Starting phenix.real_space_refine on Wed Feb 14 19:35:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7doi_30794/02_2024/7doi_30794_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7doi_30794/02_2024/7doi_30794.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7doi_30794/02_2024/7doi_30794_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7doi_30794/02_2024/7doi_30794_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7doi_30794/02_2024/7doi_30794_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7doi_30794/02_2024/7doi_30794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7doi_30794/02_2024/7doi_30794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7doi_30794/02_2024/7doi_30794_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7doi_30794/02_2024/7doi_30794_updated.pdb" } resolution = 2.6 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= 0.007 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 32 5.49 5 Mg 4 5.21 5 S 70 5.16 5 C 6337 2.51 5 N 1691 2.21 5 O 1992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A ARG 726": "NH1" <-> "NH2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A ARG 889": "NH1" <-> "NH2" Residue "A TYR 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 919": "OE1" <-> "OE2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "G ASP 99": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10128 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7305 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 875} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 875 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 526 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 68} 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: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna3p': 11} Chain: "T" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 310 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 10} Link IDs: {'rna3p': 14} Chain: "G" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 24 Unusual residues: {' MG': 4, ' ZN': 2, 'POP': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "P" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HCU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2430 SG CYS A 301 51.638 67.160 47.100 1.00 31.29 S ATOM 2471 SG CYS A 306 51.444 66.425 43.040 1.00 28.10 S ATOM 2503 SG CYS A 310 54.950 66.284 45.465 1.00 24.11 S ATOM 3911 SG CYS A 487 33.332 61.554 55.485 1.00 32.99 S ATOM 5164 SG CYS A 645 32.357 61.308 51.380 1.00 39.17 S ATOM 5170 SG CYS A 646 35.439 63.877 53.211 1.00 37.97 S Time building chain proxies: 5.69, per 1000 atoms: 0.56 Number of scatterers: 10128 At special positions: 0 Unit cell: (112.245, 94.072, 131.487, 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 70 16.00 P 32 15.00 Mg 4 11.99 O 1992 8.00 N 1691 7.00 C 6337 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.13 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 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 3 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2294 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 8 sheets defined 41.3% alpha, 12.2% beta 10 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 4.72 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 removed outlier: 3.503A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL A 14 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 89 removed outlier: 3.644A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) 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: 3.898A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 198 removed outlier: 3.507A pdb=" N TYR A 175 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 198 " --> pdb=" O ALA A 195 " (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: 4.177A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 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: 3.713A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) 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 457 removed outlier: 3.994A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.957A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) 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: 3.626A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 580 removed outlier: 6.099A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.956A 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 628 through 641 removed outlier: 4.855A 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 773 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 855 through 871 Proline residue: A 868 - end of helix removed outlier: 5.034A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 892 removed outlier: 4.353A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 924 removed outlier: 3.914A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 96 removed outlier: 4.191A pdb=" N LEU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.529A pdb=" N ILE B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 135 through 141 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 19 removed outlier: 3.723A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) 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 39 removed outlier: 3.509A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 59 removed outlier: 3.634A pdb=" N LYS C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 98 removed outlier: 3.663A pdb=" N PHE G 92 " --> pdb=" O GLN G 88 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET G 94 " --> pdb=" O MET G 90 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU G 98 " --> pdb=" O MET G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 111 Processing helix chain 'G' and resid 136 through 139 No H-bonds generated for 'chain 'G' and resid 136 through 139' Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 Processing sheet with id= B, first strand: chain 'A' and resid 31 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.684A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.607A 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: 6.555A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.449A 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 815 through 822 removed outlier: 3.565A 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: 3.503A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 127 through 132 removed outlier: 6.476A pdb=" N LEU G 189 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ILE G 156 " --> pdb=" O LEU G 189 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2404 1.33 - 1.45: 2329 1.45 - 1.57: 5500 1.57 - 1.69: 57 1.69 - 1.81: 105 Bond restraints: 10395 Sorted by residual: bond pdb=" O3 HCU P1201 " pdb=" P1 HCU P1201 " ideal model delta sigma weight residual 1.650 1.429 0.221 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C1 HCU P1201 " pdb=" O1 HCU P1201 " ideal model delta sigma weight residual 1.184 1.401 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C9 HCU P1201 " pdb=" O3 HCU P1201 " ideal model delta sigma weight residual 1.400 1.222 0.178 2.00e-02 2.50e+03 7.93e+01 bond pdb=" O4 HCU P1201 " pdb=" P1 HCU P1201 " ideal model delta sigma weight residual 1.510 1.337 0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" C SER A 15 " pdb=" N ALA A 16 " ideal model delta sigma weight residual 1.331 1.218 0.114 1.36e-02 5.41e+03 6.99e+01 ... (remaining 10390 not shown) Histogram of bond angle deviations from ideal: 88.67 - 98.54: 3 98.54 - 108.42: 756 108.42 - 118.29: 7487 118.29 - 128.16: 5886 128.16 - 138.04: 108 Bond angle restraints: 14240 Sorted by residual: angle pdb=" O2' U T 10 " pdb=" C2' U T 10 " pdb=" C1' U T 10 " ideal model delta sigma weight residual 108.40 88.67 19.73 1.50e+00 4.44e-01 1.73e+02 angle pdb=" C7 HCU P1201 " pdb=" C8 HCU P1201 " pdb=" C9 HCU P1201 " ideal model delta sigma weight residual 109.47 132.75 -23.28 3.00e+00 1.11e-01 6.02e+01 angle pdb=" C4' U P 20 " pdb=" C3' U P 20 " pdb=" O3' U P 20 " ideal model delta sigma weight residual 113.00 123.85 -10.85 1.50e+00 4.44e-01 5.23e+01 angle pdb=" O3' U P 20 " pdb=" C3' U P 20 " pdb=" C2' U P 20 " ideal model delta sigma weight residual 113.70 103.30 10.40 1.50e+00 4.44e-01 4.80e+01 angle pdb=" C3' U T 10 " pdb=" C2' U T 10 " pdb=" O2' U T 10 " ideal model delta sigma weight residual 110.70 120.83 -10.13 1.50e+00 4.44e-01 4.56e+01 ... (remaining 14235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.07: 5876 25.07 - 50.14: 261 50.14 - 75.22: 50 75.22 - 100.29: 3 100.29 - 125.36: 2 Dihedral angle restraints: 6192 sinusoidal: 2647 harmonic: 3545 Sorted by residual: dihedral pdb=" O2 POP A1008 " pdb=" O POP A1008 " pdb=" P1 POP A1008 " pdb=" P2 POP A1008 " ideal model delta sinusoidal sigma weight residual -88.77 36.59 -125.36 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O4' U T 10 " pdb=" C2' U T 10 " pdb=" C1' U T 10 " pdb=" C3' U T 10 " ideal model delta sinusoidal sigma weight residual 25.00 -13.69 38.69 1 8.00e+00 1.56e-02 3.29e+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 -165.68 108.27 1 2.00e+01 2.50e-03 3.15e+01 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.316: 1628 0.316 - 0.631: 1 0.631 - 0.947: 0 0.947 - 1.262: 0 1.262 - 1.578: 1 Chirality restraints: 1630 Sorted by residual: chirality pdb=" C8 HCU P1201 " pdb=" C10 HCU P1201 " pdb=" C7 HCU P1201 " pdb=" C9 HCU P1201 " both_signs ideal model delta sigma weight residual False -2.74 -1.17 -1.58 2.00e-01 2.50e+01 6.22e+01 chirality pdb=" CA TRP A 916 " pdb=" N TRP A 916 " pdb=" C TRP A 916 " pdb=" CB TRP A 916 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" C3' U T 10 " pdb=" C4' U T 10 " pdb=" O3' U T 10 " pdb=" C2' U T 10 " both_signs ideal model delta sigma weight residual False -2.48 -2.20 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1627 not shown) Planarity restraints: 1713 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U T 10 " -0.054 2.00e-02 2.50e+03 2.90e-02 1.89e+01 pdb=" N1 U T 10 " 0.063 2.00e-02 2.50e+03 pdb=" C2 U T 10 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U T 10 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U T 10 " 0.007 2.00e-02 2.50e+03 pdb=" C4 U T 10 " -0.000 2.00e-02 2.50e+03 pdb=" O4 U T 10 " -0.023 2.00e-02 2.50e+03 pdb=" C5 U T 10 " -0.003 2.00e-02 2.50e+03 pdb=" C6 U T 10 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 139 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.30e+00 pdb=" C LYS G 139 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS G 139 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN G 140 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP G 182 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.00e+00 pdb=" N PRO G 183 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO G 183 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 183 " -0.037 5.00e-02 4.00e+02 ... (remaining 1710 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 87 2.60 - 3.17: 7964 3.17 - 3.75: 16254 3.75 - 4.32: 23764 4.32 - 4.90: 37500 Nonbonded interactions: 85569 Sorted by model distance: nonbonded pdb=" OD2 ASP A 218 " pdb="MG MG A1006 " model vdw 2.021 2.170 nonbonded pdb="MG MG A1006 " pdb=" O4 POP A1008 " model vdw 2.073 2.170 nonbonded pdb=" OD1 ASN A 209 " pdb="MG MG A1007 " model vdw 2.120 2.170 nonbonded pdb=" N3 U T 10 " pdb=" O1 HCU P1201 " model vdw 2.153 2.520 nonbonded pdb=" OG SER A 501 " pdb=" OP1 C T 9 " model vdw 2.198 2.440 ... (remaining 85564 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 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 110 or (resid 111 and (name N or n \ ame CA or name C or name O or name CB )) or resid 112 through 179 or resid 182 t \ hrough 191)) selection = chain 'G' } 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: 0.930 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: 4.350 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 34.390 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.009 0.221 10395 Z= 0.598 Angle : 1.060 23.276 14240 Z= 0.662 Chirality : 0.075 1.578 1630 Planarity : 0.006 0.066 1713 Dihedral : 14.668 125.358 3898 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.29 % Allowed : 5.14 % Favored : 94.58 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.21), residues: 1181 helix: -1.84 (0.19), residues: 501 sheet: -0.86 (0.39), residues: 155 loop : -1.33 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 916 HIS 0.015 0.002 HIS A 613 PHE 0.031 0.003 PHE A 741 TYR 0.024 0.003 TYR A 788 ARG 0.020 0.001 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.100 Fit side-chains REVERT: A 9 ASN cc_start: 0.8044 (m-40) cc_final: 0.7840 (m110) REVERT: A 360 ASN cc_start: 0.6946 (p0) cc_final: 0.6564 (p0) REVERT: A 370 GLU cc_start: 0.7191 (pt0) cc_final: 0.6965 (pt0) REVERT: A 519 MET cc_start: 0.8630 (mtp) cc_final: 0.8239 (mtm) REVERT: A 798 LYS cc_start: 0.8194 (mmtp) cc_final: 0.7946 (mmtt) REVERT: A 916 TRP cc_start: 0.7084 (OUTLIER) cc_final: 0.6484 (p90) REVERT: B 155 GLU cc_start: 0.7823 (pt0) cc_final: 0.7443 (pt0) REVERT: B 164 SER cc_start: 0.8658 (m) cc_final: 0.8427 (p) REVERT: B 165 LYS cc_start: 0.8527 (mptt) cc_final: 0.8242 (mmtm) REVERT: B 179 ASN cc_start: 0.8381 (m110) cc_final: 0.8173 (t0) REVERT: G 103 LEU cc_start: 0.8592 (mt) cc_final: 0.8389 (mt) REVERT: G 104 ASN cc_start: 0.8556 (m-40) cc_final: 0.8275 (m-40) outliers start: 3 outliers final: 1 residues processed: 148 average time/residue: 1.2262 time to fit residues: 195.6948 Evaluate side-chains 123 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 916 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 9 ASN A 113 HIS A 158 ASN A 224 GLN A 357 GLN A 362 HIS A 381 HIS A 408 GLN A 468 GLN A 492 GLN A 568 ASN A 691 ASN A 705 ASN A 773 GLN B 105 ASN B 109 ASN B 157 GLN B 179 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN G 105 ASN G 108 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10395 Z= 0.188 Angle : 0.508 6.587 14240 Z= 0.271 Chirality : 0.041 0.192 1630 Planarity : 0.004 0.060 1713 Dihedral : 11.082 112.659 1704 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.09 % Allowed : 8.94 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.22), residues: 1181 helix: -0.58 (0.21), residues: 513 sheet: -0.52 (0.41), residues: 143 loop : -0.86 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 916 HIS 0.004 0.001 HIS A 613 PHE 0.018 0.001 PHE A 652 TYR 0.020 0.001 TYR A 921 ARG 0.002 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.080 Fit side-chains REVERT: A 69 TYR cc_start: 0.8639 (m-80) cc_final: 0.8328 (m-80) REVERT: A 360 ASN cc_start: 0.7023 (p0) cc_final: 0.6600 (p0) REVERT: A 370 GLU cc_start: 0.7053 (pt0) cc_final: 0.6755 (pt0) REVERT: A 519 MET cc_start: 0.8512 (mtp) cc_final: 0.8292 (mtm) REVERT: A 644 THR cc_start: 0.8471 (p) cc_final: 0.8112 (m) REVERT: A 798 LYS cc_start: 0.8236 (mmtp) cc_final: 0.7998 (mmtt) REVERT: A 893 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6943 (p0) REVERT: A 916 TRP cc_start: 0.7000 (OUTLIER) cc_final: 0.6257 (p90) REVERT: B 163 ASP cc_start: 0.8749 (m-30) cc_final: 0.8546 (m-30) REVERT: B 164 SER cc_start: 0.8598 (m) cc_final: 0.8272 (p) REVERT: B 171 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: B 179 ASN cc_start: 0.8444 (m-40) cc_final: 0.8076 (t0) outliers start: 22 outliers final: 7 residues processed: 129 average time/residue: 1.2410 time to fit residues: 172.3884 Evaluate side-chains 122 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain G residue 87 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.0970 chunk 33 optimal weight: 0.0670 chunk 89 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 116 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 36 optimal weight: 0.4980 chunk 86 optimal weight: 4.9990 overall best weight: 1.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 822 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN G 105 ASN G 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10395 Z= 0.161 Angle : 0.465 6.068 14240 Z= 0.248 Chirality : 0.040 0.197 1630 Planarity : 0.004 0.040 1713 Dihedral : 10.664 110.539 1704 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.04 % Allowed : 9.32 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.23), residues: 1181 helix: -0.12 (0.22), residues: 515 sheet: -0.19 (0.40), residues: 153 loop : -0.67 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 916 HIS 0.004 0.001 HIS A 613 PHE 0.016 0.001 PHE A 652 TYR 0.016 0.001 TYR A 788 ARG 0.007 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 122 time to evaluate : 1.193 Fit side-chains REVERT: A 197 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6861 (ttm-80) REVERT: A 360 ASN cc_start: 0.7062 (p0) cc_final: 0.6628 (p0) REVERT: A 370 GLU cc_start: 0.6969 (pt0) cc_final: 0.6709 (pt0) REVERT: A 519 MET cc_start: 0.8376 (mtp) cc_final: 0.8168 (mtm) REVERT: A 644 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8171 (m) REVERT: A 798 LYS cc_start: 0.8228 (mmtp) cc_final: 0.7985 (mmtt) REVERT: A 893 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6901 (p0) REVERT: A 916 TRP cc_start: 0.7068 (OUTLIER) cc_final: 0.6291 (p90) REVERT: B 109 ASN cc_start: 0.8107 (m-40) cc_final: 0.7906 (m-40) REVERT: B 164 SER cc_start: 0.8557 (m) cc_final: 0.8224 (p) REVERT: B 171 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: B 179 ASN cc_start: 0.8462 (m-40) cc_final: 0.8100 (t0) outliers start: 32 outliers final: 11 residues processed: 134 average time/residue: 1.2015 time to fit residues: 173.9852 Evaluate side-chains 131 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain G residue 87 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.0170 chunk 81 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 11 optimal weight: 0.0980 chunk 51 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 overall best weight: 2.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 642 HIS B 104 ASN C 36 HIS C 37 ASN G 88 GLN G 104 ASN G 105 ASN G 108 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10395 Z= 0.288 Angle : 0.521 6.335 14240 Z= 0.277 Chirality : 0.043 0.208 1630 Planarity : 0.004 0.053 1713 Dihedral : 10.793 111.027 1704 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.85 % Allowed : 11.32 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.23), residues: 1181 helix: -0.00 (0.22), residues: 514 sheet: -0.24 (0.40), residues: 165 loop : -0.61 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 916 HIS 0.006 0.001 HIS A 613 PHE 0.022 0.002 PHE A 741 TYR 0.018 0.002 TYR A 606 ARG 0.013 0.001 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 119 time to evaluate : 1.155 Fit side-chains REVERT: A 92 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7098 (p0) REVERT: A 197 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6834 (ttm-80) REVERT: A 360 ASN cc_start: 0.7094 (p0) cc_final: 0.6863 (p0) REVERT: A 370 GLU cc_start: 0.7019 (pt0) cc_final: 0.6779 (pt0) REVERT: A 644 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8265 (m) REVERT: A 666 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7797 (mtt) REVERT: A 798 LYS cc_start: 0.8294 (mmtp) cc_final: 0.8071 (mmmt) REVERT: A 893 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.6876 (p0) REVERT: A 916 TRP cc_start: 0.7292 (OUTLIER) cc_final: 0.6391 (p90) REVERT: B 109 ASN cc_start: 0.8143 (m-40) cc_final: 0.7932 (m-40) REVERT: B 157 GLN cc_start: 0.7680 (tt0) cc_final: 0.7456 (tt0) REVERT: B 164 SER cc_start: 0.8624 (m) cc_final: 0.8289 (p) REVERT: B 179 ASN cc_start: 0.8520 (m-40) cc_final: 0.8072 (t0) outliers start: 30 outliers final: 14 residues processed: 133 average time/residue: 1.2148 time to fit residues: 175.4686 Evaluate side-chains 135 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 182 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS G 88 GLN G 104 ASN G 105 ASN G 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10395 Z= 0.132 Angle : 0.441 6.082 14240 Z= 0.234 Chirality : 0.039 0.170 1630 Planarity : 0.003 0.047 1713 Dihedral : 10.426 107.532 1704 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.38 % Allowed : 12.84 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1181 helix: 0.24 (0.23), residues: 513 sheet: 0.03 (0.41), residues: 153 loop : -0.46 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 916 HIS 0.003 0.001 HIS A 362 PHE 0.024 0.001 PHE A 859 TYR 0.013 0.001 TYR A 788 ARG 0.007 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 1.130 Fit side-chains REVERT: A 81 GLN cc_start: 0.7715 (mt0) cc_final: 0.7500 (mt0) REVERT: A 197 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6760 (ttm-80) REVERT: A 360 ASN cc_start: 0.7073 (p0) cc_final: 0.6845 (p0) REVERT: A 629 MET cc_start: 0.8933 (mmp) cc_final: 0.8583 (mmm) REVERT: A 644 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8247 (m) REVERT: A 666 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7764 (mtt) REVERT: A 798 LYS cc_start: 0.8215 (mmtp) cc_final: 0.7999 (mmmt) REVERT: A 893 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6890 (p0) REVERT: A 916 TRP cc_start: 0.7032 (OUTLIER) cc_final: 0.6156 (p90) REVERT: B 109 ASN cc_start: 0.8035 (m-40) cc_final: 0.7832 (m-40) REVERT: B 157 GLN cc_start: 0.7629 (tt0) cc_final: 0.7414 (tt0) REVERT: B 164 SER cc_start: 0.8569 (m) cc_final: 0.8220 (p) REVERT: B 171 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: B 174 MET cc_start: 0.7055 (tpt) cc_final: 0.6770 (tpt) REVERT: B 179 ASN cc_start: 0.8510 (m-40) cc_final: 0.8072 (t0) outliers start: 25 outliers final: 13 residues processed: 134 average time/residue: 1.2241 time to fit residues: 176.8015 Evaluate side-chains 136 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 182 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 7.9990 chunk 22 optimal weight: 0.0970 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 734 ASN G 104 ASN G 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10395 Z= 0.151 Angle : 0.444 5.860 14240 Z= 0.236 Chirality : 0.040 0.195 1630 Planarity : 0.003 0.036 1713 Dihedral : 10.243 106.780 1704 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.19 % Allowed : 13.32 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1181 helix: 0.34 (0.23), residues: 514 sheet: 0.05 (0.41), residues: 153 loop : -0.38 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 916 HIS 0.003 0.001 HIS A 613 PHE 0.015 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.004 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 1.221 Fit side-chains REVERT: A 360 ASN cc_start: 0.7051 (p0) cc_final: 0.6838 (p0) REVERT: A 644 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8241 (m) REVERT: A 666 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7737 (mtt) REVERT: A 798 LYS cc_start: 0.8229 (mmtp) cc_final: 0.8009 (mmmt) REVERT: A 893 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.6963 (p0) REVERT: A 916 TRP cc_start: 0.7031 (OUTLIER) cc_final: 0.6151 (p90) REVERT: B 157 GLN cc_start: 0.7653 (tt0) cc_final: 0.7426 (tt0) REVERT: B 164 SER cc_start: 0.8568 (m) cc_final: 0.8214 (p) REVERT: B 171 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: B 179 ASN cc_start: 0.8558 (m-40) cc_final: 0.8119 (t0) outliers start: 23 outliers final: 12 residues processed: 128 average time/residue: 1.2309 time to fit residues: 169.6132 Evaluate side-chains 132 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 182 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 84 optimal weight: 0.0980 chunk 96 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 114 optimal weight: 0.0040 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 734 ASN G 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10395 Z= 0.115 Angle : 0.424 5.883 14240 Z= 0.225 Chirality : 0.039 0.203 1630 Planarity : 0.003 0.037 1713 Dihedral : 10.119 104.014 1704 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.71 % Allowed : 14.37 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.24), residues: 1181 helix: 0.43 (0.23), residues: 517 sheet: 0.15 (0.42), residues: 143 loop : -0.35 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 916 HIS 0.002 0.000 HIS A 362 PHE 0.016 0.001 PHE A 859 TYR 0.012 0.001 TYR A 788 ARG 0.010 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 1.106 Fit side-chains REVERT: A 370 GLU cc_start: 0.7267 (pm20) cc_final: 0.6761 (pm20) REVERT: A 629 MET cc_start: 0.8989 (mmp) cc_final: 0.8652 (mmm) REVERT: A 644 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8213 (m) REVERT: A 666 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7750 (mtt) REVERT: A 798 LYS cc_start: 0.8189 (mmtp) cc_final: 0.7982 (mmmt) REVERT: A 893 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.6994 (p0) REVERT: A 916 TRP cc_start: 0.7010 (OUTLIER) cc_final: 0.6195 (p90) REVERT: B 157 GLN cc_start: 0.7601 (tt0) cc_final: 0.7370 (tt0) REVERT: B 164 SER cc_start: 0.8536 (m) cc_final: 0.8177 (p) REVERT: B 179 ASN cc_start: 0.8499 (m-40) cc_final: 0.8068 (t0) outliers start: 18 outliers final: 11 residues processed: 131 average time/residue: 1.1822 time to fit residues: 167.6385 Evaluate side-chains 125 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 182 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 100 optimal weight: 0.0170 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 734 ASN G 105 ASN G 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10395 Z= 0.341 Angle : 0.544 7.087 14240 Z= 0.288 Chirality : 0.045 0.207 1630 Planarity : 0.004 0.067 1713 Dihedral : 10.504 106.892 1704 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.47 % Allowed : 13.70 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.24), residues: 1181 helix: 0.30 (0.23), residues: 512 sheet: -0.14 (0.39), residues: 161 loop : -0.48 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 916 HIS 0.006 0.001 HIS A 309 PHE 0.024 0.002 PHE A 741 TYR 0.022 0.002 TYR A 606 ARG 0.006 0.001 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 1.379 Fit side-chains REVERT: A 18 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7425 (mpt-90) REVERT: A 629 MET cc_start: 0.8986 (mmp) cc_final: 0.8722 (mmm) REVERT: A 644 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8214 (m) REVERT: A 666 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7771 (mtt) REVERT: A 798 LYS cc_start: 0.8273 (mmtp) cc_final: 0.8036 (mmmt) REVERT: A 893 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.6902 (p0) REVERT: A 916 TRP cc_start: 0.7330 (OUTLIER) cc_final: 0.6344 (p90) REVERT: B 168 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7685 (mm-40) REVERT: B 171 GLU cc_start: 0.7819 (mp0) cc_final: 0.7563 (mp0) outliers start: 26 outliers final: 16 residues processed: 129 average time/residue: 1.2333 time to fit residues: 172.3367 Evaluate side-chains 133 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 182 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 113 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS G 88 GLN G 104 ASN G 105 ASN G 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10395 Z= 0.163 Angle : 0.471 7.050 14240 Z= 0.248 Chirality : 0.041 0.217 1630 Planarity : 0.004 0.069 1713 Dihedral : 10.302 105.149 1704 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.09 % Allowed : 14.37 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1181 helix: 0.38 (0.23), residues: 513 sheet: 0.02 (0.41), residues: 149 loop : -0.43 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 916 HIS 0.003 0.001 HIS A 613 PHE 0.021 0.001 PHE A 859 TYR 0.013 0.001 TYR A 788 ARG 0.005 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.132 Fit side-chains REVERT: A 629 MET cc_start: 0.8993 (mmp) cc_final: 0.8708 (mmm) REVERT: A 644 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8232 (m) REVERT: A 666 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7749 (mtt) REVERT: A 798 LYS cc_start: 0.8250 (mmtp) cc_final: 0.8030 (mmmt) REVERT: A 893 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.6921 (p0) REVERT: A 916 TRP cc_start: 0.7223 (OUTLIER) cc_final: 0.6272 (p90) REVERT: B 164 SER cc_start: 0.8609 (m) cc_final: 0.8297 (p) REVERT: B 168 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7886 (mm-40) REVERT: B 171 GLU cc_start: 0.7821 (mp0) cc_final: 0.7597 (mp0) outliers start: 22 outliers final: 13 residues processed: 128 average time/residue: 1.2219 time to fit residues: 168.5189 Evaluate side-chains 131 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 182 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 28 optimal weight: 0.2980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 734 ASN G 104 ASN G 105 ASN G 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10395 Z= 0.243 Angle : 0.510 8.606 14240 Z= 0.269 Chirality : 0.043 0.220 1630 Planarity : 0.004 0.071 1713 Dihedral : 10.391 105.634 1704 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.90 % Allowed : 15.03 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1181 helix: 0.35 (0.23), residues: 513 sheet: 0.03 (0.41), residues: 149 loop : -0.45 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 916 HIS 0.005 0.001 HIS A 613 PHE 0.023 0.002 PHE A 859 TYR 0.017 0.002 TYR A 788 ARG 0.008 0.000 ARG A 553 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 629 MET cc_start: 0.8997 (mmp) cc_final: 0.8661 (mmm) REVERT: A 644 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8241 (m) REVERT: A 666 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7766 (mtt) REVERT: A 798 LYS cc_start: 0.8246 (mmtp) cc_final: 0.8019 (mmmt) REVERT: A 893 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.6924 (p0) REVERT: A 916 TRP cc_start: 0.7249 (OUTLIER) cc_final: 0.6309 (p90) REVERT: B 94 MET cc_start: 0.7350 (mtm) cc_final: 0.7127 (mtm) REVERT: B 164 SER cc_start: 0.8637 (m) cc_final: 0.8323 (p) REVERT: B 168 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7856 (mm-40) outliers start: 20 outliers final: 15 residues processed: 121 average time/residue: 1.2407 time to fit residues: 161.7292 Evaluate side-chains 129 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 182 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 734 ASN G 104 ASN G 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.131177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.097315 restraints weight = 12808.874| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.86 r_work: 0.3106 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10395 Z= 0.205 Angle : 0.503 11.172 14240 Z= 0.262 Chirality : 0.042 0.224 1630 Planarity : 0.004 0.065 1713 Dihedral : 10.275 104.987 1704 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.90 % Allowed : 14.84 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1181 helix: 0.40 (0.23), residues: 513 sheet: 0.04 (0.42), residues: 149 loop : -0.38 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 916 HIS 0.004 0.001 HIS A 613 PHE 0.034 0.001 PHE A 859 TYR 0.015 0.001 TYR A 788 ARG 0.008 0.000 ARG A 553 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3651.14 seconds wall clock time: 65 minutes 58.27 seconds (3958.27 seconds total)