Starting phenix.real_space_refine on Sat Dec 9 08:35:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmn_36424/12_2023/8jmn_36424_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmn_36424/12_2023/8jmn_36424.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmn_36424/12_2023/8jmn_36424_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmn_36424/12_2023/8jmn_36424_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmn_36424/12_2023/8jmn_36424_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmn_36424/12_2023/8jmn_36424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmn_36424/12_2023/8jmn_36424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmn_36424/12_2023/8jmn_36424_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmn_36424/12_2023/8jmn_36424_updated.pdb" } resolution = 2.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.082 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 1 4.86 5 Be 1 3.05 5 C 6529 2.51 5 N 1653 2.21 5 O 2233 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 ASP 84": "OD1" <-> "OD2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 95": "OD1" <-> "OD2" Residue "B TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10491 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7633 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 47, 'TRANS': 935} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 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: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 219 Unusual residues: {' MG': 1, 'PCW': 4, 'UOU': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 124 Unusual residues: {'CLR': 1, 'NAG': 3, 'PCW': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 260 Classifications: {'water': 260} Link IDs: {None: 259} Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Time building chain proxies: 6.01, per 1000 atoms: 0.57 Number of scatterers: 10491 At special positions: 0 Unit cell: (81.968, 102.272, 171.456, 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 1 17.00 S 65 16.00 P 5 15.00 Mg 1 11.99 F 3 9.00 O 2233 8.00 N 1653 7.00 C 6529 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=2.04 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: 4.03 Conformation dependent library (CDL) restraints added in 1.7 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 10 sheets defined 44.0% alpha, 12.1% 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 74 through 83 Processing helix chain 'A' and resid 97 through 104 Processing helix chain 'A' and resid 108 through 129 Processing helix chain 'A' and resid 135 through 170 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 285 Processing helix chain 'A' and resid 292 through 321 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 345 through 363 removed outlier: 3.792A pdb=" N LYS A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 373 Processing helix chain 'A' and resid 375 through 378 No H-bonds generated for 'chain 'A' and resid 375 through 378' 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 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 680 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: 3.697A pdb=" N LYS A 791 " --> pdb=" O THR A 788 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 793 " --> pdb=" O THR A 790 " (cutoff:3.500A) Proline residue: A 794 - end of helix removed outlier: 4.509A 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 821 Processing helix chain 'A' and resid 825 through 833 removed outlier: 3.603A pdb=" N LEU A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA A 832 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 4.511A 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 884 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: 3.612A pdb=" N ALA A 941 " --> pdb=" O MET A 937 " (cutoff:3.500A) removed outlier: 3.619A 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 34 through 65 Processing helix chain 'B' and resid 103 through 120 removed outlier: 4.589A pdb=" N GLY B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 removed outlier: 6.542A 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 removed outlier: 3.571A pdb=" N THR A 262 " --> pdb=" O GLN A 218 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 234 through 236 removed outlier: 4.304A pdb=" N CYS A 220 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP A 223 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 6.448A 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: 6.479A pdb=" N VAL A 381 " --> pdb=" O ALA A 722 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR A 724 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N CYS A 383 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG A 621 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N SER A 384 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 6.359A 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: 6.806A pdb=" N SER A 599 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU A 400 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 597 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE A 402 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ALA A 595 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 564 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU A 597 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 562 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER A 599 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ARG A 560 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A 503 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS A 485 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 530 through 532 Processing sheet with id= G, first strand: chain 'A' and resid 671 through 675 removed outlier: 6.603A pdb=" N GLU A 696 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE A 674 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 6.454A 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: 6.350A pdb=" N ARG A 213 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.874A 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 94 through 99 removed outlier: 4.524A pdb=" N LEU B 94 " --> pdb=" O GLU B 283 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1074 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: 3.45 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1622 1.31 - 1.43: 2697 1.43 - 1.56: 5916 1.56 - 1.69: 10 1.69 - 1.82: 98 Bond restraints: 10343 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 1.752 -0.217 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 1.750 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" CG BFD A 385 " pdb=" OD1 BFD A 385 " ideal model delta sigma weight residual 1.269 1.446 -0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" C11 PCW A1103 " pdb=" O3 PCW A1103 " ideal model delta sigma weight residual 1.326 1.455 -0.129 2.00e-02 2.50e+03 4.19e+01 ... (remaining 10338 not shown) Histogram of bond angle deviations from ideal: 86.09 - 95.72: 4 95.72 - 105.35: 264 105.35 - 114.98: 6292 114.98 - 124.61: 7294 124.61 - 134.24: 163 Bond angle restraints: 14017 Sorted by residual: angle pdb=" C5 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 111.64 86.29 25.35 3.00e+00 1.11e-01 7.14e+01 angle pdb=" C6 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 109.11 86.09 23.02 3.00e+00 1.11e-01 5.89e+01 angle pdb=" C7 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 108.24 86.90 21.34 3.00e+00 1.11e-01 5.06e+01 angle pdb=" OD1 BFD A 385 " pdb="BE BFD A 385 " pdb=" F1 BFD A 385 " ideal model delta sigma weight residual 102.38 119.00 -16.62 3.00e+00 1.11e-01 3.07e+01 angle pdb=" F2 BFD A 385 " pdb="BE BFD A 385 " pdb=" F3 BFD A 385 " ideal model delta sigma weight residual 112.60 96.08 16.52 3.00e+00 1.11e-01 3.03e+01 ... (remaining 14012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 6039 35.45 - 70.90: 275 70.90 - 106.35: 19 106.35 - 141.80: 3 141.80 - 177.25: 2 Dihedral angle restraints: 6338 sinusoidal: 2705 harmonic: 3633 Sorted by residual: dihedral pdb=" N PCW A1104 " pdb=" C4 PCW A1104 " pdb=" C5 PCW A1104 " pdb=" O4P PCW A1104 " ideal model delta sinusoidal sigma weight residual 293.34 116.09 177.25 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW A1104 " pdb=" C31 PCW A1104 " pdb=" C32 PCW A1104 " pdb=" O2 PCW A1104 " ideal model delta sinusoidal sigma weight residual 191.83 39.31 152.52 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" N PCW A1105 " pdb=" C4 PCW A1105 " pdb=" C5 PCW A1105 " pdb=" O4P PCW A1105 " ideal model delta sinusoidal sigma weight residual 293.34 151.86 141.48 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 6335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1266 0.054 - 0.108: 255 0.108 - 0.162: 36 0.162 - 0.215: 5 0.215 - 0.269: 4 Chirality restraints: 1566 Sorted by residual: 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 1.81e+00 chirality pdb=" C2 PCW A1101 " pdb=" C1 PCW A1101 " pdb=" C3 PCW A1101 " pdb=" O2 PCW A1101 " both_signs ideal model delta sigma weight residual False -2.32 -2.57 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" C2 PCW A1103 " pdb=" C1 PCW A1103 " pdb=" C3 PCW A1103 " pdb=" O2 PCW A1103 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1563 not shown) Planarity restraints: 1782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 304 " -0.348 2.00e-02 2.50e+03 2.99e-01 1.11e+03 pdb=" C7 NAG B 304 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B 304 " -0.152 2.00e-02 2.50e+03 pdb=" N2 NAG B 304 " 0.530 2.00e-02 2.50e+03 pdb=" O7 NAG B 304 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 303 " -0.311 2.00e-02 2.50e+03 2.69e-01 9.04e+02 pdb=" C7 NAG B 303 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B 303 " -0.017 2.00e-02 2.50e+03 pdb=" N2 NAG B 303 " 0.465 2.00e-02 2.50e+03 pdb=" O7 NAG B 303 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 302 " 0.048 2.00e-02 2.50e+03 3.94e-02 1.94e+01 pdb=" C7 NAG B 302 " -0.014 2.00e-02 2.50e+03 pdb=" C8 NAG B 302 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG B 302 " -0.062 2.00e-02 2.50e+03 pdb=" O7 NAG B 302 " -0.008 2.00e-02 2.50e+03 ... (remaining 1779 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 106 2.49 - 3.09: 7441 3.09 - 3.70: 17546 3.70 - 4.30: 27061 4.30 - 4.90: 41339 Nonbonded interactions: 93493 Sorted by model distance: nonbonded pdb="MG MG A1102 " pdb=" O HOH A1225 " model vdw 1.890 2.170 nonbonded pdb=" O THR A 387 " pdb="MG MG A1102 " model vdw 1.984 2.170 nonbonded pdb=" OD2 ASP A 877 " pdb=" O HOH A1201 " model vdw 2.143 2.440 nonbonded pdb=" O PRO B 145 " pdb=" OG1 THR B 148 " model vdw 2.144 2.440 nonbonded pdb=" OD2 BFD A 385 " pdb="MG MG A1102 " model vdw 2.162 2.170 ... (remaining 93488 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: 4.680 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: 19.670 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.280 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.007 0.235 10343 Z= 0.441 Angle : 0.916 25.350 14017 Z= 0.379 Chirality : 0.045 0.269 1566 Planarity : 0.011 0.299 1779 Dihedral : 18.775 177.253 3989 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.29 % Allowed : 19.45 % Favored : 77.26 % 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: 1.14 (0.24), residues: 1244 helix: 1.68 (0.21), residues: 584 sheet: 0.07 (0.40), residues: 157 loop : -0.03 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 427 HIS 0.003 0.001 HIS A 53 PHE 0.017 0.002 PHE A 970 TYR 0.013 0.001 TYR B 136 ARG 0.013 0.001 ARG A 850 *********************** 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 153 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 118 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 29 residues processed: 150 average time/residue: 1.7106 time to fit residues: 272.1049 Evaluate side-chains 143 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 29 residues processed: 1 average time/residue: 0.1394 time to fit residues: 1.8323 ------------------------------------------------------------------------------- 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: 0.7980 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 446 GLN B 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.0514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10343 Z= 0.179 Angle : 0.551 9.304 14017 Z= 0.288 Chirality : 0.043 0.259 1566 Planarity : 0.006 0.057 1779 Dihedral : 13.437 160.172 1693 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.61 % Allowed : 17.67 % Favored : 77.73 % 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: 0.99 (0.23), residues: 1244 helix: 1.34 (0.21), residues: 589 sheet: 0.33 (0.41), residues: 152 loop : 0.07 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 39 HIS 0.003 0.001 HIS B 275 PHE 0.018 0.002 PHE A 300 TYR 0.012 0.001 TYR B 48 ARG 0.006 0.000 ARG A 850 *********************** 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 167 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 118 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 33 residues processed: 155 average time/residue: 1.5669 time to fit residues: 258.1626 Evaluate side-chains 148 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 29 residues processed: 4 average time/residue: 0.8228 time to fit residues: 5.0571 ------------------------------------------------------------------------------- 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: 0.9980 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 0.0470 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 446 GLN B 76 GLN B 160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10343 Z= 0.178 Angle : 0.533 8.604 14017 Z= 0.278 Chirality : 0.043 0.256 1566 Planarity : 0.005 0.056 1779 Dihedral : 13.095 163.564 1693 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.70 % Allowed : 16.82 % Favored : 78.48 % 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: 0.93 (0.23), residues: 1244 helix: 1.20 (0.21), residues: 584 sheet: 0.32 (0.41), residues: 152 loop : 0.17 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS A 502 PHE 0.019 0.002 PHE A 497 TYR 0.012 0.001 TYR B 48 ARG 0.004 0.000 ARG A 946 *********************** 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 166 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 116 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 32 residues processed: 153 average time/residue: 1.6129 time to fit residues: 262.0350 Evaluate side-chains 144 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 1.160 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 2 average time/residue: 0.1703 time to fit residues: 2.0998 ------------------------------------------------------------------------------- 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: 0.5980 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 0.0010 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10343 Z= 0.153 Angle : 0.504 8.471 14017 Z= 0.263 Chirality : 0.042 0.250 1566 Planarity : 0.005 0.054 1779 Dihedral : 12.842 166.195 1693 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.42 % Allowed : 17.29 % Favored : 78.29 % 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: 0.95 (0.23), residues: 1244 helix: 1.22 (0.21), residues: 582 sheet: 0.34 (0.41), residues: 152 loop : 0.20 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 427 HIS 0.003 0.001 HIS A 502 PHE 0.020 0.001 PHE A 300 TYR 0.010 0.001 TYR B 48 ARG 0.007 0.000 ARG A 850 *********************** 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 159 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 112 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 31 residues processed: 148 average time/residue: 1.8136 time to fit residues: 285.1587 Evaluate side-chains 144 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 29 residues processed: 2 average time/residue: 0.1862 time to fit residues: 2.1044 ------------------------------------------------------------------------------- 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: 0.9980 chunk 68 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10343 Z= 0.221 Angle : 0.560 8.344 14017 Z= 0.292 Chirality : 0.045 0.251 1566 Planarity : 0.005 0.051 1779 Dihedral : 12.974 167.125 1693 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.23 % Allowed : 17.39 % Favored : 78.38 % 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: 0.85 (0.23), residues: 1244 helix: 1.11 (0.21), residues: 582 sheet: 0.30 (0.41), residues: 152 loop : 0.18 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 427 HIS 0.004 0.001 HIS B 275 PHE 0.017 0.002 PHE A 300 TYR 0.014 0.002 TYR A 802 ARG 0.007 0.000 ARG A 850 *********************** 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 159 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 114 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 33 residues processed: 150 average time/residue: 1.6770 time to fit residues: 267.3359 Evaluate side-chains 143 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 110 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 32 residues processed: 1 average time/residue: 0.2580 time to fit residues: 1.9507 ------------------------------------------------------------------------------- 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: 2.9990 chunk 107 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10343 Z= 0.181 Angle : 0.527 8.014 14017 Z= 0.276 Chirality : 0.043 0.252 1566 Planarity : 0.005 0.051 1779 Dihedral : 12.778 169.067 1693 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.95 % Allowed : 17.76 % Favored : 78.29 % 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: 0.90 (0.23), residues: 1244 helix: 1.13 (0.21), residues: 582 sheet: 0.26 (0.39), residues: 160 loop : 0.26 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 427 HIS 0.003 0.001 HIS B 275 PHE 0.021 0.002 PHE A 300 TYR 0.012 0.001 TYR B 48 ARG 0.009 0.000 ARG A 850 *********************** 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 158 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 116 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 32 residues processed: 149 average time/residue: 1.6082 time to fit residues: 254.8252 Evaluate side-chains 152 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 2 average time/residue: 0.1974 time to fit residues: 2.1626 ------------------------------------------------------------------------------- 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: 0.0970 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10343 Z= 0.161 Angle : 0.513 7.573 14017 Z= 0.267 Chirality : 0.043 0.252 1566 Planarity : 0.005 0.050 1779 Dihedral : 12.656 171.276 1693 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.85 % Allowed : 18.14 % Favored : 78.01 % 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: 0.96 (0.23), residues: 1244 helix: 1.17 (0.21), residues: 582 sheet: 0.27 (0.39), residues: 160 loop : 0.30 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS A 502 PHE 0.019 0.001 PHE A 970 TYR 0.011 0.001 TYR B 48 ARG 0.011 0.000 ARG A 850 *********************** 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 156 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 115 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 33 residues processed: 150 average time/residue: 1.6813 time to fit residues: 267.6137 Evaluate side-chains 145 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 112 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 31 residues processed: 3 average time/residue: 0.1721 time to fit residues: 2.4730 ------------------------------------------------------------------------------- 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: 0.6980 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 59 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 108 optimal weight: 0.0970 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10343 Z= 0.144 Angle : 0.493 7.169 14017 Z= 0.257 Chirality : 0.042 0.248 1566 Planarity : 0.005 0.050 1779 Dihedral : 12.370 174.383 1693 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.76 % Allowed : 18.42 % Favored : 77.82 % 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: 1.04 (0.24), residues: 1244 helix: 1.19 (0.22), residues: 585 sheet: 0.36 (0.41), residues: 155 loop : 0.39 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 427 HIS 0.003 0.001 HIS A 502 PHE 0.018 0.001 PHE A 300 TYR 0.009 0.001 TYR B 48 ARG 0.011 0.000 ARG A 850 *********************** 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 159 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 119 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 30 residues processed: 153 average time/residue: 1.5798 time to fit residues: 257.5567 Evaluate side-chains 145 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 30 residues processed: 0 time to fit residues: 1.5902 ------------------------------------------------------------------------------- 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: 0.5980 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10343 Z= 0.188 Angle : 0.537 6.890 14017 Z= 0.280 Chirality : 0.043 0.243 1566 Planarity : 0.005 0.055 1779 Dihedral : 12.458 174.058 1693 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.29 % Allowed : 18.80 % Favored : 77.91 % 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: 0.96 (0.23), residues: 1244 helix: 1.12 (0.21), residues: 582 sheet: 0.35 (0.41), residues: 155 loop : 0.34 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS A 502 PHE 0.023 0.002 PHE A 300 TYR 0.013 0.002 TYR B 48 ARG 0.012 0.000 ARG A 850 *********************** 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 153 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 118 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 30 residues processed: 151 average time/residue: 1.6730 time to fit residues: 268.2421 Evaluate side-chains 147 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 30 residues processed: 0 time to fit residues: 1.5457 ------------------------------------------------------------------------------- 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: 0.8980 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10343 Z= 0.219 Angle : 0.563 7.537 14017 Z= 0.294 Chirality : 0.044 0.250 1566 Planarity : 0.005 0.060 1779 Dihedral : 12.611 174.272 1693 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.10 % Allowed : 18.89 % Favored : 78.01 % 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: 0.89 (0.23), residues: 1244 helix: 1.07 (0.21), residues: 582 sheet: 0.32 (0.41), residues: 155 loop : 0.29 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 427 HIS 0.004 0.001 HIS B 275 PHE 0.020 0.002 PHE A 300 TYR 0.012 0.002 TYR A 802 ARG 0.012 0.001 ARG A 850 ********************** 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 146 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 30 residues processed: 145 average time/residue: 1.7157 time to fit residues: 263.8382 Evaluate side-chains 142 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 30 residues processed: 0 time to fit residues: 1.6175 ------------------------------------------------------------------------------- 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: 0.3980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.154149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.109050 restraints weight = 9011.575| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.30 r_work: 0.3007 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10343 Z= 0.182 Angle : 0.530 7.065 14017 Z= 0.277 Chirality : 0.043 0.256 1566 Planarity : 0.005 0.059 1779 Dihedral : 12.366 175.848 1693 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.20 % Allowed : 18.80 % Favored : 78.01 % 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: 0.95 (0.23), residues: 1244 helix: 1.13 (0.21), residues: 582 sheet: 0.33 (0.41), residues: 155 loop : 0.31 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS B 275 PHE 0.020 0.002 PHE A 300 TYR 0.012 0.001 TYR A 802 ARG 0.012 0.000 ARG A 850 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5041.89 seconds wall clock time: 91 minutes 32.93 seconds (5492.93 seconds total)