Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 14:38:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7d_10394/07_2023/6t7d_10394.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7d_10394/07_2023/6t7d_10394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7d_10394/07_2023/6t7d_10394.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7d_10394/07_2023/6t7d_10394.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7d_10394/07_2023/6t7d_10394.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7d_10394/07_2023/6t7d_10394.pdb" } resolution = 4.4 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= 0.004 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians P 234 5.49 5 C 4002 2.51 5 N 1716 2.21 5 O 2257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 8209 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 392 Classifications: {'peptide': 98} Incomplete info: {'backbone_only': 95} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 430 Unresolved non-hydrogen angles: 610 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 123 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 206 Chain: "B" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 336 Classifications: {'peptide': 84} Incomplete info: {'backbone_only': 76} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 500 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 162 Chain: "C" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 440 Classifications: {'peptide': 110} Incomplete info: {'backbone_only': 101} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 605 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 175 Chain: "D" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 380 Classifications: {'peptide': 95} Incomplete info: {'backbone_only': 90} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 376 Unresolved non-hydrogen angles: 540 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 159 Chain: "E" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 388 Classifications: {'peptide': 97} Incomplete info: {'backbone_only': 94} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 425 Unresolved non-hydrogen angles: 604 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 206 Chain: "F" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 349 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 78} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 363 Unresolved non-hydrogen angles: 515 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 167 Chain: "G" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 440 Classifications: {'peptide': 110} Incomplete info: {'backbone_only': 101} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 605 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 175 Chain: "H" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 380 Classifications: {'peptide': 95} Incomplete info: {'backbone_only': 90} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 376 Unresolved non-hydrogen angles: 540 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 159 Chain: "I" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2376 Classifications: {'DNA': 117} Link IDs: {'rna3p': 116} Chain: "J" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2421 Classifications: {'DNA': 117} Link IDs: {'rna3p': 116} Chain: "K" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 307 Classifications: {'peptide': 77} Incomplete info: {'backbone_only': 74, 'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 178 Time building chain proxies: 5.39, per 1000 atoms: 0.66 Number of scatterers: 8209 At special positions: 0 Unit cell: (74.55, 124.95, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 234 15.00 O 2257 8.00 N 1716 7.00 C 4002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 4.67 Conformation dependent library (CDL) restraints added in 962.5 milliseconds 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 67.6% alpha, 1.9% beta 117 base pairs and 202 stacking pairs defined. Time for finding SS restraints: 4.99 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.829A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.901A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.925A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.811A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.677A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.670A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.603A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.745A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.769A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.677A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 95 removed outlier: 3.668A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 90 through 95' Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.604A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 71 removed outlier: 4.078A pdb=" N ILE K 62 " --> pdb=" O VAL K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 90 Processing helix chain 'K' and resid 92 through 94 No H-bonds generated for 'chain 'K' and resid 92 through 94' Processing helix chain 'K' and resid 95 through 113 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.154A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.888A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.124A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.562A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.195A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 419 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 278 hydrogen bonds 552 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 202 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.29: 1087 1.29 - 1.37: 2209 1.37 - 1.46: 2150 1.46 - 1.54: 2868 1.54 - 1.62: 468 Bond restraints: 8782 Sorted by residual: bond pdb=" C ILE K 96 " pdb=" N PRO K 97 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.36e-02 5.41e+03 6.22e+00 bond pdb=" C3' DC I 13 " pdb=" O3' DC I 13 " ideal model delta sigma weight residual 1.422 1.492 -0.070 3.00e-02 1.11e+03 5.48e+00 bond pdb=" C3' DG I 110 " pdb=" O3' DG I 110 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.42e+00 bond pdb=" C3' DT I 38 " pdb=" O3' DT I 38 " ideal model delta sigma weight residual 1.422 1.468 -0.046 3.00e-02 1.11e+03 2.38e+00 bond pdb=" C LEU E 65 " pdb=" N PRO E 66 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.30e+00 ... (remaining 8777 not shown) Histogram of bond angle deviations from ideal: 97.09 - 104.24: 847 104.24 - 111.39: 3471 111.39 - 118.55: 2630 118.55 - 125.70: 4829 125.70 - 132.85: 757 Bond angle restraints: 12534 Sorted by residual: angle pdb=" CA LYS F 20 " pdb=" C LYS F 20 " pdb=" N VAL F 21 " ideal model delta sigma weight residual 119.63 115.92 3.71 8.10e-01 1.52e+00 2.10e+01 angle pdb=" CA LEU F 22 " pdb=" C LEU F 22 " pdb=" N ARG F 23 " ideal model delta sigma weight residual 119.63 115.95 3.68 8.10e-01 1.52e+00 2.06e+01 angle pdb=" C2' DA J 53 " pdb=" C1' DA J 53 " pdb=" N9 DA J 53 " ideal model delta sigma weight residual 113.50 119.97 -6.47 1.50e+00 4.44e-01 1.86e+01 angle pdb=" C PRO K 72 " pdb=" N ASP K 73 " pdb=" CA ASP K 73 " ideal model delta sigma weight residual 122.07 127.37 -5.30 1.43e+00 4.89e-01 1.38e+01 angle pdb=" C3' DC I 13 " pdb=" O3' DC I 13 " pdb=" P DT I 14 " ideal model delta sigma weight residual 120.20 125.32 -5.12 1.50e+00 4.44e-01 1.17e+01 ... (remaining 12529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.40: 1878 30.40 - 60.80: 1228 60.80 - 91.20: 69 91.20 - 121.60: 0 121.60 - 152.00: 3 Dihedral angle restraints: 3178 sinusoidal: 2335 harmonic: 843 Sorted by residual: dihedral pdb=" CA TYR H 34 " pdb=" C TYR H 34 " pdb=" N SER H 35 " pdb=" CA SER H 35 " ideal model delta harmonic sigma weight residual 180.00 -159.04 -20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA TYR D 34 " pdb=" C TYR D 34 " pdb=" N SER D 35 " pdb=" CA SER D 35 " ideal model delta harmonic sigma weight residual -180.00 -159.06 -20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA LYS D 43 " pdb=" C LYS D 43 " pdb=" N GLN D 44 " pdb=" CA GLN D 44 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 3175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 863 0.080 - 0.159: 68 0.159 - 0.239: 4 0.239 - 0.318: 0 0.318 - 0.398: 1 Chirality restraints: 936 Sorted by residual: chirality pdb=" C1' DA J 53 " pdb=" O4' DA J 53 " pdb=" C2' DA J 53 " pdb=" N9 DA J 53 " both_signs ideal model delta sigma weight residual False 2.42 2.02 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" P DC I 111 " pdb=" OP1 DC I 111 " pdb=" OP2 DC I 111 " pdb=" O5' DC I 111 " both_signs ideal model delta sigma weight residual True 2.35 -2.55 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" P DT I 14 " pdb=" OP1 DT I 14 " pdb=" OP2 DT I 14 " pdb=" O5' DT I 14 " both_signs ideal model delta sigma weight residual True 2.35 -2.54 -0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 933 not shown) Planarity restraints: 1077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA J 53 " -0.013 2.00e-02 2.50e+03 3.54e-02 3.44e+01 pdb=" N9 DA J 53 " 0.086 2.00e-02 2.50e+03 pdb=" C8 DA J 53 " -0.072 2.00e-02 2.50e+03 pdb=" N7 DA J 53 " 0.016 2.00e-02 2.50e+03 pdb=" C5 DA J 53 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DA J 53 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA J 53 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA J 53 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DA J 53 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA J 53 " -0.019 2.00e-02 2.50e+03 pdb=" C4 DA J 53 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 95 " -0.029 2.00e-02 2.50e+03 1.61e-02 6.45e+00 pdb=" N1 DT I 95 " 0.041 2.00e-02 2.50e+03 pdb=" C2 DT I 95 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT I 95 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DT I 95 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 95 " -0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 95 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DT I 95 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 95 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT I 95 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 60 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C VAL F 60 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL F 60 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE F 61 " 0.014 2.00e-02 2.50e+03 ... (remaining 1074 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 344 2.67 - 3.22: 6460 3.22 - 3.78: 15338 3.78 - 4.34: 17796 4.34 - 4.90: 23191 Nonbonded interactions: 63129 Sorted by model distance: nonbonded pdb=" N3 DC I 2 " pdb=" N1 DG J 145 " model vdw 2.107 2.600 nonbonded pdb=" O2 DC I 2 " pdb=" C2 DG J 145 " model vdw 2.130 3.260 nonbonded pdb=" C2 DC I 2 " pdb=" N1 DG J 145 " model vdw 2.198 3.340 nonbonded pdb=" O2 DC I 2 " pdb=" N2 DG J 145 " model vdw 2.292 2.520 nonbonded pdb=" N4 DC I 2 " pdb=" O6 DG J 145 " model vdw 2.340 2.520 ... (remaining 63124 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 18 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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 group one per residue 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: 0.100 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: 1.540 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 32.670 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 0.005 0.070 8782 Z= 0.291 Angle : 0.858 6.553 12534 Z= 0.554 Chirality : 0.047 0.398 936 Planarity : 0.005 0.035 1077 Dihedral : 32.637 152.004 3178 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.34 (0.24), residues: 833 helix: -1.43 (0.18), residues: 571 sheet: None (None), residues: 0 loop : -1.42 (0.35), residues: 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.587 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0781 time to fit residues: 3.1102 Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.632 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 chunk 52 optimal weight: 7.9990 chunk 41 optimal weight: 50.0000 chunk 80 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 60 optimal weight: 50.0000 chunk 93 optimal weight: 10.0000 overall best weight: 8.7996 ------------------------------------------------------------------------------- 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: 0.7755 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 8782 Z= 0.286 Angle : 0.657 4.728 12534 Z= 0.422 Chirality : 0.037 0.139 936 Planarity : 0.004 0.018 1077 Dihedral : 32.232 146.154 3178 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.26 (0.28), residues: 833 helix: 1.46 (0.20), residues: 584 sheet: None (None), residues: 0 loop : -0.58 (0.37), residues: 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.591 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0752 time to fit residues: 3.1137 Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.598 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 30.0000 chunk 29 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 chunk 63 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 31 optimal weight: 40.0000 chunk 75 optimal weight: 20.0000 overall best weight: 6.2192 ------------------------------------------------------------------------------- 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: 0.7742 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 8782 Z= 0.212 Angle : 0.594 4.576 12534 Z= 0.382 Chirality : 0.034 0.144 936 Planarity : 0.002 0.016 1077 Dihedral : 32.164 150.521 3178 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.81 (0.29), residues: 833 helix: 2.79 (0.21), residues: 593 sheet: None (None), residues: 0 loop : -0.61 (0.38), residues: 240 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.527 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0717 time to fit residues: 2.9233 Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 20.0000 chunk 70 optimal weight: 50.0000 chunk 48 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 44 optimal weight: 30.0000 chunk 62 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 99 optimal weight: 120.0000 chunk 49 optimal weight: 30.0000 chunk 89 optimal weight: 10.0000 chunk 26 optimal weight: 40.0000 overall best weight: 16.0000 ------------------------------------------------------------------------------- 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: 0.7874 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.058 8782 Z= 0.412 Angle : 0.738 5.961 12534 Z= 0.471 Chirality : 0.041 0.153 936 Planarity : 0.004 0.020 1077 Dihedral : 32.683 151.311 3178 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.62 (0.28), residues: 833 helix: 1.87 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -0.95 (0.38), residues: 241 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.583 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0744 time to fit residues: 3.0172 Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 41 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 0 optimal weight: 70.0000 chunk 50 optimal weight: 30.0000 chunk 89 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 overall best weight: 6.8990 ------------------------------------------------------------------------------- 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: 0.7803 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 8782 Z= 0.230 Angle : 0.605 4.487 12534 Z= 0.387 Chirality : 0.034 0.144 936 Planarity : 0.003 0.017 1077 Dihedral : 32.465 153.230 3178 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.91 (0.30), residues: 833 helix: 2.98 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -0.80 (0.38), residues: 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.650 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0807 time to fit residues: 3.2558 Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.611 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 50.0000 chunk 89 optimal weight: 10.0000 chunk 19 optimal weight: 30.0000 chunk 58 optimal weight: 30.0000 chunk 24 optimal weight: 20.0000 chunk 99 optimal weight: 50.0000 chunk 82 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 chunk 52 optimal weight: 50.0000 overall best weight: 10.7996 ------------------------------------------------------------------------------- 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: 0.7846 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 8782 Z= 0.306 Angle : 0.646 4.671 12534 Z= 0.412 Chirality : 0.036 0.144 936 Planarity : 0.003 0.018 1077 Dihedral : 32.502 151.202 3178 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.41 (0.29), residues: 833 helix: 2.62 (0.21), residues: 589 sheet: None (None), residues: 0 loop : -1.09 (0.38), residues: 244 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.538 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0732 time to fit residues: 2.9814 Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.608 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 50.0000 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 0.0170 chunk 72 optimal weight: 40.0000 chunk 83 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 99 optimal weight: 50.0000 chunk 62 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 45 optimal weight: 30.0000 chunk 61 optimal weight: 9.9990 overall best weight: 9.0028 ------------------------------------------------------------------------------- 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: 0.7823 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 8782 Z= 0.262 Angle : 0.613 4.862 12534 Z= 0.392 Chirality : 0.034 0.148 936 Planarity : 0.003 0.018 1077 Dihedral : 32.384 151.270 3178 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.76 (0.30), residues: 833 helix: 2.93 (0.21), residues: 589 sheet: None (None), residues: 0 loop : -1.09 (0.38), residues: 244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.603 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0763 time to fit residues: 3.2043 Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.588 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 20.0000 chunk 59 optimal weight: 40.0000 chunk 29 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 63 optimal weight: 40.0000 chunk 67 optimal weight: 40.0000 chunk 49 optimal weight: 30.0000 chunk 9 optimal weight: 50.0000 chunk 78 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- 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: 0.7927 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.068 8782 Z= 0.498 Angle : 0.799 7.244 12534 Z= 0.508 Chirality : 0.045 0.158 936 Planarity : 0.005 0.021 1077 Dihedral : 32.867 152.836 3178 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 29.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.28), residues: 833 helix: 1.40 (0.20), residues: 577 sheet: None (None), residues: 0 loop : -1.84 (0.34), residues: 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.669 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0757 time to fit residues: 3.1249 Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.629 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 55 optimal weight: 30.0000 chunk 40 optimal weight: 50.0000 chunk 72 optimal weight: 40.0000 chunk 28 optimal weight: 50.0000 chunk 83 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 60 optimal weight: 40.0000 chunk 97 optimal weight: 20.0000 overall best weight: 16.0000 ------------------------------------------------------------------------------- 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: 0.7907 moved from start: 0.6374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.055 8782 Z= 0.404 Angle : 0.729 6.534 12534 Z= 0.464 Chirality : 0.040 0.152 936 Planarity : 0.004 0.020 1077 Dihedral : 32.909 157.333 3178 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 23.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.28), residues: 833 helix: 1.54 (0.21), residues: 583 sheet: None (None), residues: 0 loop : -2.03 (0.34), residues: 250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.613 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0784 time to fit residues: 3.2353 Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.606 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 40.0000 chunk 46 optimal weight: 8.9990 chunk 68 optimal weight: 40.0000 chunk 102 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 chunk 63 optimal weight: 30.0000 chunk 50 optimal weight: 40.0000 chunk 64 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 overall best weight: 11.1996 ------------------------------------------------------------------------------- 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: 0.7874 moved from start: 0.6395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.038 8782 Z= 0.306 Angle : 0.664 4.964 12534 Z= 0.422 Chirality : 0.037 0.151 936 Planarity : 0.003 0.019 1077 Dihedral : 32.778 153.799 3178 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.71 (0.29), residues: 833 helix: 2.32 (0.21), residues: 577 sheet: None (None), residues: 0 loop : -1.79 (0.35), residues: 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.577 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0765 time to fit residues: 3.0896 Evaluate side-chains 16 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 12 optimal weight: 0.0980 chunk 22 optimal weight: 50.0000 chunk 81 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 chunk 10 optimal weight: 0.0970 chunk 15 optimal weight: 40.0000 chunk 71 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.076692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.053369 restraints weight = 54875.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.053445 restraints weight = 46497.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.053631 restraints weight = 36944.928| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 8782 Z= 0.186 Angle : 0.578 4.438 12534 Z= 0.368 Chirality : 0.033 0.155 936 Planarity : 0.002 0.017 1077 Dihedral : 32.450 149.994 3178 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.16 (0.31), residues: 833 helix: 3.48 (0.22), residues: 583 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 250 =============================================================================== Job complete usr+sys time: 895.96 seconds wall clock time: 17 minutes 11.92 seconds (1031.92 seconds total)