Starting phenix.real_space_refine (version: dev) on Mon Dec 12 13:58:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7m_9941/12_2022/6k7m_9941_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7m_9941/12_2022/6k7m_9941.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7m_9941/12_2022/6k7m_9941_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7m_9941/12_2022/6k7m_9941_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7m_9941/12_2022/6k7m_9941_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7m_9941/12_2022/6k7m_9941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7m_9941/12_2022/6k7m_9941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7m_9941/12_2022/6k7m_9941_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7m_9941/12_2022/6k7m_9941_updated.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 139": "NH1" <-> "NH2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 482": "OD1" <-> "OD2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A ASP 650": "OD1" <-> "OD2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A ASP 672": "OD1" <-> "OD2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 290": "NH1" <-> "NH2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "C TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 10591 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7827 Classifications: {'peptide': 983} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 952} Chain breaks: 3 Chain: "C" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2604 Classifications: {'peptide': 324} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 298} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {' MG': 1, 'ALF': 1, 'D39': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.57, per 1000 atoms: 0.62 Number of scatterers: 10591 At special positions: 0 Unit cell: (73.87, 106.24, 174.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 56 16.00 P 1 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1912 8.00 N 1745 7.00 C 6871 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.04 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 ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 4.46 Conformation dependent library (CDL) restraints added in 1.5 seconds 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 9 sheets defined 41.5% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 64 through 72 Processing helix chain 'A' and resid 76 through 89 removed outlier: 4.077A pdb=" N GLN A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 132 removed outlier: 3.912A pdb=" N LYS A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 186 through 189 No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 209 through 214 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 278 No H-bonds generated for 'chain 'A' and resid 275 through 278' Processing helix chain 'A' and resid 289 through 323 Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 358 through 375 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 398 through 401 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 459 through 471 removed outlier: 4.651A pdb=" N GLU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 503 removed outlier: 3.847A pdb=" N LEU A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 566 Processing helix chain 'A' and resid 574 through 587 Processing helix chain 'A' and resid 601 through 616 removed outlier: 5.511A pdb=" N GLU A 606 " --> pdb=" O SER A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 629 Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 731 through 737 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 763 through 777 Processing helix chain 'A' and resid 788 through 795 removed outlier: 3.792A pdb=" N VAL A 791 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER A 792 " --> pdb=" O ASN A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.513A pdb=" N LYS A 826 " --> pdb=" O LYS A 823 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 828 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 829 " --> pdb=" O LYS A 826 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET A 830 " --> pdb=" O ASN A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 865 removed outlier: 3.833A pdb=" N ASN A 851 " --> pdb=" O CYS A 847 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 857 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE A 859 " --> pdb=" O TYR A 855 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 878 No H-bonds generated for 'chain 'A' and resid 875 through 878' Processing helix chain 'A' and resid 887 through 895 removed outlier: 3.890A pdb=" N LEU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.024A pdb=" N SER A 915 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 962 through 983 Processing helix chain 'A' and resid 990 through 1011 Processing helix chain 'A' and resid 1026 through 1031 Processing helix chain 'A' and resid 1034 through 1060 removed outlier: 3.925A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 5.368A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 74 Proline residue: C 52 - end of helix Proline residue: C 63 - end of helix removed outlier: 3.580A pdb=" N ASN C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 132 through 135 No H-bonds generated for 'chain 'C' and resid 132 through 135' Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 207 through 210 No H-bonds generated for 'chain 'C' and resid 207 through 210' Processing helix chain 'C' and resid 223 through 226 No H-bonds generated for 'chain 'C' and resid 223 through 226' Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 324 through 348 Processing sheet with id= A, first strand: chain 'A' and resid 37 through 41 Processing sheet with id= B, first strand: chain 'A' and resid 134 through 136 Processing sheet with id= C, first strand: chain 'A' and resid 156 through 159 removed outlier: 6.882A pdb=" N ASP A 168 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 194 through 198 removed outlier: 3.773A pdb=" N TYR A 182 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 694 through 696 removed outlier: 6.421A pdb=" N ALA A 755 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE A 729 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 757 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL A 780 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE A 406 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A 782 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N SER A 408 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 784 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 799 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLY A 785 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 801 " --> pdb=" O GLY A 785 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR A 817 " --> pdb=" O GLY A 802 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 506 through 508 removed outlier: 4.608A pdb=" N VAL A 515 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 419 through 425 removed outlier: 6.832A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N CYS A 424 " --> pdb=" O ALA A 641 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA A 641 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG A 546 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU A 528 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 77 through 81 removed outlier: 5.983A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 102 through 110 removed outlier: 4.344A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1191 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: 3.55 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1849 1.32 - 1.45: 2835 1.45 - 1.57: 6062 1.57 - 1.70: 1 1.70 - 1.82: 89 Bond restraints: 10836 Sorted by residual: bond pdb=" O3 D39 A1304 " pdb=" P D39 A1304 " ideal model delta sigma weight residual 1.664 1.540 0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" F3 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.685 1.790 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.684 1.786 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.685 1.787 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" F4 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.686 1.786 -0.100 2.00e-02 2.50e+03 2.48e+01 ... (remaining 10831 not shown) Histogram of bond angle deviations from ideal: 89.21 - 106.99: 358 106.99 - 124.77: 14098 124.77 - 142.55: 242 142.55 - 160.33: 0 160.33 - 178.11: 2 Bond angle restraints: 14700 Sorted by residual: angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F2 ALF A1301 " ideal model delta sigma weight residual 108.68 177.19 -68.51 3.00e+00 1.11e-01 5.21e+02 angle pdb=" F3 ALF A1301 " pdb="AL ALF A1301 " pdb=" F4 ALF A1301 " ideal model delta sigma weight residual 109.63 178.11 -68.48 3.00e+00 1.11e-01 5.21e+02 angle pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " pdb=" F3 ALF A1301 " ideal model delta sigma weight residual 109.59 89.21 20.38 3.00e+00 1.11e-01 4.61e+01 angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F3 ALF A1301 " ideal model delta sigma weight residual 109.69 89.91 19.78 3.00e+00 1.11e-01 4.35e+01 angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F4 ALF A1301 " ideal model delta sigma weight residual 109.02 89.36 19.66 3.00e+00 1.11e-01 4.29e+01 ... (remaining 14695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.37: 6165 28.37 - 56.74: 248 56.74 - 85.11: 21 85.11 - 113.48: 0 113.48 - 141.85: 2 Dihedral angle restraints: 6436 sinusoidal: 2622 harmonic: 3814 Sorted by residual: dihedral pdb=" CA ASN C 163 " pdb=" C ASN C 163 " pdb=" N GLU C 164 " pdb=" CA GLU C 164 " ideal model delta harmonic sigma weight residual -180.00 -139.55 -40.45 0 5.00e+00 4.00e-02 6.55e+01 dihedral pdb=" CB CYS C 91 " pdb=" SG CYS C 91 " pdb=" SG CYS C 104 " pdb=" CB CYS C 104 " ideal model delta sinusoidal sigma weight residual 93.00 158.33 -65.33 1 1.00e+01 1.00e-02 5.59e+01 dihedral pdb=" CA PRO A 477 " pdb=" C PRO A 477 " pdb=" N GLU A 478 " pdb=" CA GLU A 478 " ideal model delta harmonic sigma weight residual 180.00 -143.08 -36.92 0 5.00e+00 4.00e-02 5.45e+01 ... (remaining 6433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1307 0.076 - 0.152: 330 0.152 - 0.228: 35 0.228 - 0.304: 6 0.304 - 0.380: 1 Chirality restraints: 1679 Sorted by residual: chirality pdb=" C4 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C5 NAG B 2 " pdb=" O4 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.51 -2.13 -0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" C1 MAN B 3 " pdb=" O4 NAG B 2 " pdb=" C2 MAN B 3 " pdb=" O5 MAN B 3 " both_signs ideal model delta sigma weight residual False 2.40 2.43 -0.03 2.00e-02 2.50e+03 2.19e+00 chirality pdb=" CG LEU A 854 " pdb=" CB LEU A 854 " pdb=" CD1 LEU A 854 " pdb=" CD2 LEU A 854 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1676 not shown) Planarity restraints: 1834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.209 2.00e-02 2.50e+03 1.74e-01 3.77e+02 pdb=" C7 NAG C 402 " 0.055 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.149 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.286 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.137 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" C7 NAG B 1 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.027 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.193 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.131 2.00e-02 2.50e+03 1.07e-01 1.44e+02 pdb=" C7 NAG C 401 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.099 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.170 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.023 2.00e-02 2.50e+03 ... (remaining 1831 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 83 2.58 - 3.16: 8170 3.16 - 3.74: 16615 3.74 - 4.32: 24476 4.32 - 4.90: 40197 Nonbonded interactions: 89541 Sorted by model distance: nonbonded pdb=" F2 ALF A1301 " pdb="MG MG A1303 " model vdw 2.002 2.120 nonbonded pdb=" OD1 ASP A 786 " pdb="MG MG A1303 " model vdw 2.045 2.170 nonbonded pdb=" OD1 ASN A 331 " pdb=" OH TYR C 160 " model vdw 2.229 2.440 nonbonded pdb=" O TYR A 881 " pdb=" OG1 THR A 886 " model vdw 2.281 2.440 nonbonded pdb=" OD2 ASP A 409 " pdb=" F2 ALF A1301 " model vdw 2.284 2.390 ... (remaining 89536 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 Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 1 5.49 5 Mg 1 5.21 5 S 56 5.16 5 C 6871 2.51 5 N 1745 2.21 5 O 1912 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.480 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 30.890 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 : 0.012 0.124 10836 Z= 0.746 Angle : 1.433 68.506 14700 Z= 0.680 Chirality : 0.066 0.380 1679 Planarity : 0.010 0.174 1831 Dihedral : 15.234 141.848 3967 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.78 % Favored : 93.14 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.48 % 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: -3.41 (0.19), residues: 1297 helix: -2.41 (0.16), residues: 573 sheet: -0.57 (0.39), residues: 151 loop : -2.49 (0.23), residues: 573 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 1.208 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 151 average time/residue: 1.2612 time to fit residues: 205.3288 Evaluate side-chains 104 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 1.284 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.7587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 118 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 278 GLN A 333 ASN ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 ASN A 487 GLN A 580 HIS A 789 ASN C 36 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10836 Z= 0.182 Angle : 0.614 8.598 14700 Z= 0.321 Chirality : 0.044 0.246 1679 Planarity : 0.005 0.053 1831 Dihedral : 8.835 110.103 1489 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.87 (0.22), residues: 1297 helix: -0.83 (0.20), residues: 582 sheet: -0.08 (0.42), residues: 154 loop : -1.97 (0.24), residues: 561 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 1.479 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 138 average time/residue: 1.0964 time to fit residues: 165.9025 Evaluate side-chains 106 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0894 time to fit residues: 1.7462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 10836 Z= 0.203 Angle : 0.593 9.004 14700 Z= 0.307 Chirality : 0.044 0.183 1679 Planarity : 0.005 0.054 1831 Dihedral : 8.266 88.807 1489 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 3.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.23 (0.23), residues: 1297 helix: -0.21 (0.21), residues: 582 sheet: 0.23 (0.43), residues: 151 loop : -1.74 (0.25), residues: 564 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 100 time to evaluate : 1.267 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 17 residues processed: 132 average time/residue: 1.0040 time to fit residues: 146.2294 Evaluate side-chains 111 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 1.257 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.0812 time to fit residues: 1.7395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 56 optimal weight: 0.0970 chunk 79 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10836 Z= 0.193 Angle : 0.570 8.909 14700 Z= 0.295 Chirality : 0.043 0.186 1679 Planarity : 0.004 0.057 1831 Dihedral : 7.635 63.378 1489 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.81 (0.23), residues: 1297 helix: 0.18 (0.22), residues: 574 sheet: 0.41 (0.44), residues: 147 loop : -1.51 (0.25), residues: 576 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 105 time to evaluate : 1.293 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 19 residues processed: 136 average time/residue: 1.0604 time to fit residues: 158.9922 Evaluate side-chains 116 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 0.0980 time to fit residues: 1.8956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 107 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN C 190 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 10836 Z= 0.266 Angle : 0.597 8.890 14700 Z= 0.309 Chirality : 0.045 0.188 1679 Planarity : 0.004 0.058 1831 Dihedral : 7.358 58.966 1489 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.73 (0.23), residues: 1297 helix: 0.17 (0.22), residues: 580 sheet: 0.69 (0.44), residues: 151 loop : -1.48 (0.26), residues: 566 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 103 time to evaluate : 1.243 Fit side-chains outliers start: 36 outliers final: 19 residues processed: 133 average time/residue: 1.0505 time to fit residues: 153.5303 Evaluate side-chains 116 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 0.0994 time to fit residues: 1.8661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.3980 chunk 113 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 0.2980 chunk 104 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 10836 Z= 0.291 Angle : 0.610 8.874 14700 Z= 0.316 Chirality : 0.047 0.378 1679 Planarity : 0.005 0.059 1831 Dihedral : 7.173 57.231 1489 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 3.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.75 (0.23), residues: 1297 helix: 0.17 (0.22), residues: 585 sheet: 0.67 (0.44), residues: 151 loop : -1.53 (0.26), residues: 561 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 100 time to evaluate : 1.143 Fit side-chains outliers start: 41 outliers final: 24 residues processed: 136 average time/residue: 1.0533 time to fit residues: 157.6042 Evaluate side-chains 121 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 2 average time/residue: 0.1043 time to fit residues: 2.2545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10836 Z= 0.166 Angle : 0.546 10.003 14700 Z= 0.281 Chirality : 0.043 0.192 1679 Planarity : 0.004 0.059 1831 Dihedral : 6.532 57.169 1489 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.43 (0.23), residues: 1297 helix: 0.54 (0.22), residues: 579 sheet: 0.53 (0.42), residues: 160 loop : -1.40 (0.26), residues: 558 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 104 time to evaluate : 1.249 Fit side-chains outliers start: 34 outliers final: 20 residues processed: 136 average time/residue: 1.0199 time to fit residues: 152.5428 Evaluate side-chains 117 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 1.6954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 98 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 838 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10836 Z= 0.164 Angle : 0.550 10.071 14700 Z= 0.282 Chirality : 0.043 0.190 1679 Planarity : 0.004 0.058 1831 Dihedral : 6.195 56.865 1489 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.27 (0.24), residues: 1297 helix: 0.66 (0.22), residues: 581 sheet: 0.63 (0.43), residues: 160 loop : -1.31 (0.26), residues: 556 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 1.364 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 21 residues processed: 128 average time/residue: 1.0892 time to fit residues: 157.4246 Evaluate side-chains 120 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 1.8361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 110 optimal weight: 0.4980 chunk 76 optimal weight: 0.7980 chunk 123 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10836 Z= 0.161 Angle : 0.549 10.163 14700 Z= 0.280 Chirality : 0.044 0.432 1679 Planarity : 0.004 0.059 1831 Dihedral : 5.987 58.268 1489 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.17 (0.24), residues: 1297 helix: 0.71 (0.22), residues: 588 sheet: 0.69 (0.42), residues: 160 loop : -1.26 (0.26), residues: 549 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 1.215 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 23 residues processed: 129 average time/residue: 1.0186 time to fit residues: 145.2516 Evaluate side-chains 122 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 2 average time/residue: 0.1715 time to fit residues: 2.1308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 119 optimal weight: 0.0570 chunk 103 optimal weight: 6.9990 chunk 10 optimal weight: 0.0370 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 838 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 10836 Z= 0.150 Angle : 0.555 16.614 14700 Z= 0.279 Chirality : 0.043 0.243 1679 Planarity : 0.004 0.058 1831 Dihedral : 5.818 59.219 1489 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.02 (0.24), residues: 1297 helix: 0.85 (0.22), residues: 587 sheet: 0.73 (0.42), residues: 160 loop : -1.18 (0.26), residues: 550 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 1.271 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 130 average time/residue: 1.0105 time to fit residues: 145.2750 Evaluate side-chains 122 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 1.7828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 15 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.191880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.151187 restraints weight = 10897.358| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.15 r_work: 0.3127 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10836 Z= 0.169 Angle : 0.558 13.317 14700 Z= 0.282 Chirality : 0.043 0.256 1679 Planarity : 0.004 0.058 1831 Dihedral : 5.815 59.753 1489 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.08 (0.24), residues: 1297 helix: 0.86 (0.22), residues: 582 sheet: 0.90 (0.42), residues: 162 loop : -1.07 (0.26), residues: 553 =============================================================================== Job complete usr+sys time: 3363.72 seconds wall clock time: 60 minutes 54.52 seconds (3654.52 seconds total)