Starting phenix.real_space_refine on Sat Dec 9 15:24:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4a_32299/12_2023/7w4a_32299_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4a_32299/12_2023/7w4a_32299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4a_32299/12_2023/7w4a_32299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4a_32299/12_2023/7w4a_32299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4a_32299/12_2023/7w4a_32299_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4a_32299/12_2023/7w4a_32299_updated.pdb" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 1623 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 P 1 5.49 5 Mg 1 5.21 5 S 64 5.16 5 Na 1 4.78 5 Be 1 3.05 5 C 6318 2.51 5 N 1638 2.21 5 O 1827 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 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 602": "OD1" <-> "OD2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 712": "OE1" <-> "OE2" Residue "A PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9855 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7642 Classifications: {'peptide': 984} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 47, 'TRANS': 936} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "B" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2076 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 4, 'PTRANS': 17, 'TRANS': 239} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' NA': 1, '8CK': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 96 Unusual residues: {'NAG': 3, 'PCW': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 5.56, per 1000 atoms: 0.56 Number of scatterers: 9855 At special positions: 0 Unit cell: (118.064, 91.744, 170.704, 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) S 64 16.00 P 1 15.00 Mg 1 11.99 Na 1 11.00 F 4 9.00 O 1827 8.00 N 1638 7.00 C 6318 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 262 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 301 " - " ASN B 99 " " NAG B 302 " - " ASN B 130 " " NAG B 303 " - " ASN B 161 " Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 1.8 seconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2330 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 10 sheets defined 44.6% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 51 through 54 No H-bonds generated for 'chain 'A' and resid 51 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 104 Processing helix chain 'A' and resid 108 through 129 Processing helix chain 'A' and resid 136 through 170 removed outlier: 3.655A pdb=" N SER A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N PHE A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) 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 322 Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 344 through 363 removed outlier: 3.708A 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 Processing helix chain 'A' and resid 425 through 437 Processing helix chain 'A' and resid 460 through 472 Processing helix chain 'A' and resid 476 through 482 removed outlier: 3.829A pdb=" N GLU A 481 " --> pdb=" O MET A 477 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 526 removed outlier: 4.623A pdb=" N GLU A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 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 676 through 681 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 805 removed outlier: 3.549A pdb=" N ASN A 780 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 790 " --> pdb=" O TYR A 787 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 791 " --> pdb=" O THR A 788 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 793 " --> pdb=" O THR A 790 " (cutoff:3.500A) Proline residue: A 794 - end of helix removed outlier: 4.215A pdb=" N THR A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) Proline residue: A 798 - end of helix removed outlier: 4.076A pdb=" N VAL A 805 " --> pdb=" O TYR A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 823 through 833 Proline residue: A 827 - end of helix removed outlier: 3.942A pdb=" N ALA A 832 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 864 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 889 through 892 No H-bonds generated for 'chain 'A' and resid 889 through 892' Processing helix chain 'A' and resid 896 through 899 No H-bonds generated for 'chain 'A' and resid 896 through 899' Processing helix chain 'A' and resid 917 through 947 removed outlier: 3.729A pdb=" N ALA A 941 " --> pdb=" O MET A 937 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 944 " --> pdb=" O ILE A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 979 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 119 removed outlier: 4.167A pdb=" N GLY B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 125 Processing helix chain 'B' and resid 156 through 163 removed outlier: 6.253A 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 182 removed outlier: 3.546A pdb=" N ARG A 182 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 199 through 202 removed outlier: 4.016A 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: 4.379A pdb=" N CYS A 220 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASP A 223 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 6.550A 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: 6.400A pdb=" N VAL A 381 " --> pdb=" O ALA A 722 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR A 724 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N CYS A 383 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG A 621 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N SER A 384 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 6.403A 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: 3.562A pdb=" N THR A 396 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER A 599 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 400 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 597 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N PHE A 402 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N ALA A 595 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE A 564 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU A 597 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 562 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A 599 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG A 560 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N CYS A 487 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 535 through 538 removed outlier: 6.702A pdb=" N LEU A 592 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ILE A 530 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE A 594 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 5.966A 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: 6.884A pdb=" N GLU A 696 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE A 674 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 6.708A 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: 3.851A pdb=" N ASP A 211 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN A 269 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG A 213 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL A 267 " --> pdb=" O ARG A 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 82 through 85 removed outlier: 3.576A pdb=" N VAL B 245 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 95 through 99 removed outlier: 8.571A pdb=" N ILE B 96 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LYS B 285 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N TYR B 98 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS B 287 " --> pdb=" O TYR B 98 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1149 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: 2.92 Time building geometry restraints manager: 4.32 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: 3142 1.34 - 1.46: 1780 1.46 - 1.58: 5049 1.58 - 1.70: 2 1.70 - 1.82: 95 Bond restraints: 10068 Sorted by residual: bond pdb=" F3 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.529 1.763 -0.234 2.00e-02 2.50e+03 1.36e+02 bond pdb=" F2 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.535 1.754 -0.219 2.00e-02 2.50e+03 1.19e+02 bond pdb=" F1 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.542 1.753 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" CG BFD A 385 " pdb=" OD1 BFD A 385 " ideal model delta sigma weight residual 1.269 1.450 -0.181 2.00e-02 2.50e+03 8.15e+01 bond pdb=" C31 PCW B 304 " pdb=" O2 PCW B 304 " ideal model delta sigma weight residual 1.333 1.454 -0.121 2.00e-02 2.50e+03 3.68e+01 ... (remaining 10063 not shown) Histogram of bond angle deviations from ideal: 95.71 - 103.40: 134 103.40 - 111.08: 3822 111.08 - 118.76: 4198 118.76 - 126.44: 5387 126.44 - 134.13: 140 Bond angle restraints: 13681 Sorted by residual: angle pdb=" F2 BFD A 385 " pdb="BE BFD A 385 " pdb=" F3 BFD A 385 " ideal model delta sigma weight residual 112.60 95.74 16.86 3.00e+00 1.11e-01 3.16e+01 angle pdb=" OD1 BFD A 385 " pdb="BE BFD A 385 " pdb=" F1 BFD A 385 " ideal model delta sigma weight residual 102.38 118.72 -16.34 3.00e+00 1.11e-01 2.97e+01 angle pdb=" F1 BFD A 385 " pdb="BE BFD A 385 " pdb=" F3 BFD A 385 " ideal model delta sigma weight residual 111.29 95.71 15.58 3.00e+00 1.11e-01 2.70e+01 angle pdb=" C ASN A 792 " pdb=" N ILE A 793 " pdb=" CA ILE A 793 " ideal model delta sigma weight residual 120.24 123.49 -3.25 6.30e-01 2.52e+00 2.67e+01 angle pdb=" OD1 BFD A 385 " pdb="BE BFD A 385 " pdb=" F3 BFD A 385 " ideal model delta sigma weight residual 109.93 95.90 14.03 3.00e+00 1.11e-01 2.19e+01 ... (remaining 13676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 5728 22.41 - 44.81: 315 44.81 - 67.22: 31 67.22 - 89.62: 15 89.62 - 112.03: 3 Dihedral angle restraints: 6092 sinusoidal: 2475 harmonic: 3617 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 152 " pdb=" CB CYS B 152 " ideal model delta sinusoidal sigma weight residual 93.00 37.85 55.15 1 1.00e+01 1.00e-02 4.11e+01 dihedral pdb=" C3 NAG B 302 " pdb=" C1 NAG B 302 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " ideal model delta sinusoidal sigma weight residual -55.55 56.48 -112.03 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" N2 NAG B 302 " pdb=" C1 NAG B 302 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " ideal model delta sinusoidal sigma weight residual -178.19 -67.58 -110.61 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 6089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1250 0.053 - 0.106: 256 0.106 - 0.158: 39 0.158 - 0.211: 2 0.211 - 0.264: 2 Chirality restraints: 1549 Sorted by residual: chirality pdb=" C1 NAG B 302 " pdb=" ND2 ASN B 130 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB VAL A 930 " pdb=" CA VAL A 930 " pdb=" CG1 VAL A 930 " pdb=" CG2 VAL A 930 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C2 PCW B 304 " pdb=" C1 PCW B 304 " pdb=" C3 PCW B 304 " pdb=" O2 PCW B 304 " both_signs ideal model delta sigma weight residual False -2.32 -2.52 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1546 not shown) Planarity restraints: 1757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 232 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO A 233 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 233 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 233 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 99 " 0.001 2.00e-02 2.50e+03 1.92e-02 4.62e+00 pdb=" CG ASN B 99 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 99 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN B 99 " -0.020 2.00e-02 2.50e+03 pdb=" C1 NAG B 301 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 237 " -0.034 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO A 238 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 238 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 238 " -0.029 5.00e-02 4.00e+02 ... (remaining 1754 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 78 2.62 - 3.19: 8801 3.19 - 3.76: 15587 3.76 - 4.33: 21613 4.33 - 4.90: 35376 Nonbonded interactions: 81455 Sorted by model distance: nonbonded pdb=" F2 BFD A 385 " pdb="MG MG A1103 " model vdw 2.048 2.120 nonbonded pdb=" OD2 BFD A 385 " pdb="MG MG A1103 " model vdw 2.082 2.170 nonbonded pdb=" ND2 ASN A 792 " pdb=" O HOH A1201 " model vdw 2.146 2.520 nonbonded pdb=" OH TYR A1011 " pdb=" OH TYR B 43 " model vdw 2.174 2.440 nonbonded pdb=" O SER A 244 " pdb=" OG1 THR A 248 " model vdw 2.240 2.440 ... (remaining 81450 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 4.560 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.150 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 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 : 0.006 0.234 10068 Z= 0.335 Angle : 0.712 16.855 13681 Z= 0.344 Chirality : 0.044 0.264 1549 Planarity : 0.004 0.062 1754 Dihedral : 13.796 112.026 3753 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.29 (0.24), residues: 1238 helix: 1.76 (0.21), residues: 575 sheet: -0.01 (0.37), residues: 162 loop : 0.21 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 427 HIS 0.009 0.001 HIS B 114 PHE 0.030 0.002 PHE A 124 TYR 0.018 0.001 TYR A 802 ARG 0.008 0.000 ARG A 844 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.086 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 1.2149 time to fit residues: 180.5090 Evaluate side-chains 105 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5237 ------------------------------------------------------------------------------- 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: 4.9990 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 0.0270 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 0.0980 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 0.0970 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 706 GLN A 792 ASN A 986 ASN B 146 ASN B 147 HIS B 289 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10068 Z= 0.136 Angle : 0.482 6.069 13681 Z= 0.248 Chirality : 0.041 0.158 1549 Planarity : 0.004 0.054 1754 Dihedral : 7.890 94.798 1480 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.42 % Allowed : 7.68 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.53 (0.24), residues: 1238 helix: 1.98 (0.22), residues: 568 sheet: 0.16 (0.38), residues: 162 loop : 0.31 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 427 HIS 0.005 0.001 HIS B 227 PHE 0.015 0.001 PHE A 970 TYR 0.011 0.001 TYR A 878 ARG 0.005 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 133 average time/residue: 1.1850 time to fit residues: 171.4760 Evaluate side-chains 117 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.2606 time to fit residues: 1.9086 ------------------------------------------------------------------------------- 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: 8.9990 chunk 34 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 112 optimal weight: 0.4980 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A 792 ASN A 986 ASN B 289 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10068 Z= 0.355 Angle : 0.642 6.385 13681 Z= 0.334 Chirality : 0.048 0.315 1549 Planarity : 0.006 0.061 1754 Dihedral : 8.388 88.650 1480 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.46 % Allowed : 9.48 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.82 (0.23), residues: 1238 helix: 1.21 (0.21), residues: 574 sheet: -0.08 (0.37), residues: 161 loop : 0.13 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 998 HIS 0.007 0.001 HIS B 111 PHE 0.023 0.002 PHE A 315 TYR 0.016 0.002 TYR A 551 ARG 0.006 0.001 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 1.012 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 9 residues processed: 128 average time/residue: 1.1324 time to fit residues: 158.1858 Evaluate side-chains 117 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.424 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.1518 time to fit residues: 2.8313 ------------------------------------------------------------------------------- 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: 10.0000 chunk 84 optimal weight: 0.0060 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 792 ASN B 289 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10068 Z= 0.151 Angle : 0.487 6.624 13681 Z= 0.251 Chirality : 0.041 0.171 1549 Planarity : 0.004 0.055 1754 Dihedral : 7.605 83.479 1480 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.52 % Allowed : 11.56 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.21 (0.24), residues: 1238 helix: 1.68 (0.22), residues: 576 sheet: 0.11 (0.38), residues: 162 loop : 0.13 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 401 HIS 0.004 0.001 HIS B 227 PHE 0.021 0.001 PHE A 970 TYR 0.010 0.001 TYR A 878 ARG 0.003 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 130 average time/residue: 1.1208 time to fit residues: 158.2504 Evaluate side-chains 117 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1671 time to fit residues: 1.9576 ------------------------------------------------------------------------------- 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: 1.9990 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 107 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 792 ASN A 986 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10068 Z= 0.166 Angle : 0.497 6.718 13681 Z= 0.254 Chirality : 0.041 0.180 1549 Planarity : 0.004 0.054 1754 Dihedral : 7.466 81.768 1480 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.65 % Allowed : 12.61 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.24 (0.24), residues: 1238 helix: 1.69 (0.22), residues: 574 sheet: 0.16 (0.38), residues: 162 loop : 0.14 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 998 HIS 0.004 0.001 HIS B 227 PHE 0.027 0.001 PHE A 333 TYR 0.011 0.001 TYR A 878 ARG 0.002 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 115 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 131 average time/residue: 1.0261 time to fit residues: 146.7597 Evaluate side-chains 127 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.1023 time to fit residues: 2.1099 ------------------------------------------------------------------------------- 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: 5.9990 chunk 107 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 566 GLN A 792 ASN A 986 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10068 Z= 0.184 Angle : 0.511 6.799 13681 Z= 0.260 Chirality : 0.042 0.178 1549 Planarity : 0.004 0.056 1754 Dihedral : 7.440 79.482 1480 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.27 % Allowed : 13.46 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1238 helix: 1.63 (0.22), residues: 576 sheet: 0.19 (0.38), residues: 162 loop : 0.10 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 998 HIS 0.004 0.001 HIS B 227 PHE 0.015 0.001 PHE A 970 TYR 0.011 0.001 TYR A 140 ARG 0.002 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 132 average time/residue: 1.0519 time to fit residues: 151.5643 Evaluate side-chains 125 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 5 average time/residue: 0.1474 time to fit residues: 2.7546 ------------------------------------------------------------------------------- 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: 0.2980 chunk 13 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 74 optimal weight: 0.0070 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 792 ASN A 986 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10068 Z= 0.157 Angle : 0.496 6.757 13681 Z= 0.251 Chirality : 0.041 0.172 1549 Planarity : 0.004 0.054 1754 Dihedral : 7.228 77.602 1480 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.46 % Allowed : 14.03 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.30 (0.24), residues: 1238 helix: 1.74 (0.22), residues: 576 sheet: 0.26 (0.38), residues: 162 loop : 0.14 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 401 HIS 0.004 0.001 HIS B 227 PHE 0.032 0.001 PHE A 333 TYR 0.020 0.001 TYR B 60 ARG 0.002 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 1.133 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 132 average time/residue: 1.0256 time to fit residues: 147.9670 Evaluate side-chains 122 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 5 average time/residue: 0.1555 time to fit residues: 2.6344 ------------------------------------------------------------------------------- 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: 0.9980 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 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 193 GLN A 792 ASN A 898 GLN A 902 HIS A 986 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10068 Z= 0.164 Angle : 0.519 7.882 13681 Z= 0.261 Chirality : 0.041 0.171 1549 Planarity : 0.004 0.054 1754 Dihedral : 7.632 76.575 1480 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.27 % Allowed : 14.41 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.29 (0.24), residues: 1238 helix: 1.73 (0.22), residues: 576 sheet: 0.26 (0.38), residues: 162 loop : 0.15 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 401 HIS 0.005 0.001 HIS A 694 PHE 0.021 0.001 PHE A 970 TYR 0.012 0.001 TYR A 157 ARG 0.002 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 1.002 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 131 average time/residue: 1.0577 time to fit residues: 151.2437 Evaluate side-chains 130 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.1462 time to fit residues: 2.2082 ------------------------------------------------------------------------------- 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: 3.9990 chunk 104 optimal weight: 0.0670 chunk 111 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 48 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 792 ASN A 986 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10068 Z= 0.151 Angle : 0.513 7.391 13681 Z= 0.255 Chirality : 0.041 0.164 1549 Planarity : 0.004 0.053 1754 Dihedral : 7.290 74.840 1480 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.80 % Allowed : 15.45 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.37 (0.24), residues: 1238 helix: 1.81 (0.22), residues: 574 sheet: 0.31 (0.38), residues: 162 loop : 0.18 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 401 HIS 0.004 0.001 HIS B 227 PHE 0.032 0.001 PHE A 333 TYR 0.013 0.001 TYR A 157 ARG 0.002 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 1.186 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 133 average time/residue: 1.0243 time to fit residues: 149.0952 Evaluate side-chains 121 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.2618 time to fit residues: 1.9487 ------------------------------------------------------------------------------- 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: 5.9990 chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 0.0970 chunk 78 optimal weight: 0.3980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 792 ASN A 902 HIS A 986 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10068 Z= 0.140 Angle : 0.510 8.044 13681 Z= 0.254 Chirality : 0.040 0.164 1549 Planarity : 0.004 0.053 1754 Dihedral : 7.046 72.911 1480 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.61 % Allowed : 15.36 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.49 (0.24), residues: 1238 helix: 1.90 (0.22), residues: 574 sheet: 0.39 (0.38), residues: 162 loop : 0.23 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 401 HIS 0.004 0.001 HIS A 694 PHE 0.013 0.001 PHE A 161 TYR 0.020 0.001 TYR B 60 ARG 0.002 0.000 ARG A 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.216 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 135 average time/residue: 1.0156 time to fit residues: 150.2798 Evaluate side-chains 127 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.2422 time to fit residues: 1.8408 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 792 ASN A 986 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.181914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132685 restraints weight = 11425.309| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.54 r_work: 0.3272 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10068 Z= 0.160 Angle : 0.539 10.586 13681 Z= 0.270 Chirality : 0.046 0.742 1549 Planarity : 0.004 0.054 1754 Dihedral : 7.098 72.282 1480 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.71 % Allowed : 16.02 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.49 (0.24), residues: 1238 helix: 1.93 (0.22), residues: 562 sheet: 0.40 (0.38), residues: 162 loop : 0.22 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 106 HIS 0.004 0.001 HIS A 694 PHE 0.014 0.001 PHE A 254 TYR 0.012 0.001 TYR A 157 ARG 0.002 0.000 ARG A 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3908.47 seconds wall clock time: 70 minutes 33.84 seconds (4233.84 seconds total)