Starting phenix.real_space_refine on Sat Dec 9 08:47:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijv_35500/12_2023/8ijv_35500_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijv_35500/12_2023/8ijv_35500.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijv_35500/12_2023/8ijv_35500_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijv_35500/12_2023/8ijv_35500_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijv_35500/12_2023/8ijv_35500_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijv_35500/12_2023/8ijv_35500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijv_35500/12_2023/8ijv_35500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijv_35500/12_2023/8ijv_35500_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijv_35500/12_2023/8ijv_35500_updated.pdb" } resolution = 2.1 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= -0.002 sd= 0.094 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: 9 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 65 5.16 5 Cl 4 4.86 5 Be 1 3.05 5 C 6570 2.51 5 N 1654 2.21 5 O 2229 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10532 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7631 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 47, 'TRANS': 935} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2142 Classifications: {'peptide': 268} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 245} Chain: "A" Number of atoms: 238 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 216 Unusual residues: {' MG': 1, 'PCW': 4, 'PWI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 6, 216 Unusual residues: {' MG': 1, 'PCW': 4, 'PWI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 189 Chain: "B" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Unusual residues: {'CLR': 2, 'NAG': 3, 'PCW': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 255 Classifications: {'water': 255} Link IDs: {None: 254} Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C01APWI A1106 " occ=0.46 ... (42 atoms not shown) pdb="CL2 BPWI A1106 " occ=0.54 Time building chain proxies: 6.46, per 1000 atoms: 0.61 Number of scatterers: 10532 At special positions: 0 Unit cell: (81.216, 97.76, 174.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Cl 4 17.00 S 65 16.00 P 5 15.00 Mg 1 11.99 F 3 9.00 O 2229 8.00 N 1654 7.00 C 6570 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 262 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 130 " " NAG B 304 " - " ASN B 161 " Time building additional restraints: 4.69 Conformation dependent library (CDL) restraints added in 2.1 seconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 9 sheets defined 44.0% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 97 through 105 removed outlier: 3.943A pdb=" N PHE A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 128 Processing helix chain 'A' and resid 136 through 170 removed outlier: 3.902A pdb=" N PHE A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 292 through 321 Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 345 through 363 removed outlier: 3.757A pdb=" N LYS A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 removed outlier: 3.518A pdb=" N GLU A 374 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU A 376 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 460 through 472 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 542 through 556 Processing helix chain 'A' and resid 608 through 617 Processing helix chain 'A' and resid 630 through 640 Processing helix chain 'A' and resid 650 through 657 Processing helix chain 'A' and resid 661 through 663 No H-bonds generated for 'chain 'A' and resid 661 through 663' Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 676 through 681 removed outlier: 3.580A pdb=" N ASP A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 693 Processing helix chain 'A' and resid 704 through 716 Processing helix chain 'A' and resid 728 through 736 Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 749 through 754 Processing helix chain 'A' and resid 764 through 804 removed outlier: 3.635A pdb=" N LYS A 791 " --> pdb=" O THR A 788 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 793 " --> pdb=" O THR A 790 " (cutoff:3.500A) Proline residue: A 794 - end of helix removed outlier: 4.594A pdb=" N THR A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) Proline residue: A 798 - end of helix Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 825 through 833 removed outlier: 3.608A pdb=" N LEU A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA A 832 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 842 No H-bonds generated for 'chain 'A' and resid 840 through 842' Processing helix chain 'A' and resid 856 through 864 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 889 through 892 No H-bonds generated for 'chain 'A' and resid 889 through 892' Processing helix chain 'A' and resid 896 through 900 Processing helix chain 'A' and resid 917 through 947 removed outlier: 3.622A pdb=" N ALA A 941 " --> pdb=" O MET A 937 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 947 " --> pdb=" O VAL A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 956 No H-bonds generated for 'chain 'A' and resid 953 through 956' Processing helix chain 'A' and resid 962 through 980 Processing helix chain 'A' and resid 984 through 987 No H-bonds generated for 'chain 'A' and resid 984 through 987' Processing helix chain 'A' and resid 995 through 1000 Processing helix chain 'A' and resid 1002 through 1021 Processing helix chain 'A' and resid 1026 through 1031 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 34 through 65 Processing helix chain 'B' and resid 103 through 119 removed outlier: 4.557A pdb=" N GLY B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 removed outlier: 6.664A pdb=" N ASN B 161 " --> pdb=" O MET B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing sheet with id= A, first strand: chain 'A' and resid 177 through 182 Processing sheet with id= B, first strand: chain 'A' and resid 199 through 203 Processing sheet with id= C, first strand: chain 'A' and resid 234 through 236 removed outlier: 4.403A pdb=" N CYS A 220 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 260 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASP A 223 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N CYS A 258 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.454A pdb=" N VAL A 381 " --> pdb=" O ALA A 722 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N THR A 724 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N CYS A 383 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG A 621 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N SER A 384 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A 623 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 405 through 408 removed outlier: 6.834A pdb=" N SER A 599 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU A 400 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A 597 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE A 402 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 9.981A pdb=" N ALA A 595 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE A 564 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU A 597 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 562 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER A 599 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG A 560 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS A 512 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS A 487 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR A 503 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYS A 485 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 671 through 675 removed outlier: 6.643A pdb=" N GLU A 696 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE A 674 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 698 " --> pdb=" O ILE A 674 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 211 through 214 removed outlier: 6.140A pdb=" N ARG A 213 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL A 267 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 82 through 85 Processing sheet with id= I, first strand: chain 'B' and resid 94 through 99 removed outlier: 4.493A pdb=" N LEU B 94 " --> pdb=" O GLU B 283 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1143 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1623 1.29 - 1.42: 2593 1.42 - 1.55: 6056 1.55 - 1.68: 17 1.68 - 1.82: 101 Bond restraints: 10390 Sorted by residual: bond pdb=" F3 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.529 1.764 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" F2 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.535 1.753 -0.218 2.00e-02 2.50e+03 1.18e+02 bond pdb=" F1 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.542 1.752 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C16APWI A1106 " pdb=" C17APWI A1106 " ideal model delta sigma weight residual 1.527 1.341 0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" C14APWI A1106 " pdb=" C15APWI A1106 " ideal model delta sigma weight residual 1.526 1.341 0.185 2.00e-02 2.50e+03 8.52e+01 ... (remaining 10385 not shown) Histogram of bond angle deviations from ideal: 82.90 - 100.40: 14 100.40 - 117.90: 7832 117.90 - 135.41: 6232 135.41 - 152.91: 0 152.91 - 170.41: 4 Bond angle restraints: 14082 Sorted by residual: angle pdb=" C19 CLR B 306 " pdb=" C10 CLR B 306 " pdb=" C9 CLR B 306 " ideal model delta sigma weight residual 111.86 84.38 27.48 3.00e+00 1.11e-01 8.39e+01 angle pdb=" C1 CLR B 306 " pdb=" C10 CLR B 306 " pdb=" C19 CLR B 306 " ideal model delta sigma weight residual 109.60 82.90 26.70 3.00e+00 1.11e-01 7.92e+01 angle pdb=" C5 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 111.64 86.86 24.78 3.00e+00 1.11e-01 6.82e+01 angle pdb=" C19 CLR B 306 " pdb=" C10 CLR B 306 " pdb=" C5 CLR B 306 " ideal model delta sigma weight residual 108.37 83.64 24.73 3.00e+00 1.11e-01 6.79e+01 angle pdb=" C6 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 109.11 86.89 22.22 3.00e+00 1.11e-01 5.48e+01 ... (remaining 14077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 6098 35.55 - 71.10: 269 71.10 - 106.65: 27 106.65 - 142.19: 5 142.19 - 177.74: 7 Dihedral angle restraints: 6406 sinusoidal: 2773 harmonic: 3633 Sorted by residual: dihedral pdb=" C19 CLR B 306 " pdb=" C10 CLR B 306 " pdb=" C5 CLR B 306 " pdb=" C6 CLR B 306 " ideal model delta sinusoidal sigma weight residual 252.42 74.68 177.74 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C13BPWI A1106 " pdb=" C14BPWI A1106 " pdb=" O01BPWI A1106 " pdb=" C15BPWI A1106 " ideal model delta sinusoidal sigma weight residual -177.81 -0.10 -177.71 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C11 CLR B 306 " pdb=" C10 CLR B 306 " pdb=" C9 CLR B 306 " pdb=" C19 CLR B 306 " ideal model delta sinusoidal sigma weight residual 51.90 -124.69 176.59 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 6403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.358: 1573 0.358 - 0.716: 0 0.716 - 1.074: 0 1.074 - 1.432: 0 1.432 - 1.790: 1 Chirality restraints: 1574 Sorted by residual: chirality pdb=" C10 CLR B 306 " pdb=" C1 CLR B 306 " pdb=" C5 CLR B 306 " pdb=" C9 CLR B 306 " both_signs ideal model delta sigma weight residual False -2.85 -1.06 -1.79 2.00e-01 2.50e+01 8.01e+01 chirality pdb=" C1 NAG B 303 " pdb=" ND2 ASN B 130 " pdb=" C2 NAG B 303 " pdb=" O5 NAG B 303 " both_signs ideal model delta sigma weight residual False -2.40 -2.74 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C1 NAG B 302 " pdb=" ND2 ASN B 99 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1571 not shown) Planarity restraints: 1780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 130 " 0.216 2.00e-02 2.50e+03 1.94e-01 4.71e+02 pdb=" CG ASN B 130 " -0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN B 130 " -0.148 2.00e-02 2.50e+03 pdb=" ND2 ASN B 130 " -0.230 2.00e-02 2.50e+03 pdb=" C1 NAG B 303 " 0.244 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01APWI A1106 " 0.006 2.00e-02 2.50e+03 5.57e-02 6.98e+01 pdb=" C07APWI A1106 " 0.000 2.00e-02 2.50e+03 pdb=" C08APWI A1106 " 0.048 2.00e-02 2.50e+03 pdb=" C09APWI A1106 " 0.101 2.00e-02 2.50e+03 pdb=" C10APWI A1106 " 0.043 2.00e-02 2.50e+03 pdb=" C11APWI A1106 " -0.014 2.00e-02 2.50e+03 pdb=" C12APWI A1106 " -0.027 2.00e-02 2.50e+03 pdb=" C13APWI A1106 " -0.089 2.00e-02 2.50e+03 pdb="CL2 APWI A1106 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01APWI A1106 " -0.028 2.00e-02 2.50e+03 4.56e-02 4.16e+01 pdb=" C02APWI A1106 " -0.045 2.00e-02 2.50e+03 pdb=" C03APWI A1106 " -0.016 2.00e-02 2.50e+03 pdb=" C04APWI A1106 " -0.001 2.00e-02 2.50e+03 pdb=" C05APWI A1106 " -0.026 2.00e-02 2.50e+03 pdb=" C06APWI A1106 " -0.036 2.00e-02 2.50e+03 pdb=" C07APWI A1106 " 0.089 2.00e-02 2.50e+03 pdb="CL1 APWI A1106 " 0.062 2.00e-02 2.50e+03 ... (remaining 1777 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 129 2.56 - 3.14: 8449 3.14 - 3.73: 17992 3.73 - 4.31: 26118 4.31 - 4.90: 39941 Nonbonded interactions: 92629 Sorted by model distance: nonbonded pdb=" O THR A 387 " pdb="MG MG A1102 " model vdw 1.973 2.170 nonbonded pdb="MG MG A1102 " pdb=" O HOH A1204 " model vdw 2.021 2.170 nonbonded pdb=" F2 BFD A 385 " pdb="MG MG A1102 " model vdw 2.104 2.120 nonbonded pdb=" CE LYS B 135 " pdb=" O HOH B 463 " model vdw 2.141 3.440 nonbonded pdb=" F1 BFD A 385 " pdb=" OG1 THR A 626 " model vdw 2.152 2.390 ... (remaining 92624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 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: 4.840 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: 19.000 Check model and map are aligned: 0.220 Set scattering table: 0.100 Process input model: 34.250 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.008 0.235 10390 Z= 0.572 Angle : 1.110 27.477 14082 Z= 0.475 Chirality : 0.066 1.790 1574 Planarity : 0.006 0.125 1777 Dihedral : 20.132 177.742 4057 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.73 % Allowed : 17.78 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.17 (0.24), residues: 1244 helix: 1.65 (0.22), residues: 579 sheet: 0.43 (0.41), residues: 155 loop : -0.04 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 997 HIS 0.003 0.001 HIS B 227 PHE 0.022 0.002 PHE A 333 TYR 0.017 0.001 TYR A 802 ARG 0.006 0.000 ARG A1020 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 29 residues processed: 145 average time/residue: 1.5006 time to fit residues: 232.6512 Evaluate side-chains 145 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 29 residues processed: 0 time to fit residues: 1.4761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 0.3980 chunk 50 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.0436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10390 Z= 0.156 Angle : 0.677 29.922 14082 Z= 0.308 Chirality : 0.063 1.811 1574 Planarity : 0.005 0.056 1777 Dihedral : 16.903 175.433 1764 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.70 % Allowed : 14.86 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.17 (0.24), residues: 1244 helix: 1.65 (0.22), residues: 585 sheet: 0.47 (0.41), residues: 154 loop : -0.07 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 997 HIS 0.003 0.001 HIS A 53 PHE 0.014 0.001 PHE A 161 TYR 0.012 0.001 TYR A 878 ARG 0.003 0.000 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 119 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 31 residues processed: 160 average time/residue: 1.4380 time to fit residues: 246.6417 Evaluate side-chains 147 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 27 residues processed: 4 average time/residue: 0.9495 time to fit residues: 5.8612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.0553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10390 Z= 0.200 Angle : 0.706 30.339 14082 Z= 0.325 Chirality : 0.064 1.829 1574 Planarity : 0.005 0.054 1777 Dihedral : 16.892 176.142 1764 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.23 % Allowed : 14.96 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.07 (0.24), residues: 1244 helix: 1.56 (0.22), residues: 585 sheet: 0.40 (0.41), residues: 155 loop : -0.11 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 997 HIS 0.004 0.001 HIS B 227 PHE 0.020 0.002 PHE A 970 TYR 0.014 0.002 TYR A 802 ARG 0.002 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 117 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 36 residues processed: 155 average time/residue: 1.4696 time to fit residues: 243.3304 Evaluate side-chains 151 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 115 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 30 residues processed: 6 average time/residue: 0.8076 time to fit residues: 6.8679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 113 optimal weight: 0.0870 chunk 119 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 665 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10390 Z= 0.165 Angle : 0.683 30.180 14082 Z= 0.310 Chirality : 0.063 1.827 1574 Planarity : 0.005 0.053 1777 Dihedral : 16.674 176.577 1764 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.33 % Allowed : 14.68 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.09 (0.24), residues: 1244 helix: 1.55 (0.22), residues: 587 sheet: 0.39 (0.40), residues: 155 loop : -0.06 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 997 HIS 0.003 0.001 HIS A 53 PHE 0.013 0.001 PHE A 970 TYR 0.013 0.001 TYR A 802 ARG 0.002 0.000 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 116 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 34 residues processed: 156 average time/residue: 1.4645 time to fit residues: 244.3296 Evaluate side-chains 149 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 1.242 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 31 residues processed: 3 average time/residue: 0.1629 time to fit residues: 2.4561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 0.2980 chunk 49 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 61 optimal weight: 0.0060 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 665 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10390 Z= 0.165 Angle : 0.683 30.180 14082 Z= 0.310 Chirality : 0.063 1.827 1574 Planarity : 0.005 0.053 1777 Dihedral : 16.674 176.577 1764 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.01 % Allowed : 16.18 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.09 (0.24), residues: 1244 helix: 1.55 (0.22), residues: 587 sheet: 0.39 (0.40), residues: 155 loop : -0.06 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 997 HIS 0.003 0.001 HIS A 53 PHE 0.013 0.001 PHE A 970 TYR 0.013 0.001 TYR A 802 ARG 0.002 0.000 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 31 residues processed: 147 average time/residue: 1.5110 time to fit residues: 237.6406 Evaluate side-chains 146 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 1.401 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 31 residues processed: 0 time to fit residues: 1.6677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.0980 chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10390 Z= 0.165 Angle : 0.683 30.180 14082 Z= 0.310 Chirality : 0.063 1.827 1574 Planarity : 0.005 0.053 1777 Dihedral : 16.674 176.577 1764 Min Nonbonded Distance : 1.587 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.92 % Allowed : 16.37 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.09 (0.24), residues: 1244 helix: 1.55 (0.22), residues: 587 sheet: 0.39 (0.40), residues: 155 loop : -0.06 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 997 HIS 0.003 0.001 HIS A 53 PHE 0.013 0.001 PHE A 970 TYR 0.013 0.001 TYR A 802 ARG 0.002 0.000 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 31 residues processed: 146 average time/residue: 1.5149 time to fit residues: 236.1481 Evaluate side-chains 146 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 31 residues processed: 0 time to fit residues: 1.6303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10390 Z= 0.198 Angle : 0.698 30.220 14082 Z= 0.320 Chirality : 0.064 1.834 1574 Planarity : 0.005 0.052 1777 Dihedral : 16.682 176.466 1764 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.48 % Allowed : 15.62 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.08 (0.24), residues: 1244 helix: 1.54 (0.22), residues: 587 sheet: 0.39 (0.40), residues: 155 loop : -0.06 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 997 HIS 0.003 0.001 HIS A 53 PHE 0.024 0.002 PHE A 970 TYR 0.013 0.001 TYR A 802 ARG 0.005 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 118 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 31 residues processed: 152 average time/residue: 1.5048 time to fit residues: 244.7436 Evaluate side-chains 147 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 30 residues processed: 1 average time/residue: 0.1007 time to fit residues: 1.8745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.0634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10390 Z= 0.198 Angle : 0.698 30.220 14082 Z= 0.320 Chirality : 0.064 1.834 1574 Planarity : 0.005 0.052 1777 Dihedral : 16.682 176.466 1764 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.82 % Allowed : 15.99 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.08 (0.24), residues: 1244 helix: 1.54 (0.22), residues: 587 sheet: 0.39 (0.40), residues: 155 loop : -0.06 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 997 HIS 0.003 0.001 HIS A 53 PHE 0.024 0.002 PHE A 970 TYR 0.013 0.001 TYR A 802 ARG 0.005 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 30 residues processed: 146 average time/residue: 1.5748 time to fit residues: 245.4741 Evaluate side-chains 146 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 30 residues processed: 0 time to fit residues: 1.6279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10390 Z= 0.198 Angle : 0.698 30.220 14082 Z= 0.320 Chirality : 0.064 1.834 1574 Planarity : 0.005 0.052 1777 Dihedral : 16.682 176.466 1764 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.82 % Allowed : 16.18 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.08 (0.24), residues: 1244 helix: 1.54 (0.22), residues: 587 sheet: 0.39 (0.40), residues: 155 loop : -0.06 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 997 HIS 0.003 0.001 HIS A 53 PHE 0.024 0.002 PHE A 970 TYR 0.013 0.001 TYR A 802 ARG 0.005 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 30 residues processed: 146 average time/residue: 1.5463 time to fit residues: 241.6946 Evaluate side-chains 146 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 30 residues processed: 0 time to fit residues: 1.6118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 0.0010 chunk 78 optimal weight: 5.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 10390 Z= 0.189 Angle : 0.696 30.224 14082 Z= 0.319 Chirality : 0.064 1.831 1574 Planarity : 0.005 0.052 1777 Dihedral : 16.707 176.535 1764 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.92 % Allowed : 16.09 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.08 (0.24), residues: 1244 helix: 1.53 (0.22), residues: 587 sheet: 0.39 (0.40), residues: 155 loop : -0.06 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 997 HIS 0.003 0.001 HIS A 53 PHE 0.016 0.002 PHE A 970 TYR 0.013 0.001 TYR A 802 ARG 0.005 0.000 ARG A 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 31 residues processed: 146 average time/residue: 1.5588 time to fit residues: 243.2227 Evaluate side-chains 147 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 30 residues processed: 1 average time/residue: 1.3262 time to fit residues: 3.1713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.168081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120765 restraints weight = 9196.869| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.58 r_work: 0.3138 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 10390 Z= 0.189 Angle : 0.696 30.224 14082 Z= 0.319 Chirality : 0.064 1.831 1574 Planarity : 0.005 0.052 1777 Dihedral : 16.707 176.535 1764 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.82 % Allowed : 16.18 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.08 (0.24), residues: 1244 helix: 1.53 (0.22), residues: 587 sheet: 0.39 (0.40), residues: 155 loop : -0.06 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 997 HIS 0.003 0.001 HIS A 53 PHE 0.016 0.002 PHE A 970 TYR 0.013 0.001 TYR A 802 ARG 0.005 0.000 ARG A 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4996.06 seconds wall clock time: 89 minutes 32.15 seconds (5372.15 seconds total)