG CYS A 310 76.742 41.105 49.964 1.00 25.23 S ATOM 3925 SG CYS A 487 89.052 47.626 68.104 1.00 30.40 S ATOM 5178 SG CYS A 645 90.808 48.944 65.420 1.00 35.57 S ATOM 5184 SG CYS A 646 90.164 45.454 65.537 1.00 35.17 S Time building chain proxies: 5.77, per 1000 atoms: 0.58 Number of scatterers: 9932 At special positions: 0 Unit cell: (104.14, 103.32, 124.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 70 16.00 P 19 15.00 O 1927 8.00 N 1669 7.00 C 6245 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=0, symmetry=0 Time building additional restraints: 3.84 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 3 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2302 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 43.8% alpha, 11.4% beta 9 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 removed outlier: 3.753A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 198 removed outlier: 3.684A pdb=" N ALA A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.508A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.627A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 303 through 318 removed outlier: 4.070A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 removed outlier: 3.645A pdb=" N ASP A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.785A pdb=" N ASP A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA A 423 " --> pdb=" O PHE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.598A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.346A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.812A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.640A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 708 removed outlier: 3.915A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.921A pdb=" N ILE A 715 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 790 removed outlier: 4.126A pdb=" N SER A 784 " --> pdb=" O LYS A 780 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 843 Processing helix chain 'A' and resid 855 through 864 removed outlier: 3.899A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 863 " --> pdb=" O PHE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 896 removed outlier: 3.591A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 926 removed outlier: 3.924A pdb=" N TYR A 925 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.893A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.342A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.570A pdb=" N TYR B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.689A pdb=" N LEU B 180 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 26 through 41 Processing helix chain 'C' and resid 44 through 62 removed outlier: 4.047A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 94 Processing helix chain 'D' and resid 100 through 112 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.509A pdb=" N GLN A 57 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE A 56 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER A 68 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU A 58 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 66 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 38 removed outlier: 3.505A pdb=" N ILE A 37 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.282A pdb=" N PHE A 102 " --> pdb=" O HIS A 113 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS A 113 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 104 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 111 " --> pdb=" O PHE A 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.527A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.570A pdb=" N VAL A 342 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 3.554A pdb=" N MET A 542 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR B 187 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA B 191 " --> pdb=" O TRP B 154 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N TRP B 154 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 612 through 616 removed outlier: 3.525A pdb=" N PHE A 766 " --> pdb=" O HIS A 613 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 754 " --> pdb=" O CYS A 765 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 612 through 616 removed outlier: 3.525A pdb=" N PHE A 766 " --> pdb=" O HIS A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AB1, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.597A pdb=" N THR D 187 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 142 through 143 379 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 4.17 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: 3113 1.34 - 1.46: 1710 1.46 - 1.57: 5220 1.57 - 1.69: 36 1.69 - 1.81: 105 Bond restraints: 10184 Sorted by residual: bond pdb=" C TRP B 182 " pdb=" N PRO B 183 " ideal model delta sigma weight residual 1.335 1.350 -0.015 8.70e-03 1.32e+04 3.10e+00 bond pdb=" CA SER A 709 " pdb=" C SER A 709 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.80e-02 3.09e+03 1.80e+00 bond pdb=" N ILE A 847 " pdb=" CA ILE A 847 " ideal model delta sigma weight residual 1.474 1.456 0.018 1.57e-02 4.06e+03 1.33e+00 bond pdb=" CA VAL A 844 " pdb=" CB VAL A 844 " ideal model delta sigma weight residual 1.550 1.539 0.012 1.03e-02 9.43e+03 1.28e+00 bond pdb=" CA VAL D 167 " pdb=" CB VAL D 167 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.05e-02 9.07e+03 1.24e+00 ... (remaining 10179 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.09: 276 106.09 - 113.08: 5522 113.08 - 120.06: 3623 120.06 - 127.04: 4367 127.04 - 134.02: 128 Bond angle restraints: 13916 Sorted by residual: angle pdb=" C LEU A 119 " pdb=" N THR A 120 " pdb=" CA THR A 120 " ideal model delta sigma weight residual 121.54 127.94 -6.40 1.91e+00 2.74e-01 1.12e+01 angle pdb=" C TYR A 787 " pdb=" N TYR A 788 " pdb=" CA TYR A 788 " ideal model delta sigma weight residual 122.26 117.24 5.02 1.73e+00 3.34e-01 8.43e+00 angle pdb=" C TRP A 916 " pdb=" N GLU A 917 " pdb=" CA GLU A 917 " ideal model delta sigma weight residual 121.95 132.43 -10.48 3.74e+00 7.15e-02 7.84e+00 angle pdb=" C ASP A 846 " pdb=" N ILE A 847 " pdb=" CA ILE A 847 " ideal model delta sigma weight residual 121.65 119.11 2.54 9.40e-01 1.13e+00 7.33e+00 angle pdb=" N ILE A 847 " pdb=" CA ILE A 847 " pdb=" C ILE A 847 " ideal model delta sigma weight residual 106.21 109.10 -2.89 1.07e+00 8.73e-01 7.30e+00 ... (remaining 13911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.37: 5848 28.37 - 56.73: 215 56.73 - 85.10: 33 85.10 - 113.46: 3 113.46 - 141.83: 1 Dihedral angle restraints: 6100 sinusoidal: 2541 harmonic: 3559 Sorted by residual: dihedral pdb=" CA ILE A 106 " pdb=" C ILE A 106 " pdb=" N ASP A 107 " pdb=" CA ASP A 107 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ASP A 107 " pdb=" C ASP A 107 " pdb=" N GLY A 108 " pdb=" CA GLY A 108 " ideal model delta harmonic sigma weight residual -180.00 -152.19 -27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ILE A 757 " pdb=" C ILE A 757 " pdb=" N LEU A 758 " pdb=" CA LEU A 758 " ideal model delta harmonic sigma weight residual 180.00 154.74 25.26 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 6097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1311 0.056 - 0.111: 263 0.111 - 0.167: 17 0.167 - 0.222: 1 0.222 - 0.278: 1 Chirality restraints: 1593 Sorted by residual: chirality pdb=" CB THR A 120 " pdb=" CA THR A 120 " pdb=" OG1 THR A 120 " pdb=" CG2 THR A 120 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C3' G F -3 " pdb=" C4' G F -3 " pdb=" O3' G F -3 " pdb=" C2' G F -3 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA TRP D 182 " pdb=" N TRP D 182 " pdb=" C TRP D 182 " pdb=" CB TRP D 182 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.61e-01 ... (remaining 1590 not shown) Planarity restraints: 1712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 177 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.38e+00 pdb=" N PRO B 178 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 182 " 0.026 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO D 183 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 183 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 183 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G F -1 " -0.019 2.00e-02 2.50e+03 7.91e-03 1.88e+00 pdb=" N9 G F -1 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G F -1 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G F -1 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G F -1 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G F -1 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G F -1 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G F -1 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G F -1 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G F -1 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G F -1 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G F -1 " 0.003 2.00e-02 2.50e+03 ... (remaining 1709 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 964 2.74 - 3.28: 10318 3.28 - 3.82: 16222 3.82 - 4.36: 20084 4.36 - 4.90: 33800 Nonbonded interactions: 81388 Sorted by model distance: nonbonded pdb=" OG SER A 239 " pdb=" OD1 ASP A 465 " model vdw 2.199 2.440 nonbonded pdb=" OH TYR A 294 " pdb=" OD1 ASN A 314 " model vdw 2.233 2.440 nonbonded pdb=" OD2 ASP A 390 " pdb=" OH TYR A 674 " model vdw 2.237 2.440 nonbonded pdb=" OG SER A 433 " pdb=" O VAL A 435 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR A 420 " pdb=" OG SER C 4 " model vdw 2.259 2.440 ... (remaining 81383 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 84 through 122 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB )) or resid 128 through 188 or (resid 189 and (name N o \ r name CA or name C or name O or name CB )) or resid 190 through 191)) selection = (chain 'D' and (resid 84 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 191)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 6.180 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 32.970 Find NCS groups from input model: 0.310 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 0.033 10184 Z= 0.224 Angle : 0.610 10.475 13916 Z= 0.347 Chirality : 0.043 0.278 1593 Planarity : 0.003 0.039 1712 Dihedral : 15.055 141.826 3798 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -4.42 (0.19), residues: 1188 helix: -1.96 (0.19), residues: 500 sheet: -3.57 (0.36), residues: 133 loop : -3.74 (0.20), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 182 HIS 0.005 0.001 HIS A 113 PHE 0.015 0.001 PHE A 753 TYR 0.013 0.001 TYR A 921 ARG 0.002 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 452 ASP cc_start: 0.7776 (t70) cc_final: 0.7492 (t70) REVERT: D 106 ILE cc_start: 0.5964 (mm) cc_final: 0.5570 (mt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2598 time to fit residues: 58.2834 Evaluate side-chains 120 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 10.0000 chunk 90 optimal weight: 0.0770 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 56 optimal weight: 0.0170 chunk 69 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 81 GLN A 113 HIS A 133 HIS ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN A 356 ASN A 357 GLN A 439 HIS A 573 GLN A 650 HIS A 705 ASN A 724 GLN A 789 GLN A 815 GLN B 108 ASN B 109 ASN B 168 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN D 104 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10184 Z= 0.160 Angle : 0.544 7.210 13916 Z= 0.287 Chirality : 0.041 0.191 1593 Planarity : 0.003 0.044 1712 Dihedral : 11.955 144.856 1600 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.04 % Allowed : 12.44 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -2.97 (0.22), residues: 1188 helix: -0.58 (0.22), residues: 491 sheet: -2.74 (0.40), residues: 127 loop : -3.13 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 182 HIS 0.004 0.001 HIS A 309 PHE 0.016 0.001 PHE A 741 TYR 0.015 0.001 TYR A 887 ARG 0.006 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: D 94 MET cc_start: 0.6161 (mtt) cc_final: 0.5860 (mtp) REVERT: D 106 ILE cc_start: 0.6011 (mm) cc_final: 0.5614 (mt) outliers start: 11 outliers final: 7 residues processed: 142 average time/residue: 0.2061 time to fit residues: 41.6589 Evaluate side-chains 125 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 153 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 116 optimal weight: 0.0770 chunk 96 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 86 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10184 Z= 0.153 Angle : 0.516 5.528 13916 Z= 0.272 Chirality : 0.041 0.192 1593 Planarity : 0.003 0.050 1712 Dihedral : 11.780 144.585 1600 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.71 % Allowed : 15.10 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -2.29 (0.23), residues: 1188 helix: 0.02 (0.24), residues: 485 sheet: -2.19 (0.44), residues: 127 loop : -2.81 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 182 HIS 0.004 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.015 0.001 TYR A 887 ARG 0.005 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 0.984 Fit side-chains REVERT: D 94 MET cc_start: 0.6118 (mtt) cc_final: 0.5775 (mtp) REVERT: D 106 ILE cc_start: 0.6033 (mm) cc_final: 0.5620 (mt) outliers start: 18 outliers final: 10 residues processed: 141 average time/residue: 0.2293 time to fit residues: 45.6866 Evaluate side-chains 128 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain D residue 101 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN A 572 HIS A 705 ASN A 815 GLN C 36 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 10184 Z= 0.465 Angle : 0.710 7.215 13916 Z= 0.372 Chirality : 0.048 0.223 1593 Planarity : 0.004 0.053 1712 Dihedral : 11.840 136.213 1600 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 3.32 % Allowed : 17.09 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -2.67 (0.23), residues: 1188 helix: -0.39 (0.23), residues: 486 sheet: -2.21 (0.43), residues: 131 loop : -2.99 (0.23), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 154 HIS 0.004 0.001 HIS A 113 PHE 0.016 0.002 PHE A 753 TYR 0.020 0.003 TYR A 867 ARG 0.006 0.001 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 121 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: A 331 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7439 (ttt-90) REVERT: D 106 ILE cc_start: 0.6115 (mm) cc_final: 0.5678 (mt) outliers start: 35 outliers final: 26 residues processed: 144 average time/residue: 0.2298 time to fit residues: 47.3388 Evaluate side-chains 147 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 114 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN A 198 ASN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10184 Z= 0.214 Angle : 0.560 6.042 13916 Z= 0.294 Chirality : 0.042 0.200 1593 Planarity : 0.003 0.047 1712 Dihedral : 11.686 139.456 1600 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.18 % Allowed : 19.09 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -2.27 (0.23), residues: 1188 helix: -0.05 (0.23), residues: 492 sheet: -2.07 (0.45), residues: 128 loop : -2.77 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 29 HIS 0.004 0.001 HIS A 309 PHE 0.016 0.001 PHE A 102 TYR 0.016 0.002 TYR A 453 ARG 0.003 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 340 PHE cc_start: 0.8483 (m-10) cc_final: 0.8257 (m-10) REVERT: A 437 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7108 (tt) REVERT: A 924 MET cc_start: 0.6010 (mmt) cc_final: 0.5661 (mmt) REVERT: D 106 ILE cc_start: 0.6056 (mm) cc_final: 0.5632 (mt) outliers start: 23 outliers final: 15 residues processed: 140 average time/residue: 0.2175 time to fit residues: 43.5562 Evaluate side-chains 137 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 114 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10184 Z= 0.187 Angle : 0.538 6.312 13916 Z= 0.282 Chirality : 0.041 0.198 1593 Planarity : 0.003 0.044 1712 Dihedral : 11.580 141.404 1600 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.04 % Allowed : 19.28 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.96 (0.24), residues: 1188 helix: 0.26 (0.24), residues: 484 sheet: -2.10 (0.44), residues: 138 loop : -2.56 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 182 HIS 0.004 0.001 HIS A 309 PHE 0.016 0.001 PHE A 741 TYR 0.013 0.001 TYR A 887 ARG 0.002 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 131 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 340 PHE cc_start: 0.8503 (m-10) cc_final: 0.8298 (m-10) REVERT: A 437 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7092 (tt) REVERT: A 665 GLU cc_start: 0.7812 (pm20) cc_final: 0.7455 (pm20) REVERT: A 667 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8286 (p) outliers start: 32 outliers final: 20 residues processed: 155 average time/residue: 0.2037 time to fit residues: 45.7880 Evaluate side-chains 146 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 114 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10184 Z= 0.300 Angle : 0.615 8.619 13916 Z= 0.319 Chirality : 0.044 0.209 1593 Planarity : 0.003 0.045 1712 Dihedral : 11.631 138.862 1600 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.23 % Allowed : 19.47 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -2.08 (0.24), residues: 1188 helix: 0.11 (0.24), residues: 485 sheet: -1.97 (0.46), residues: 128 loop : -2.63 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 154 HIS 0.003 0.001 HIS A 309 PHE 0.020 0.002 PHE A 102 TYR 0.015 0.002 TYR A 867 ARG 0.003 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 437 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7142 (tt) REVERT: D 169 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6641 (mp) outliers start: 34 outliers final: 25 residues processed: 150 average time/residue: 0.2186 time to fit residues: 46.6098 Evaluate side-chains 149 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 169 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 90 optimal weight: 0.0570 chunk 104 optimal weight: 0.0670 chunk 109 optimal weight: 0.0050 chunk 100 optimal weight: 6.9990 overall best weight: 1.2254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10184 Z= 0.211 Angle : 0.570 8.743 13916 Z= 0.296 Chirality : 0.042 0.199 1593 Planarity : 0.003 0.039 1712 Dihedral : 11.586 140.826 1600 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 3.13 % Allowed : 20.23 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.89 (0.24), residues: 1188 helix: 0.26 (0.24), residues: 485 sheet: -2.05 (0.44), residues: 138 loop : -2.47 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.004 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.019 0.001 TYR A 453 ARG 0.002 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 123 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 608 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6843 (m-30) REVERT: A 855 MET cc_start: 0.5128 (tpp) cc_final: 0.4615 (tpp) outliers start: 33 outliers final: 24 residues processed: 146 average time/residue: 0.2081 time to fit residues: 43.9034 Evaluate side-chains 143 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 114 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 1.9990 chunk 109 optimal weight: 0.0870 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10184 Z= 0.205 Angle : 0.569 7.901 13916 Z= 0.293 Chirality : 0.042 0.199 1593 Planarity : 0.003 0.038 1712 Dihedral : 11.556 141.482 1600 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.66 % Allowed : 20.70 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.81 (0.24), residues: 1188 helix: 0.34 (0.24), residues: 484 sheet: -1.99 (0.44), residues: 138 loop : -2.44 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.004 0.001 HIS A 309 PHE 0.020 0.001 PHE A 102 TYR 0.019 0.001 TYR A 286 ARG 0.002 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 665 GLU cc_start: 0.7734 (pm20) cc_final: 0.7242 (pm20) REVERT: A 921 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6980 (m-80) REVERT: D 169 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6621 (mp) outliers start: 28 outliers final: 25 residues processed: 143 average time/residue: 0.2061 time to fit residues: 42.7882 Evaluate side-chains 150 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 846 ASP Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 169 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 109 optimal weight: 0.0370 chunk 94 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 100 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 198 ASN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10184 Z= 0.147 Angle : 0.534 8.184 13916 Z= 0.274 Chirality : 0.040 0.191 1593 Planarity : 0.003 0.034 1712 Dihedral : 11.495 143.911 1600 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.47 % Allowed : 21.18 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.56 (0.24), residues: 1188 helix: 0.57 (0.24), residues: 483 sheet: -1.89 (0.44), residues: 137 loop : -2.30 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 29 HIS 0.005 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.015 0.001 TYR A 286 ARG 0.002 0.000 ARG A 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 452 ASP cc_start: 0.7348 (t70) cc_final: 0.7063 (t0) REVERT: A 665 GLU cc_start: 0.7736 (pm20) cc_final: 0.7224 (pm20) REVERT: A 667 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8225 (p) REVERT: A 921 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.6919 (m-80) outliers start: 26 outliers final: 22 residues processed: 149 average time/residue: 0.2027 time to fit residues: 43.6267 Evaluate side-chains 148 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain D residue 114 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 0.0170 chunk 94 optimal weight: 0.2980 chunk 39 optimal weight: 0.2980 chunk 97 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 68 optimal weight: 0.0050 overall best weight: 0.1430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 177 ASN A 209 ASN A 698 GLN A 752 HIS A 789 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.167478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.142936 restraints weight = 15736.870| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.60 r_work: 0.3724 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10184 Z= 0.132 Angle : 0.525 8.103 13916 Z= 0.268 Chirality : 0.040 0.183 1593 Planarity : 0.003 0.035 1712 Dihedral : 11.454 145.872 1600 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.71 % Allowed : 22.41 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.19 (0.25), residues: 1188 helix: 0.86 (0.25), residues: 485 sheet: -1.67 (0.45), residues: 137 loop : -2.09 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 29 HIS 0.006 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.012 0.001 TYR A 887 ARG 0.002 0.000 ARG A 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2232.16 seconds wall clock time: 41 minutes 7.51 seconds (2467.51 seconds total)