Starting phenix.real_space_refine on Mon Mar 18 03:40:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/03_2024/8wa5_37391_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/03_2024/8wa5_37391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/03_2024/8wa5_37391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/03_2024/8wa5_37391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/03_2024/8wa5_37391_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa5_37391/03_2024/8wa5_37391_updated.pdb" } resolution = 2.51 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= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9918 atoms to isotropic. 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 K 3 8.98 5 Al 1 5.89 5 P 1 5.49 5 Mg 1 5.21 5 S 66 5.16 5 C 6368 2.51 5 N 1648 2.21 5 O 1837 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 459": "OD1" <-> "OD2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "A PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 610": "OD1" <-> "OD2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A ASP 652": "OD1" <-> "OD2" Residue "A ASP 681": "OD1" <-> "OD2" Residue "A ASP 749": "OD1" <-> "OD2" Residue "A GLU 772": "OE1" <-> "OE2" Residue "A ASP 779": "OD1" <-> "OD2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A TYR 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A GLU 856": "OE1" <-> "OE2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9929 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7662 Classifications: {'peptide': 987} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 939} 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: "B" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2100 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 240} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 37 Unusual residues: {' K': 3, ' MG': 1, 'ALF': 1, 'CLR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 124 Unusual residues: {'NAG': 5, 'PCW': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 5.90, per 1000 atoms: 0.59 Number of scatterers: 9929 At special positions: 0 Unit cell: (82.17, 87.98, 174.3, 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) K 3 19.00 S 66 16.00 P 1 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1837 8.00 N 1648 7.00 C 6368 6.00 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=1, symmetry=0 Links applied NAG-ASN " NAG B 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 161 " " NAG B 304 " - " ASN B 221 " " NAG B 305 " - " ASN B 193 " " NAG B 306 " - " ASN B 146 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.7 seconds 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 10 sheets defined 45.6% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 108 through 129 Processing helix chain 'A' and resid 136 through 159 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 225 through 228 No H-bonds generated for 'chain 'A' and resid 225 through 228' 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 323 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 345 through 363 removed outlier: 3.699A pdb=" N LYS A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.710A pdb=" N GLU A 374 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 375 " --> pdb=" O ALA A 372 " (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 481 Processing helix chain 'A' and resid 520 through 526 Processing helix chain 'A' and resid 541 through 557 removed outlier: 3.826A pdb=" N LEU A 557 " --> pdb=" O SER A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' 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 Processing helix chain 'A' and resid 684 through 693 Processing helix chain 'A' and resid 704 through 717 removed outlier: 3.626A pdb=" N LEU A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) 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 766 through 805 removed outlier: 4.117A pdb=" N LYS A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN A 792 " --> pdb=" O THR A 788 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE A 793 " --> pdb=" O LEU A 789 " (cutoff:3.500A) Proline residue: A 794 - end of helix Proline residue: A 798 - end of helix Processing helix chain 'A' and resid 813 through 821 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: 4.494A pdb=" N ALA A 832 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 4.783A 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 884 removed outlier: 3.921A pdb=" N ILE A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 869 " --> pdb=" O GLN A 865 " (cutoff:3.500A) 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 899 No H-bonds generated for 'chain 'A' and resid 896 through 899' Processing helix chain 'A' and resid 917 through 947 removed outlier: 3.821A 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 1021 Proline residue: A1001 - end of helix removed outlier: 4.640A pdb=" N PHE A1004 " --> pdb=" O VAL A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1030 Processing helix chain 'B' and resid 34 through 65 Processing helix chain 'B' and resid 103 through 120 removed outlier: 3.955A pdb=" N ALA B 107 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLY B 108 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 118 " --> pdb=" O ARG B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 156 through 163 removed outlier: 6.665A 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 178 through 180 Processing sheet with id= B, first strand: chain 'A' and resid 199 through 202 Processing sheet with id= C, first strand: chain 'A' and resid 220 through 222 removed outlier: 4.430A pdb=" N CYS A 220 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 365 through 367 removed outlier: 3.541A pdb=" N ILE A 739 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 743 " --> pdb=" O GLY A 725 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 381 " --> pdb=" O ALA A 722 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N THR A 724 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N CYS A 383 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG A 621 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER A 384 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 6.635A 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: 6.869A pdb=" N SER A 599 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A 400 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 597 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE A 402 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N ALA A 595 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE A 564 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU A 597 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A 562 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER A 599 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ARG A 560 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR A 503 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS A 485 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 535 through 538 removed outlier: 7.044A pdb=" N LEU A 592 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE A 530 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE A 594 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE A 532 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 671 through 674 removed outlier: 6.613A pdb=" N GLU A 696 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE A 674 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 698 " --> pdb=" O ILE A 674 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 211 through 214 removed outlier: 6.014A pdb=" N ARG A 213 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL A 267 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 82 through 85 Processing sheet with id= J, first strand: chain 'B' and resid 95 through 99 removed outlier: 8.293A pdb=" N ILE B 96 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LYS B 285 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N TYR B 98 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS B 287 " --> pdb=" O TYR B 98 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1203 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: 3.52 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3173 1.34 - 1.46: 1696 1.46 - 1.58: 5176 1.58 - 1.70: 2 1.70 - 1.82: 99 Bond restraints: 10146 Sorted by residual: bond pdb=" C11 PCW B 301 " pdb=" O3 PCW B 301 " ideal model delta sigma weight residual 1.326 1.450 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C31 PCW B 301 " pdb=" O2 PCW B 301 " ideal model delta sigma weight residual 1.333 1.454 -0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" F3 ALF A1104 " pdb="AL ALF A1104 " ideal model delta sigma weight residual 1.685 1.800 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" F1 ALF A1104 " pdb="AL ALF A1104 " ideal model delta sigma weight residual 1.684 1.799 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" F2 ALF A1104 " pdb="AL ALF A1104 " ideal model delta sigma weight residual 1.685 1.798 -0.113 2.00e-02 2.50e+03 3.20e+01 ... (remaining 10141 not shown) Histogram of bond angle deviations from ideal: 89.51 - 107.54: 406 107.54 - 125.58: 13225 125.58 - 143.62: 153 143.62 - 161.66: 0 161.66 - 179.70: 2 Bond angle restraints: 13786 Sorted by residual: angle pdb=" F1 ALF A1104 " pdb="AL ALF A1104 " pdb=" F2 ALF A1104 " ideal model delta sigma weight residual 108.68 179.48 -70.80 3.00e+00 1.11e-01 5.57e+02 angle pdb=" F3 ALF A1104 " pdb="AL ALF A1104 " pdb=" F4 ALF A1104 " ideal model delta sigma weight residual 109.63 179.70 -70.07 3.00e+00 1.11e-01 5.46e+02 angle pdb=" F2 ALF A1104 " pdb="AL ALF A1104 " pdb=" F3 ALF A1104 " ideal model delta sigma weight residual 109.59 89.70 19.89 3.00e+00 1.11e-01 4.40e+01 angle pdb=" F2 ALF A1104 " pdb="AL ALF A1104 " pdb=" F4 ALF A1104 " ideal model delta sigma weight residual 110.21 90.39 19.82 3.00e+00 1.11e-01 4.36e+01 angle pdb=" F1 ALF A1104 " pdb="AL ALF A1104 " pdb=" F4 ALF A1104 " ideal model delta sigma weight residual 109.02 89.51 19.51 3.00e+00 1.11e-01 4.23e+01 ... (remaining 13781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.65: 6002 34.65 - 69.29: 192 69.29 - 103.94: 16 103.94 - 138.59: 0 138.59 - 173.24: 1 Dihedral angle restraints: 6211 sinusoidal: 2583 harmonic: 3628 Sorted by residual: dihedral pdb=" N PCW B 301 " pdb=" C4 PCW B 301 " pdb=" C5 PCW B 301 " pdb=" O4P PCW B 301 " ideal model delta sinusoidal sigma weight residual -66.66 106.58 -173.24 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA LEU A 376 " pdb=" C LEU A 376 " pdb=" N GLY A 377 " pdb=" CA GLY A 377 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE A 764 " pdb=" C PHE A 764 " pdb=" N ALA A 765 " pdb=" CA ALA A 765 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 6208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1421 0.074 - 0.148: 143 0.148 - 0.222: 4 0.222 - 0.296: 2 0.296 - 0.370: 1 Chirality restraints: 1571 Sorted by residual: chirality pdb=" C1 NAG B 304 " pdb=" ND2 ASN B 221 " pdb=" C2 NAG B 304 " pdb=" O5 NAG B 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C1 NAG B 306 " pdb=" ND2 ASN B 146 " pdb=" C2 NAG B 306 " pdb=" O5 NAG B 306 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ASN B 221 " pdb=" N ASN B 221 " pdb=" C ASN B 221 " pdb=" CB ASN B 221 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1568 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 302 " -0.270 2.00e-02 2.50e+03 2.26e-01 6.40e+02 pdb=" C7 NAG B 302 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 302 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG B 302 " 0.382 2.00e-02 2.50e+03 pdb=" O7 NAG B 302 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 303 " -0.175 2.00e-02 2.50e+03 1.45e-01 2.61e+02 pdb=" C7 NAG B 303 " 0.049 2.00e-02 2.50e+03 pdb=" C8 NAG B 303 " -0.129 2.00e-02 2.50e+03 pdb=" N2 NAG B 303 " 0.233 2.00e-02 2.50e+03 pdb=" O7 NAG B 303 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 304 " 0.056 2.00e-02 2.50e+03 4.56e-02 2.60e+01 pdb=" C7 NAG B 304 " -0.015 2.00e-02 2.50e+03 pdb=" C8 NAG B 304 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG B 304 " -0.072 2.00e-02 2.50e+03 pdb=" O7 NAG B 304 " -0.011 2.00e-02 2.50e+03 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.57: 55 2.57 - 3.21: 9104 3.21 - 3.85: 20313 3.85 - 4.50: 27938 4.50 - 5.14: 43897 Nonbonded interactions: 101307 Sorted by model distance: nonbonded pdb=" F2 ALF A1104 " pdb="MG MG A1105 " model vdw 1.926 2.120 nonbonded pdb=" OD1 ASP A 726 " pdb="MG MG A1105 " model vdw 2.003 2.170 nonbonded pdb=" O THR A 387 " pdb="MG MG A1105 " model vdw 2.004 2.170 nonbonded pdb=" OD2 ASP A 385 " pdb="MG MG A1105 " model vdw 2.153 2.170 nonbonded pdb=" O PRO B 145 " pdb=" OG1 THR B 148 " model vdw 2.200 2.440 ... (remaining 101302 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=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: 6.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 15.570 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.670 Find NCS groups from input model: 0.290 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 0.004 0.124 10146 Z= 0.286 Angle : 1.100 70.797 13786 Z= 0.427 Chirality : 0.044 0.370 1571 Planarity : 0.008 0.226 1761 Dihedral : 16.205 173.237 3864 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.85 % Allowed : 15.99 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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 (0.23), residues: 1245 helix: 1.94 (0.21), residues: 572 sheet: -0.13 (0.38), residues: 177 loop : -0.19 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 401 HIS 0.003 0.001 HIS A 629 PHE 0.025 0.001 PHE A 300 TYR 0.016 0.001 TYR A 802 ARG 0.010 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.6777 (mtm-85) cc_final: 0.6537 (mtm-85) REVERT: A 677 MET cc_start: 0.6969 (mmp) cc_final: 0.6715 (mmt) outliers start: 9 outliers final: 6 residues processed: 126 average time/residue: 1.4193 time to fit residues: 190.1918 Evaluate side-chains 121 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain B residue 35 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10146 Z= 0.216 Angle : 0.789 31.089 13786 Z= 0.337 Chirality : 0.045 0.448 1571 Planarity : 0.005 0.048 1761 Dihedral : 8.049 166.056 1575 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.33 % Allowed : 12.51 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.01 (0.23), residues: 1245 helix: 1.58 (0.21), residues: 588 sheet: 0.10 (0.42), residues: 139 loop : -0.13 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 915 HIS 0.005 0.001 HIS A 629 PHE 0.028 0.002 PHE A 300 TYR 0.019 0.001 TYR A 802 ARG 0.007 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 112 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 54 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6265 (mt0) REVERT: A 103 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7600 (ttp-170) REVERT: A 171 LYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6583 (ttmt) REVERT: A 216 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7311 (pt0) REVERT: A 414 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8132 (p0) REVERT: A 560 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6965 (mtm-85) REVERT: A 650 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.7987 (p) REVERT: A 677 MET cc_start: 0.6976 (mmp) cc_final: 0.6740 (mmt) REVERT: A 772 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: A 933 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8645 (tp) REVERT: B 115 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6690 (ptt90) REVERT: B 287 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8292 (tttp) outliers start: 46 outliers final: 9 residues processed: 143 average time/residue: 1.4000 time to fit residues: 213.0553 Evaluate side-chains 126 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 111 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 865 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10146 Z= 0.276 Angle : 0.809 31.253 13786 Z= 0.352 Chirality : 0.046 0.304 1571 Planarity : 0.005 0.053 1761 Dihedral : 8.066 170.659 1571 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.05 % Allowed : 13.17 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 0.87 (0.23), residues: 1245 helix: 1.40 (0.21), residues: 586 sheet: 0.06 (0.41), residues: 150 loop : -0.13 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 106 HIS 0.006 0.001 HIS A 629 PHE 0.030 0.002 PHE A 300 TYR 0.016 0.002 TYR A 802 ARG 0.008 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 117 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6368 (pm20) REVERT: A 202 MET cc_start: 0.7297 (mmp) cc_final: 0.7003 (mtm) REVERT: A 216 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7336 (pt0) REVERT: A 414 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8285 (p0) REVERT: A 442 PHE cc_start: 0.5665 (OUTLIER) cc_final: 0.4332 (t80) REVERT: A 560 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.7023 (mtm-85) REVERT: A 650 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.7989 (p) REVERT: A 677 MET cc_start: 0.7019 (mmp) cc_final: 0.6790 (mmt) REVERT: A 772 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: A 844 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7447 (mtp-110) REVERT: A 933 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8631 (tp) REVERT: B 84 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8584 (pt) REVERT: B 115 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6688 (ptt90) REVERT: B 135 LYS cc_start: 0.8121 (ptmm) cc_final: 0.7153 (ptmt) outliers start: 43 outliers final: 10 residues processed: 146 average time/residue: 1.4829 time to fit residues: 230.0970 Evaluate side-chains 137 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 183 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10146 Z= 0.178 Angle : 0.761 30.530 13786 Z= 0.320 Chirality : 0.043 0.303 1571 Planarity : 0.004 0.045 1761 Dihedral : 7.736 167.325 1570 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.76 % Allowed : 13.64 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 0.97 (0.23), residues: 1245 helix: 1.57 (0.22), residues: 584 sheet: 0.05 (0.40), residues: 152 loop : -0.17 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 401 HIS 0.004 0.001 HIS A 629 PHE 0.028 0.001 PHE A 300 TYR 0.014 0.001 TYR A 802 ARG 0.008 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 110 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6544 (mt0) REVERT: A 171 LYS cc_start: 0.7282 (ttmt) cc_final: 0.7026 (ttmm) REVERT: A 176 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6355 (pm20) REVERT: A 203 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7060 (ttpm) REVERT: A 414 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8309 (p0) REVERT: A 442 PHE cc_start: 0.5816 (OUTLIER) cc_final: 0.4308 (t80) REVERT: A 470 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6927 (tp30) REVERT: A 677 MET cc_start: 0.7008 (mmp) cc_final: 0.6767 (mmt) REVERT: A 772 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: A 844 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7422 (mtt-85) REVERT: B 84 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8404 (pt) REVERT: B 115 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6639 (ptt90) REVERT: B 135 LYS cc_start: 0.8127 (ptmm) cc_final: 0.7159 (ptmt) outliers start: 40 outliers final: 17 residues processed: 134 average time/residue: 1.4724 time to fit residues: 209.9180 Evaluate side-chains 131 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG 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: 1.9990 chunk 1 optimal weight: 0.0270 chunk 89 optimal weight: 0.0870 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 0.0050 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 61 optimal weight: 0.0980 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.4432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10146 Z= 0.148 Angle : 0.739 30.319 13786 Z= 0.307 Chirality : 0.042 0.263 1571 Planarity : 0.004 0.043 1761 Dihedral : 7.484 166.619 1570 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.29 % Allowed : 14.58 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.12 (0.24), residues: 1245 helix: 1.69 (0.22), residues: 588 sheet: 0.23 (0.40), residues: 152 loop : -0.14 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 401 HIS 0.003 0.001 HIS A 629 PHE 0.028 0.001 PHE A 300 TYR 0.012 0.001 TYR A 802 ARG 0.009 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 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: 35 poor density : 112 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6531 (mt0) REVERT: A 171 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6974 (ttmm) REVERT: A 202 MET cc_start: 0.7427 (ttm) cc_final: 0.7167 (ttm) REVERT: A 414 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8310 (p0) REVERT: A 442 PHE cc_start: 0.5736 (OUTLIER) cc_final: 0.4267 (t80) REVERT: A 470 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6965 (tp30) REVERT: A 521 GLU cc_start: 0.7032 (pm20) cc_final: 0.6767 (pm20) REVERT: A 772 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: A 844 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7427 (mtt-85) REVERT: A 1031 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8474 (mt) REVERT: B 78 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8148 (mmtm) REVERT: B 115 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6563 (ptt90) outliers start: 35 outliers final: 14 residues processed: 135 average time/residue: 1.4933 time to fit residues: 214.1985 Evaluate side-chains 134 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 115 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.0870 chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10146 Z= 0.157 Angle : 0.740 30.375 13786 Z= 0.308 Chirality : 0.042 0.243 1571 Planarity : 0.004 0.043 1761 Dihedral : 7.293 166.464 1570 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.29 % Allowed : 15.33 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.18 (0.24), residues: 1245 helix: 1.74 (0.22), residues: 585 sheet: 0.34 (0.40), residues: 152 loop : -0.13 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 401 HIS 0.003 0.001 HIS A 629 PHE 0.028 0.001 PHE A 300 TYR 0.014 0.001 TYR A 802 ARG 0.010 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 108 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6930 (ttmm) REVERT: A 176 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6360 (pm20) REVERT: A 202 MET cc_start: 0.7334 (ttm) cc_final: 0.7100 (ttm) REVERT: A 414 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8301 (p0) REVERT: A 442 PHE cc_start: 0.5768 (OUTLIER) cc_final: 0.4293 (t80) REVERT: A 470 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6969 (tp30) REVERT: A 521 GLU cc_start: 0.7039 (pm20) cc_final: 0.6819 (pm20) REVERT: A 650 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.7928 (m) REVERT: A 772 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: A 844 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7431 (mtt-85) REVERT: A 1031 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8470 (mt) REVERT: B 78 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8146 (mmtm) outliers start: 35 outliers final: 15 residues processed: 129 average time/residue: 1.5123 time to fit residues: 208.1534 Evaluate side-chains 127 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 141 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10146 Z= 0.216 Angle : 0.771 30.857 13786 Z= 0.327 Chirality : 0.044 0.239 1571 Planarity : 0.004 0.045 1761 Dihedral : 7.407 165.572 1570 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.48 % Allowed : 15.43 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.06 (0.23), residues: 1245 helix: 1.60 (0.22), residues: 585 sheet: 0.22 (0.39), residues: 152 loop : -0.12 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 401 HIS 0.004 0.001 HIS A 629 PHE 0.029 0.002 PHE A 300 TYR 0.015 0.001 TYR A 802 ARG 0.013 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 106 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7664 (mm-40) REVERT: A 171 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.7017 (ttmm) REVERT: A 176 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6361 (pm20) REVERT: A 442 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.4367 (t80) REVERT: A 521 GLU cc_start: 0.7028 (pm20) cc_final: 0.6716 (pm20) REVERT: A 560 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6917 (mtm-85) REVERT: A 650 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.7938 (m) REVERT: A 772 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: A 844 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7452 (mtp-110) REVERT: A 1031 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8470 (mt) outliers start: 37 outliers final: 15 residues processed: 130 average time/residue: 1.4562 time to fit residues: 201.4333 Evaluate side-chains 128 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 141 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 0.0020 chunk 108 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10146 Z= 0.162 Angle : 0.756 30.363 13786 Z= 0.315 Chirality : 0.043 0.236 1571 Planarity : 0.004 0.043 1761 Dihedral : 7.237 165.039 1570 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.10 % Allowed : 15.71 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.14 (0.24), residues: 1245 helix: 1.69 (0.22), residues: 585 sheet: 0.27 (0.39), residues: 155 loop : -0.11 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 401 HIS 0.003 0.001 HIS A 629 PHE 0.028 0.001 PHE A 300 TYR 0.013 0.001 TYR A 802 ARG 0.011 0.000 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 106 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6648 (mt0) REVERT: A 171 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.7011 (ttmm) REVERT: A 176 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.6341 (pm20) REVERT: A 442 PHE cc_start: 0.6145 (OUTLIER) cc_final: 0.4373 (t80) REVERT: A 521 GLU cc_start: 0.7062 (pm20) cc_final: 0.6747 (pm20) REVERT: A 560 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6878 (mtm-85) REVERT: A 650 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.7911 (m) REVERT: A 772 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: A 844 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7406 (mtt-85) REVERT: A 1031 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8463 (mt) REVERT: B 78 LYS cc_start: 0.8415 (mmpt) cc_final: 0.8158 (mmtm) outliers start: 33 outliers final: 16 residues processed: 128 average time/residue: 1.4982 time to fit residues: 204.0383 Evaluate side-chains 130 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 183 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9990 chunk 104 optimal weight: 0.0040 chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10146 Z= 0.171 Angle : 0.757 30.489 13786 Z= 0.318 Chirality : 0.043 0.237 1571 Planarity : 0.004 0.047 1761 Dihedral : 7.176 164.318 1570 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.54 % Allowed : 16.37 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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 (0.24), residues: 1245 helix: 1.68 (0.22), residues: 585 sheet: 0.31 (0.39), residues: 155 loop : -0.09 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 401 HIS 0.003 0.001 HIS A 629 PHE 0.028 0.001 PHE A 300 TYR 0.014 0.001 TYR A 802 ARG 0.012 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6628 (ttmt) REVERT: A 176 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6348 (pm20) REVERT: A 188 GLN cc_start: 0.7878 (mt0) cc_final: 0.7337 (mm-40) REVERT: A 442 PHE cc_start: 0.6250 (OUTLIER) cc_final: 0.4454 (t80) REVERT: A 521 GLU cc_start: 0.7049 (pm20) cc_final: 0.6735 (pm20) REVERT: A 560 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6880 (mtm-85) REVERT: A 650 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.7907 (m) REVERT: A 772 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: A 844 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7397 (mtt-85) REVERT: A 1031 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8466 (mt) REVERT: B 78 LYS cc_start: 0.8396 (mmpt) cc_final: 0.8148 (mmtm) outliers start: 27 outliers final: 15 residues processed: 122 average time/residue: 1.5461 time to fit residues: 200.1490 Evaluate side-chains 128 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 183 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10146 Z= 0.220 Angle : 0.780 30.829 13786 Z= 0.332 Chirality : 0.045 0.265 1571 Planarity : 0.005 0.060 1761 Dihedral : 7.312 162.532 1570 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.54 % Allowed : 16.56 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.06 (0.24), residues: 1245 helix: 1.57 (0.22), residues: 585 sheet: 0.23 (0.39), residues: 158 loop : -0.07 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 401 HIS 0.004 0.001 HIS A 629 PHE 0.028 0.002 PHE A 300 TYR 0.016 0.001 TYR A 802 ARG 0.014 0.000 ARG A 850 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6646 (ttmt) REVERT: A 176 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6378 (pm20) REVERT: A 442 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.4825 (t80) REVERT: A 521 GLU cc_start: 0.7030 (pm20) cc_final: 0.6707 (pm20) REVERT: A 560 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6907 (mtm-85) REVERT: A 650 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.7938 (m) REVERT: A 772 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: A 844 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7445 (mtp-110) REVERT: A 1031 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8487 (mt) REVERT: B 78 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8142 (mmtm) outliers start: 27 outliers final: 12 residues processed: 123 average time/residue: 1.5095 time to fit residues: 198.2212 Evaluate side-chains 124 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108876 restraints weight = 10967.440| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.78 r_work: 0.3122 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10146 Z= 0.177 Angle : 0.760 30.505 13786 Z= 0.320 Chirality : 0.043 0.236 1571 Planarity : 0.004 0.062 1761 Dihedral : 7.157 163.090 1570 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.45 % Allowed : 16.65 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.11 (0.24), residues: 1245 helix: 1.64 (0.22), residues: 585 sheet: 0.32 (0.39), residues: 155 loop : -0.12 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 401 HIS 0.003 0.001 HIS A 629 PHE 0.029 0.001 PHE A 497 TYR 0.013 0.001 TYR A 802 ARG 0.014 0.000 ARG A 850 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4098.49 seconds wall clock time: 76 minutes 8.75 seconds (4568.75 seconds total)