Starting phenix.real_space_refine on Sun Dec 10 14:44:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccq_30339/12_2023/7ccq_30339.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccq_30339/12_2023/7ccq_30339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccq_30339/12_2023/7ccq_30339.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccq_30339/12_2023/7ccq_30339.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccq_30339/12_2023/7ccq_30339.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccq_30339/12_2023/7ccq_30339.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 294 5.49 5 S 29 5.16 5 C 8443 2.51 5 N 2743 2.21 5 O 3348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "K ARG 236": "NH1" <-> "NH2" Residue "K TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14857 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 787 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 789 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "K" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2958 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 348} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 7.49, per 1000 atoms: 0.50 Number of scatterers: 14857 At special positions: 0 Unit cell: (125, 113, 139, 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 294 15.00 O 3348 8.00 N 2743 7.00 C 8443 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: 7.11 Conformation dependent library (CDL) restraints added in 2.0 seconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 66.2% alpha, 6.0% beta 134 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 6.63 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.596A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.607A 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 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.730A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.157A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.677A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.531A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 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: 4.238A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.531A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'K' and resid 161 through 176 Processing helix chain 'K' and resid 178 through 198 removed outlier: 4.309A pdb=" N ALA K 182 " --> pdb=" O ASP K 178 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS K 198 " --> pdb=" O LEU K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 204 removed outlier: 3.875A pdb=" N ARG K 204 " --> pdb=" O SER K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 266 removed outlier: 3.663A pdb=" N GLN K 264 " --> pdb=" O ASN K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 289 removed outlier: 4.354A pdb=" N ASN K 289 " --> pdb=" O LYS K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 335 Processing helix chain 'K' and resid 345 through 354 Processing helix chain 'K' and resid 379 through 389 Processing helix chain 'K' and resid 405 through 424 Processing helix chain 'K' and resid 425 through 427 No H-bonds generated for 'chain 'K' and resid 425 through 427' Processing helix chain 'K' and resid 434 through 449 removed outlier: 3.911A pdb=" N VAL K 438 " --> pdb=" O SER K 434 " (cutoff:3.500A) Processing helix chain 'K' and resid 452 through 458 removed outlier: 3.853A pdb=" N ASP K 456 " --> pdb=" O SER K 453 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ARG K 457 " --> pdb=" O GLN K 454 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LYS K 458 " --> pdb=" O TRP K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 477 Processing helix chain 'K' and resid 497 through 513 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.030A 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 'B' and resid 96 through 98 removed outlier: 5.959A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.264A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.859A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.737A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.991A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 206 through 208 removed outlier: 3.518A pdb=" N PHE K 230 " --> pdb=" O THR K 321 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 206 through 208 removed outlier: 3.518A pdb=" N PHE K 230 " --> pdb=" O THR K 321 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU K 311 " --> pdb=" O ILE K 297 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE K 297 " --> pdb=" O LEU K 311 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 237 through 241 Processing sheet with id=AB5, first strand: chain 'K' and resid 324 through 326 removed outlier: 3.893A pdb=" N TYR K 358 " --> pdb=" O SER K 378 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 336 hydrogen bonds 668 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 7.19 Time building geometry restraints manager: 7.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2815 1.33 - 1.45: 4992 1.45 - 1.57: 7290 1.57 - 1.69: 584 1.69 - 1.81: 44 Bond restraints: 15725 Sorted by residual: bond pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " ideal model delta sigma weight residual 1.422 1.347 0.075 3.00e-02 1.11e+03 6.18e+00 bond pdb=" C3' DC J 6 " pdb=" O3' DC J 6 " ideal model delta sigma weight residual 1.422 1.350 0.072 3.00e-02 1.11e+03 5.81e+00 bond pdb=" C3' DG I 8 " pdb=" O3' DG I 8 " ideal model delta sigma weight residual 1.422 1.355 0.067 3.00e-02 1.11e+03 5.05e+00 bond pdb=" O5' DC I -28 " pdb=" C5' DC I -28 " ideal model delta sigma weight residual 1.423 1.357 0.066 3.00e-02 1.11e+03 4.86e+00 bond pdb=" C3' DG I -4 " pdb=" O3' DG I -4 " ideal model delta sigma weight residual 1.422 1.356 0.066 3.00e-02 1.11e+03 4.78e+00 ... (remaining 15720 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.32: 1425 105.32 - 112.51: 8521 112.51 - 119.71: 5438 119.71 - 126.90: 6330 126.90 - 134.09: 759 Bond angle restraints: 22473 Sorted by residual: angle pdb=" O5' DT I 31 " pdb=" C5' DT I 31 " pdb=" C4' DT I 31 " ideal model delta sigma weight residual 110.80 103.62 7.18 1.50e+00 4.44e-01 2.29e+01 angle pdb=" O4' DG I -35 " pdb=" C1' DG I -35 " pdb=" N9 DG I -35 " ideal model delta sigma weight residual 108.40 101.73 6.67 1.50e+00 4.44e-01 1.98e+01 angle pdb=" O4' DG I -8 " pdb=" C1' DG I -8 " pdb=" N9 DG I -8 " ideal model delta sigma weight residual 108.40 102.10 6.30 1.50e+00 4.44e-01 1.76e+01 angle pdb=" C4' DC I -26 " pdb=" C3' DC I -26 " pdb=" O3' DC I -26 " ideal model delta sigma weight residual 110.00 104.17 5.83 1.50e+00 4.44e-01 1.51e+01 angle pdb=" O4' DA I -3 " pdb=" C1' DA I -3 " pdb=" N9 DA I -3 " ideal model delta sigma weight residual 108.40 102.60 5.80 1.50e+00 4.44e-01 1.50e+01 ... (remaining 22468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.00: 7258 32.00 - 63.99: 1432 63.99 - 95.99: 42 95.99 - 127.98: 1 127.98 - 159.98: 2 Dihedral angle restraints: 8735 sinusoidal: 5530 harmonic: 3205 Sorted by residual: dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual -180.00 -148.37 -31.63 0 5.00e+00 4.00e-02 4.00e+01 dihedral pdb=" CA PRO K 361 " pdb=" C PRO K 361 " pdb=" N LYS K 362 " pdb=" CA LYS K 362 " ideal model delta harmonic sigma weight residual 180.00 151.94 28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA ILE K 312 " pdb=" C ILE K 312 " pdb=" N SER K 313 " pdb=" CA SER K 313 " ideal model delta harmonic sigma weight residual 180.00 154.05 25.95 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 8732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2126 0.084 - 0.169: 383 0.169 - 0.253: 22 0.253 - 0.337: 1 0.337 - 0.421: 4 Chirality restraints: 2536 Sorted by residual: chirality pdb=" C1' DC I -27 " pdb=" O4' DC I -27 " pdb=" C2' DC I -27 " pdb=" N1 DC I -27 " both_signs ideal model delta sigma weight residual False 2.47 2.05 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" C1' DT J 13 " pdb=" O4' DT J 13 " pdb=" C2' DT J 13 " pdb=" N1 DT J 13 " both_signs ideal model delta sigma weight residual False 2.47 2.07 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" C1' DT I 31 " pdb=" O4' DT I 31 " pdb=" C2' DT I 31 " pdb=" N1 DT I 31 " both_signs ideal model delta sigma weight residual False 2.47 2.10 0.37 2.00e-01 2.50e+01 3.40e+00 ... (remaining 2533 not shown) Planarity restraints: 1830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 31 " 0.052 2.00e-02 2.50e+03 5.17e-02 6.69e+01 pdb=" N1 DT I 31 " -0.131 2.00e-02 2.50e+03 pdb=" C2 DT I 31 " 0.079 2.00e-02 2.50e+03 pdb=" O2 DT I 31 " -0.012 2.00e-02 2.50e+03 pdb=" N3 DT I 31 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DT I 31 " -0.001 2.00e-02 2.50e+03 pdb=" O4 DT I 31 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DT I 31 " 0.007 2.00e-02 2.50e+03 pdb=" C7 DT I 31 " 0.017 2.00e-02 2.50e+03 pdb=" C6 DT I 31 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -2 " -0.048 2.00e-02 2.50e+03 4.15e-02 3.88e+01 pdb=" N1 DC I -2 " 0.102 2.00e-02 2.50e+03 pdb=" C2 DC I -2 " -0.050 2.00e-02 2.50e+03 pdb=" O2 DC I -2 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DC I -2 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DC I -2 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC I -2 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DC I -2 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DC I -2 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 44 " -0.026 2.00e-02 2.50e+03 3.57e-02 3.18e+01 pdb=" N1 DT I 44 " 0.087 2.00e-02 2.50e+03 pdb=" C2 DT I 44 " -0.063 2.00e-02 2.50e+03 pdb=" O2 DT I 44 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DT I 44 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DT I 44 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT I 44 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DT I 44 " -0.006 2.00e-02 2.50e+03 pdb=" C7 DT I 44 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DT I 44 " -0.013 2.00e-02 2.50e+03 ... (remaining 1827 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2684 2.77 - 3.30: 12926 3.30 - 3.83: 29462 3.83 - 4.37: 33969 4.37 - 4.90: 49238 Nonbonded interactions: 128279 Sorted by model distance: nonbonded pdb=" N2 DG I 21 " pdb=" O2 DC J -21 " model vdw 2.235 2.496 nonbonded pdb=" OH TYR H 40 " pdb=" OP1 DG I 48 " model vdw 2.291 2.440 nonbonded pdb=" NH2 ARG C 32 " pdb=" OE1 GLU D 35 " model vdw 2.321 2.520 nonbonded pdb=" OH TYR K 249 " pdb=" OG SER K 333 " model vdw 2.331 2.440 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 78 " model vdw 2.331 2.440 ... (remaining 128274 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' selection = (chain 'E' and resid 40 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 16 through 116) selection = (chain 'G' and resid 16 through 116) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 32 through 123) } 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: 1.320 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: 0.020 Extract box with map and model: 6.450 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 47.720 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.010 0.093 15725 Z= 0.576 Angle : 1.033 9.515 22473 Z= 0.606 Chirality : 0.063 0.421 2536 Planarity : 0.009 0.063 1830 Dihedral : 24.879 159.981 6661 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.89 (0.20), residues: 1081 helix: -1.61 (0.15), residues: 699 sheet: -2.19 (0.58), residues: 46 loop : -2.16 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP K 375 HIS 0.010 0.003 HIS B 75 PHE 0.028 0.004 PHE C 25 TYR 0.050 0.004 TYR F 98 ARG 0.012 0.001 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.3879 time to fit residues: 172.0594 Evaluate side-chains 197 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 260 ASN K 494 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15725 Z= 0.245 Angle : 0.639 8.253 22473 Z= 0.370 Chirality : 0.038 0.178 2536 Planarity : 0.005 0.050 1830 Dihedral : 29.754 161.608 4426 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.11 % Allowed : 9.60 % Favored : 88.29 % 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: -0.42 (0.24), residues: 1081 helix: 0.47 (0.18), residues: 708 sheet: -1.15 (0.75), residues: 36 loop : -1.68 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 375 HIS 0.007 0.001 HIS B 75 PHE 0.018 0.002 PHE A 67 TYR 0.042 0.002 TYR F 88 ARG 0.009 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 239 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 251 average time/residue: 0.2961 time to fit residues: 104.9327 Evaluate side-chains 215 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 202 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1743 time to fit residues: 5.2837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.0670 chunk 101 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 75 HIS H 67 ASN K 449 ASN K 466 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15725 Z= 0.305 Angle : 0.633 6.717 22473 Z= 0.363 Chirality : 0.038 0.152 2536 Planarity : 0.005 0.045 1830 Dihedral : 29.873 161.846 4426 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.90 % Allowed : 13.71 % Favored : 84.39 % 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: 0.48 (0.25), residues: 1081 helix: 1.22 (0.18), residues: 709 sheet: -0.45 (0.93), residues: 29 loop : -1.53 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 375 HIS 0.007 0.001 HIS B 75 PHE 0.017 0.002 PHE K 357 TYR 0.049 0.003 TYR F 88 ARG 0.007 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 223 time to evaluate : 1.232 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 229 average time/residue: 0.2938 time to fit residues: 96.1116 Evaluate side-chains 212 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 203 time to evaluate : 1.290 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1657 time to fit residues: 4.2054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 58 optimal weight: 0.0980 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN G 38 ASN K 217 HIS ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 449 ASN K 466 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 15725 Z= 0.388 Angle : 0.672 8.383 22473 Z= 0.380 Chirality : 0.040 0.175 2536 Planarity : 0.005 0.072 1830 Dihedral : 30.097 163.171 4426 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.32 % Allowed : 15.19 % Favored : 82.49 % 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: 0.58 (0.25), residues: 1081 helix: 1.28 (0.18), residues: 714 sheet: -0.34 (0.84), residues: 39 loop : -1.51 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 455 HIS 0.005 0.001 HIS B 75 PHE 0.020 0.002 PHE A 67 TYR 0.069 0.003 TYR F 88 ARG 0.006 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 204 time to evaluate : 1.243 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 213 average time/residue: 0.2877 time to fit residues: 88.1531 Evaluate side-chains 212 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 197 time to evaluate : 1.263 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1539 time to fit residues: 5.6214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 110 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15725 Z= 0.251 Angle : 0.601 7.935 22473 Z= 0.346 Chirality : 0.036 0.180 2536 Planarity : 0.004 0.045 1830 Dihedral : 29.838 164.966 4426 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.05 % Allowed : 16.98 % Favored : 81.96 % 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: 0.93 (0.25), residues: 1081 helix: 1.59 (0.18), residues: 712 sheet: -0.35 (0.84), residues: 39 loop : -1.43 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 455 HIS 0.004 0.001 HIS D 49 PHE 0.013 0.001 PHE A 67 TYR 0.054 0.003 TYR D 83 ARG 0.006 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 215 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 219 average time/residue: 0.2818 time to fit residues: 89.3548 Evaluate side-chains 206 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 201 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1984 time to fit residues: 3.1166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15725 Z= 0.352 Angle : 0.646 8.359 22473 Z= 0.368 Chirality : 0.038 0.186 2536 Planarity : 0.005 0.043 1830 Dihedral : 29.973 164.954 4426 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.11 % Allowed : 17.19 % Favored : 80.70 % 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: 0.83 (0.25), residues: 1081 helix: 1.46 (0.18), residues: 714 sheet: -0.36 (0.86), residues: 39 loop : -1.38 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 343 HIS 0.005 0.001 HIS B 75 PHE 0.040 0.002 PHE A 67 TYR 0.061 0.003 TYR F 88 ARG 0.004 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 205 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 213 average time/residue: 0.2803 time to fit residues: 86.4840 Evaluate side-chains 206 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 196 time to evaluate : 1.314 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1313 time to fit residues: 4.1072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 217 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15725 Z= 0.261 Angle : 0.613 8.779 22473 Z= 0.352 Chirality : 0.036 0.173 2536 Planarity : 0.004 0.048 1830 Dihedral : 29.798 165.773 4426 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.05 % Allowed : 18.25 % Favored : 80.70 % 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: 1.00 (0.25), residues: 1081 helix: 1.60 (0.18), residues: 713 sheet: -0.22 (0.89), residues: 39 loop : -1.32 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 455 HIS 0.005 0.001 HIS D 49 PHE 0.032 0.001 PHE A 67 TYR 0.050 0.003 TYR F 88 ARG 0.006 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 213 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 217 average time/residue: 0.2810 time to fit residues: 89.9795 Evaluate side-chains 204 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 199 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1399 time to fit residues: 2.8378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 25 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15725 Z= 0.297 Angle : 0.637 12.643 22473 Z= 0.363 Chirality : 0.037 0.176 2536 Planarity : 0.004 0.046 1830 Dihedral : 29.830 165.880 4426 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.95 % Allowed : 19.09 % Favored : 79.96 % 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: 1.00 (0.25), residues: 1081 helix: 1.57 (0.18), residues: 713 sheet: -0.22 (0.94), residues: 34 loop : -1.25 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 455 HIS 0.005 0.001 HIS D 49 PHE 0.031 0.002 PHE A 67 TYR 0.061 0.003 TYR D 83 ARG 0.006 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 208 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 211 average time/residue: 0.2896 time to fit residues: 89.0815 Evaluate side-chains 201 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 193 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1412 time to fit residues: 3.5598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 15725 Z= 0.456 Angle : 0.727 10.933 22473 Z= 0.409 Chirality : 0.042 0.192 2536 Planarity : 0.005 0.044 1830 Dihedral : 30.191 166.063 4426 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.16 % Allowed : 19.20 % Favored : 79.64 % 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 (0.25), residues: 1081 helix: 1.29 (0.18), residues: 712 sheet: -0.26 (0.94), residues: 34 loop : -1.30 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 455 HIS 0.006 0.001 HIS B 75 PHE 0.032 0.002 PHE A 67 TYR 0.105 0.004 TYR D 83 ARG 0.005 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 198 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 203 average time/residue: 0.2858 time to fit residues: 84.2072 Evaluate side-chains 192 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 186 time to evaluate : 1.255 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1447 time to fit residues: 3.2027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15725 Z= 0.364 Angle : 0.694 14.449 22473 Z= 0.394 Chirality : 0.039 0.187 2536 Planarity : 0.005 0.046 1830 Dihedral : 30.110 167.261 4426 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.53 % Allowed : 20.25 % Favored : 79.22 % 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: 0.71 (0.25), residues: 1081 helix: 1.33 (0.18), residues: 711 sheet: -0.34 (0.93), residues: 34 loop : -1.28 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 455 HIS 0.005 0.001 HIS D 49 PHE 0.030 0.002 PHE A 67 TYR 0.100 0.004 TYR D 83 ARG 0.005 0.000 ARG B 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 202 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 203 average time/residue: 0.2874 time to fit residues: 84.2868 Evaluate side-chains 196 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1298 time to fit residues: 2.5613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 93 optimal weight: 0.0070 chunk 6 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.100452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.068777 restraints weight = 48402.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.070298 restraints weight = 26357.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.071243 restraints weight = 19337.092| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15725 Z= 0.198 Angle : 0.623 10.233 22473 Z= 0.357 Chirality : 0.036 0.206 2536 Planarity : 0.004 0.054 1830 Dihedral : 29.520 169.513 4426 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.11 % Allowed : 20.89 % Favored : 79.01 % 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: 1.08 (0.26), residues: 1081 helix: 1.67 (0.19), residues: 706 sheet: -0.53 (0.95), residues: 32 loop : -1.19 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 455 HIS 0.004 0.001 HIS D 49 PHE 0.027 0.001 PHE A 67 TYR 0.025 0.002 TYR K 242 ARG 0.006 0.000 ARG B 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2817.53 seconds wall clock time: 52 minutes 9.23 seconds (3129.23 seconds total)