Starting phenix.real_space_refine on Thu Nov 16 00:08:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9h_41111/11_2023/8t9h_41111.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9h_41111/11_2023/8t9h_41111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9h_41111/11_2023/8t9h_41111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9h_41111/11_2023/8t9h_41111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9h_41111/11_2023/8t9h_41111.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9h_41111/11_2023/8t9h_41111.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1622 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 201 5.49 5 S 29 5.16 5 C 6930 2.51 5 N 2237 2.21 5 O 2642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 12039 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 750 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "H" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 709 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2012 Classifications: {'DNA': 99} Link IDs: {'rna3p': 98} Chain: "J" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2110 Classifications: {'DNA': 102} Link IDs: {'rna3p': 101} Chain: "K" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1969 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 243} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Time building chain proxies: 6.34, per 1000 atoms: 0.53 Number of scatterers: 12039 At special positions: 0 Unit cell: (92.064, 118.368, 127.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 201 15.00 O 2642 8.00 N 2237 7.00 C 6930 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: 6.12 Conformation dependent library (CDL) restraints added in 1.4 seconds 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 13 sheets defined 65.9% alpha, 5.5% beta 96 base pairs and 141 stacking pairs defined. Time for finding SS restraints: 4.82 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.990A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.523A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.569A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.530A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.511A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.505A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.173A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (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 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.669A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.492A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 39 through 50 removed outlier: 3.524A pdb=" N TYR H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.609A pdb=" N ALA H 108 " --> pdb=" O PRO H 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 88 Processing helix chain 'K' and resid 88 through 94 Processing helix chain 'K' and resid 134 through 148 removed outlier: 3.697A pdb=" N LYS K 138 " --> pdb=" O GLN K 134 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU K 142 " --> pdb=" O LYS K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 158 Processing helix chain 'K' and resid 160 through 169 removed outlier: 3.652A pdb=" N LEU K 168 " --> pdb=" O ARG K 164 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN K 169 " --> pdb=" O HIS K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 188 removed outlier: 3.509A pdb=" N ILE K 184 " --> pdb=" O GLU K 180 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR K 185 " --> pdb=" O HIS K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 235 through 243 removed outlier: 3.709A pdb=" N ASN K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET K 241 " --> pdb=" O ILE K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 270 removed outlier: 3.683A pdb=" N PHE K 270 " --> pdb=" O PRO K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 328 Processing helix chain 'K' and resid 329 through 333 Processing helix chain 'K' and resid 354 through 361 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.154A pdb=" N ARG A 83 " --> pdb=" O VAL F 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 'B' and resid 20 through 22 removed outlier: 3.570A pdb=" N CYS K 260 " --> pdb=" O SER K 255 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA K 261 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA K 232 " --> pdb=" O LEU K 263 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU K 265 " --> pdb=" O CYS K 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.652A pdb=" N ARG B 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.453A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.049A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.287A pdb=" N ARG G 42 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'K' and resid 195 through 199 removed outlier: 3.697A pdb=" N GLU K 301 " --> pdb=" O ALA K 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 279 through 283 483 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 247 hydrogen bonds 486 hydrogen bond angles 0 basepair planarities 96 basepair parallelities 141 stacking parallelities Total time for adding SS restraints: 4.48 Time building geometry restraints manager: 6.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2831 1.33 - 1.45: 3313 1.45 - 1.57: 6062 1.57 - 1.69: 400 1.69 - 1.81: 44 Bond restraints: 12650 Sorted by residual: bond pdb=" C3' DG I 94 " pdb=" O3' DG I 94 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" C3' DA J 44 " pdb=" O3' DA J 44 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" CA ILE C 79 " pdb=" CB ILE C 79 " ideal model delta sigma weight residual 1.546 1.536 0.010 8.80e-03 1.29e+04 1.23e+00 bond pdb=" O5' DA I 49 " pdb=" C5' DA I 49 " ideal model delta sigma weight residual 1.423 1.455 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" C3' DT I 48 " pdb=" O3' DT I 48 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 9.75e-01 ... (remaining 12645 not shown) Histogram of bond angle deviations from ideal: 97.33 - 104.65: 843 104.65 - 111.97: 6822 111.97 - 119.29: 3798 119.29 - 126.61: 5842 126.61 - 133.94: 623 Bond angle restraints: 17928 Sorted by residual: angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 111.02 116.36 -5.34 1.86e+00 2.89e-01 8.23e+00 angle pdb=" C3' DT I 48 " pdb=" C2' DT I 48 " pdb=" C1' DT I 48 " ideal model delta sigma weight residual 101.60 97.33 4.27 1.50e+00 4.44e-01 8.12e+00 angle pdb=" C ASN G 73 " pdb=" N LYS G 74 " pdb=" CA LYS G 74 " ideal model delta sigma weight residual 121.54 126.03 -4.49 1.91e+00 2.74e-01 5.52e+00 angle pdb=" C4' DA I 49 " pdb=" C3' DA I 49 " pdb=" C2' DA I 49 " ideal model delta sigma weight residual 102.40 98.93 3.47 1.50e+00 4.44e-01 5.36e+00 angle pdb=" N PRO D 103 " pdb=" CA PRO D 103 " pdb=" C PRO D 103 " ideal model delta sigma weight residual 110.21 113.95 -3.74 1.64e+00 3.72e-01 5.21e+00 ... (remaining 17923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 6007 35.17 - 70.34: 896 70.34 - 105.50: 42 105.50 - 140.67: 0 140.67 - 175.84: 3 Dihedral angle restraints: 6948 sinusoidal: 4038 harmonic: 2910 Sorted by residual: dihedral pdb=" C4' DA J 44 " pdb=" C3' DA J 44 " pdb=" O3' DA J 44 " pdb=" P DT J 45 " ideal model delta sinusoidal sigma weight residual 220.00 44.16 175.84 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 94 " pdb=" C3' DG I 94 " pdb=" O3' DG I 94 " pdb=" P DC I 95 " ideal model delta sinusoidal sigma weight residual 220.00 51.01 168.99 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DG I 85 " pdb=" C3' DG I 85 " pdb=" O3' DG I 85 " pdb=" P DT I 86 " ideal model delta sinusoidal sigma weight residual 220.00 55.01 164.99 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 6945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1456 0.031 - 0.063: 428 0.063 - 0.094: 89 0.094 - 0.125: 53 0.125 - 0.156: 5 Chirality restraints: 2031 Sorted by residual: chirality pdb=" C3' DT I 48 " pdb=" C4' DT I 48 " pdb=" O3' DT I 48 " pdb=" C2' DT I 48 " both_signs ideal model delta sigma weight residual False -2.66 -2.82 0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" P DT I 86 " pdb=" OP1 DT I 86 " pdb=" OP2 DT I 86 " pdb=" O5' DT I 86 " both_signs ideal model delta sigma weight residual True 2.35 -2.49 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 2028 not shown) Planarity restraints: 1592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 49 " 0.031 2.00e-02 2.50e+03 1.38e-02 5.22e+00 pdb=" N9 DA I 49 " -0.029 2.00e-02 2.50e+03 pdb=" C8 DA I 49 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 49 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DA I 49 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 49 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 49 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DA I 49 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 49 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 49 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DA I 49 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 98 " 0.001 2.00e-02 2.50e+03 1.40e-02 4.44e+00 pdb=" N1 DC J 98 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DC J 98 " -0.034 2.00e-02 2.50e+03 pdb=" O2 DC J 98 " 0.017 2.00e-02 2.50e+03 pdb=" N3 DC J 98 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DC J 98 " -0.013 2.00e-02 2.50e+03 pdb=" N4 DC J 98 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC J 98 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC J 98 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 88 " -0.024 2.00e-02 2.50e+03 1.15e-02 3.31e+00 pdb=" N1 DT I 88 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DT I 88 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 88 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 88 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 88 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT I 88 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 88 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 88 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT I 88 " 0.004 2.00e-02 2.50e+03 ... (remaining 1589 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2498 2.78 - 3.31: 11748 3.31 - 3.84: 23449 3.84 - 4.37: 25860 4.37 - 4.90: 39469 Nonbonded interactions: 103024 Sorted by model distance: nonbonded pdb=" OD1 ASP B 85 " pdb=" OH TYR D 83 " model vdw 2.255 2.440 nonbonded pdb=" NE2 GLN K 262 " pdb=" O LEU K 263 " model vdw 2.256 2.520 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.256 2.440 nonbonded pdb=" O GLU K 236 " pdb=" ND2 ASN K 240 " model vdw 2.264 2.520 nonbonded pdb=" O ILE K 271 " pdb=" OH TYR K 307 " model vdw 2.264 2.440 ... (remaining 103019 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 44 through 135) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 35 through 125) 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 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 7.380 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 37.920 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 : 0.003 0.038 12650 Z= 0.174 Angle : 0.519 5.574 17928 Z= 0.317 Chirality : 0.035 0.156 2031 Planarity : 0.004 0.034 1592 Dihedral : 24.793 175.838 5068 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.97 % Allowed : 6.18 % Favored : 92.85 % 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: 1.98 (0.27), residues: 981 helix: 2.29 (0.21), residues: 624 sheet: -0.80 (0.82), residues: 44 loop : -0.37 (0.33), residues: 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 196 time to evaluate : 1.153 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 202 average time/residue: 0.2384 time to fit residues: 69.0404 Evaluate side-chains 170 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1019 time to fit residues: 1.6554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 40.0000 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 112 GLN G 112 GLN K 134 GLN K 174 GLN ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 346 ASN ** K 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12650 Z= 0.263 Angle : 0.561 5.784 17928 Z= 0.328 Chirality : 0.037 0.149 2031 Planarity : 0.004 0.033 1592 Dihedral : 29.964 176.784 3137 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.70 % Allowed : 12.48 % Favored : 85.82 % 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: 2.15 (0.27), residues: 981 helix: 2.42 (0.21), residues: 638 sheet: -0.87 (0.83), residues: 44 loop : -0.41 (0.33), residues: 299 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 176 average time/residue: 0.2381 time to fit residues: 60.7712 Evaluate side-chains 170 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1142 time to fit residues: 3.1392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12650 Z= 0.192 Angle : 0.534 6.099 17928 Z= 0.315 Chirality : 0.036 0.154 2031 Planarity : 0.003 0.035 1592 Dihedral : 29.891 176.932 3137 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.33 % Allowed : 12.12 % Favored : 86.55 % 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: 2.26 (0.27), residues: 981 helix: 2.51 (0.21), residues: 637 sheet: -0.90 (0.82), residues: 44 loop : -0.37 (0.34), residues: 300 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 180 time to evaluate : 1.070 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 183 average time/residue: 0.2460 time to fit residues: 64.0344 Evaluate side-chains 170 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1067 time to fit residues: 1.7471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 0.0060 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN F 93 GLN ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12650 Z= 0.217 Angle : 0.547 6.481 17928 Z= 0.320 Chirality : 0.036 0.156 2031 Planarity : 0.003 0.031 1592 Dihedral : 29.929 177.615 3137 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.97 % Allowed : 13.94 % Favored : 85.09 % 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: 2.23 (0.27), residues: 981 helix: 2.46 (0.21), residues: 640 sheet: -0.95 (0.82), residues: 44 loop : -0.32 (0.34), residues: 297 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 173 time to evaluate : 1.105 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 174 average time/residue: 0.2402 time to fit residues: 60.3893 Evaluate side-chains 169 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1154 time to fit residues: 1.9469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 30.0000 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12650 Z= 0.264 Angle : 0.572 7.583 17928 Z= 0.332 Chirality : 0.037 0.164 2031 Planarity : 0.004 0.032 1592 Dihedral : 30.062 178.384 3137 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.09 % Allowed : 14.91 % Favored : 84.00 % 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: 2.20 (0.27), residues: 981 helix: 2.44 (0.21), residues: 639 sheet: -0.97 (0.82), residues: 44 loop : -0.33 (0.34), residues: 298 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 166 time to evaluate : 1.089 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 170 average time/residue: 0.2236 time to fit residues: 55.8890 Evaluate side-chains 171 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1093 time to fit residues: 2.1347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12650 Z= 0.186 Angle : 0.542 8.457 17928 Z= 0.316 Chirality : 0.036 0.160 2031 Planarity : 0.003 0.038 1592 Dihedral : 29.970 178.079 3137 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.73 % Allowed : 16.36 % Favored : 82.91 % 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: 2.26 (0.27), residues: 981 helix: 2.52 (0.21), residues: 637 sheet: -0.94 (0.82), residues: 44 loop : -0.38 (0.34), residues: 300 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 183 time to evaluate : 1.156 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 184 average time/residue: 0.2537 time to fit residues: 66.0531 Evaluate side-chains 172 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1184 time to fit residues: 1.7501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS D 84 ASN F 93 GLN ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12650 Z= 0.197 Angle : 0.559 8.886 17928 Z= 0.321 Chirality : 0.036 0.163 2031 Planarity : 0.003 0.034 1592 Dihedral : 29.947 178.305 3137 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.36 % Allowed : 17.45 % Favored : 82.18 % 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: 2.27 (0.27), residues: 981 helix: 2.52 (0.21), residues: 636 sheet: -0.94 (0.81), residues: 44 loop : -0.34 (0.34), residues: 301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 171 time to evaluate : 1.088 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 171 average time/residue: 0.2500 time to fit residues: 60.9187 Evaluate side-chains 168 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1269 time to fit residues: 1.7116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12650 Z= 0.184 Angle : 0.562 10.338 17928 Z= 0.321 Chirality : 0.036 0.161 2031 Planarity : 0.003 0.035 1592 Dihedral : 29.876 178.162 3137 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.24 % Allowed : 17.94 % Favored : 81.82 % 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: 2.25 (0.27), residues: 981 helix: 2.51 (0.21), residues: 636 sheet: -0.92 (0.81), residues: 44 loop : -0.35 (0.34), residues: 301 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 173 time to evaluate : 1.213 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 173 average time/residue: 0.2279 time to fit residues: 57.5077 Evaluate side-chains 170 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1312 time to fit residues: 1.5230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.1980 chunk 106 optimal weight: 0.0770 chunk 62 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12650 Z= 0.170 Angle : 0.561 9.580 17928 Z= 0.320 Chirality : 0.036 0.159 2031 Planarity : 0.004 0.039 1592 Dihedral : 29.745 177.949 3137 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.12 % Allowed : 17.94 % Favored : 81.94 % 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: 2.21 (0.27), residues: 981 helix: 2.46 (0.21), residues: 637 sheet: -0.89 (0.81), residues: 44 loop : -0.35 (0.34), residues: 300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.044 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.2411 time to fit residues: 63.3015 Evaluate side-chains 172 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 12650 Z= 0.386 Angle : 0.664 9.823 17928 Z= 0.372 Chirality : 0.039 0.186 2031 Planarity : 0.004 0.030 1592 Dihedral : 30.137 179.622 3137 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.24 % Allowed : 18.42 % Favored : 81.33 % 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: 1.95 (0.27), residues: 981 helix: 2.24 (0.21), residues: 638 sheet: -1.14 (0.79), residues: 44 loop : -0.41 (0.33), residues: 299 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 1.179 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 165 average time/residue: 0.2495 time to fit residues: 59.2047 Evaluate side-chains 161 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1124 time to fit residues: 1.5829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 0.0010 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.068899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.046015 restraints weight = 56080.376| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.38 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12650 Z= 0.188 Angle : 0.597 13.364 17928 Z= 0.336 Chirality : 0.036 0.161 2031 Planarity : 0.004 0.041 1592 Dihedral : 29.915 178.227 3137 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.24 % Allowed : 18.42 % Favored : 81.33 % 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: 2.04 (0.27), residues: 981 helix: 2.31 (0.21), residues: 637 sheet: -0.97 (0.81), residues: 44 loop : -0.37 (0.33), residues: 300 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2188.80 seconds wall clock time: 40 minutes 46.18 seconds (2446.18 seconds total)