Starting phenix.real_space_refine on Sat Mar 16 18:50:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6p_22691/03_2024/7k6p_22691_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6p_22691/03_2024/7k6p_22691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6p_22691/03_2024/7k6p_22691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6p_22691/03_2024/7k6p_22691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6p_22691/03_2024/7k6p_22691_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6p_22691/03_2024/7k6p_22691_updated.pdb" } resolution = 3.2 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= 0.004 sd= 1.015 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 292 5.49 5 S 32 5.16 5 C 8834 2.51 5 N 2828 2.21 5 O 3461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 94": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "K GLU 197": "OE1" <-> "OE2" Residue "K GLU 267": "OE1" <-> "OE2" Residue "K GLU 422": "OE1" <-> "OE2" Residue "K GLU 453": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15447 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 715 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 672 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2961 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 362} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "L" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 465 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ARG L 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG L 74 " occ=0.45 residue: pdb=" N GLY L 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY L 75 " occ=0.25 Time building chain proxies: 7.60, per 1000 atoms: 0.49 Number of scatterers: 15447 At special positions: 0 Unit cell: (125.235, 123.165, 120.06, 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 32 16.00 P 292 15.00 O 3461 8.00 N 2828 7.00 C 8834 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: 8.01 Conformation dependent library (CDL) restraints added in 1.8 seconds 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 4 sheets defined 53.6% alpha, 5.0% beta 139 base pairs and 265 stacking pairs defined. Time for finding SS restraints: 7.54 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 48 through 75 removed outlier: 3.813A pdb=" N TYR B 51 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU B 52 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 53 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 66 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.409A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.551A pdb=" N THR D 122 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.406A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.444A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 83 Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 105 through 123 Processing helix chain 'K' and resid 196 through 201 Processing helix chain 'K' and resid 264 through 277 Processing helix chain 'K' and resid 284 through 302 removed outlier: 3.803A pdb=" N LEU K 293 " --> pdb=" O LYS K 289 " (cutoff:3.500A) Proline residue: K 294 - end of helix Processing helix chain 'K' and resid 305 through 319 Processing helix chain 'K' and resid 324 through 333 Processing helix chain 'K' and resid 339 through 353 removed outlier: 3.914A pdb=" N HIS K 343 " --> pdb=" O ARG K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 355 through 357 No H-bonds generated for 'chain 'K' and resid 355 through 357' Processing helix chain 'K' and resid 359 through 363 Processing helix chain 'K' and resid 377 through 387 Processing helix chain 'K' and resid 404 through 413 Processing helix chain 'K' and resid 425 through 445 Processing helix chain 'K' and resid 464 through 472 Proline residue: K 471 - end of helix Processing helix chain 'K' and resid 485 through 497 removed outlier: 4.835A pdb=" N THR K 497 " --> pdb=" O LYS K 493 " (cutoff:3.500A) Processing helix chain 'K' and resid 526 through 528 No H-bonds generated for 'chain 'K' and resid 526 through 528' Processing helix chain 'K' and resid 566 through 569 No H-bonds generated for 'chain 'K' and resid 566 through 569' Processing helix chain 'L' and resid 23 through 34 Processing helix chain 'L' and resid 38 through 40 No H-bonds generated for 'chain 'L' and resid 38 through 40' Processing helix chain 'L' and resid 57 through 59 No H-bonds generated for 'chain 'L' and resid 57 through 59' Processing sheet with id= A, first strand: chain 'K' and resid 186 through 188 Processing sheet with id= B, first strand: chain 'K' and resid 236 through 240 Processing sheet with id= C, first strand: chain 'K' and resid 529 through 536 removed outlier: 4.136A pdb=" N GLY K 548 " --> pdb=" O LEU K 536 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU K 417 " --> pdb=" O PHE K 395 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ASP K 397 " --> pdb=" O LEU K 417 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE K 419 " --> pdb=" O ASP K 397 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 12 through 16 480 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 265 stacking parallelities Total time for adding SS restraints: 6.74 Time building geometry restraints manager: 8.52 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: 3639 1.33 - 1.45: 4489 1.45 - 1.58: 7562 1.58 - 1.70: 578 1.70 - 1.82: 51 Bond restraints: 16319 Sorted by residual: bond pdb=" O3' DA I 91 " pdb=" P DC I 92 " ideal model delta sigma weight residual 1.607 1.547 0.060 1.50e-02 4.44e+03 1.60e+01 bond pdb=" O3' DA I 90 " pdb=" P DA I 91 " ideal model delta sigma weight residual 1.607 1.561 0.046 1.50e-02 4.44e+03 9.56e+00 bond pdb=" N ASP H 51 " pdb=" CA ASP H 51 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.18e-02 7.18e+03 9.48e+00 bond pdb=" O3' DA I 131 " pdb=" P DG I 132 " ideal model delta sigma weight residual 1.607 1.566 0.041 1.50e-02 4.44e+03 7.64e+00 bond pdb=" N ARG B 45 " pdb=" CA ARG B 45 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.27e-02 6.20e+03 7.07e+00 ... (remaining 16314 not shown) Histogram of bond angle deviations from ideal: 97.50 - 104.78: 1205 104.78 - 112.07: 8627 112.07 - 119.35: 5278 119.35 - 126.64: 7361 126.64 - 133.92: 872 Bond angle restraints: 23343 Sorted by residual: angle pdb=" O3' DA I 90 " pdb=" C3' DA I 90 " pdb=" C2' DA I 90 " ideal model delta sigma weight residual 111.50 104.64 6.86 1.50e+00 4.44e-01 2.09e+01 angle pdb=" O3' DT I 89 " pdb=" C3' DT I 89 " pdb=" C2' DT I 89 " ideal model delta sigma weight residual 111.50 105.78 5.72 1.50e+00 4.44e-01 1.45e+01 angle pdb=" O3' DT J 15 " pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 111.50 117.00 -5.50 1.50e+00 4.44e-01 1.35e+01 angle pdb=" C4' DT I 89 " pdb=" C3' DT I 89 " pdb=" O3' DT I 89 " ideal model delta sigma weight residual 110.00 104.65 5.35 1.50e+00 4.44e-01 1.27e+01 angle pdb=" C2' DC I 111 " pdb=" C1' DC I 111 " pdb=" N1 DC I 111 " ideal model delta sigma weight residual 113.50 118.27 -4.77 1.50e+00 4.44e-01 1.01e+01 ... (remaining 23338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.08: 7423 30.08 - 60.16: 1583 60.16 - 90.24: 56 90.24 - 120.31: 0 120.31 - 150.39: 3 Dihedral angle restraints: 9065 sinusoidal: 5504 harmonic: 3561 Sorted by residual: dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual 180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 69.61 150.39 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 9062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2242 0.059 - 0.118: 409 0.118 - 0.176: 32 0.176 - 0.235: 3 0.235 - 0.294: 1 Chirality restraints: 2687 Sorted by residual: chirality pdb=" C3' DT J 15 " pdb=" C4' DT J 15 " pdb=" O3' DT J 15 " pdb=" C2' DT J 15 " both_signs ideal model delta sigma weight residual False -2.66 -2.37 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C3' DT I 89 " pdb=" C4' DT I 89 " pdb=" O3' DT I 89 " pdb=" C2' DT I 89 " both_signs ideal model delta sigma weight residual False -2.66 -2.89 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C3' DA I 90 " pdb=" C4' DA I 90 " pdb=" O3' DA I 90 " pdb=" C2' DA I 90 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2684 not shown) Planarity restraints: 1951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 88 " 0.030 2.00e-02 2.50e+03 1.52e-02 5.79e+00 pdb=" N1 DT I 88 " -0.036 2.00e-02 2.50e+03 pdb=" C2 DT I 88 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT I 88 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT I 88 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DT I 88 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 88 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DT I 88 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 88 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT I 88 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 121 " -0.031 2.00e-02 2.50e+03 1.34e-02 5.37e+00 pdb=" N9 DG I 121 " 0.030 2.00e-02 2.50e+03 pdb=" C8 DG I 121 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 121 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG I 121 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 121 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 121 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG I 121 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 121 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 121 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DG I 121 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG I 121 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 86 " 0.193 9.50e-02 1.11e+02 8.65e-02 4.93e+00 pdb=" NE ARG D 86 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D 86 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 86 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 86 " 0.004 2.00e-02 2.50e+03 ... (remaining 1948 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 192 2.62 - 3.19: 12849 3.19 - 3.76: 28305 3.76 - 4.33: 38200 4.33 - 4.90: 55939 Nonbonded interactions: 135485 Sorted by model distance: nonbonded pdb=" O THR G 16 " pdb=" OG SER G 19 " model vdw 2.051 2.440 nonbonded pdb=" OH TYR K 247 " pdb=" OE1 GLU K 249 " model vdw 2.063 2.440 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.105 2.440 nonbonded pdb=" OH TYR K 274 " pdb=" OD2 ASP K 344 " model vdw 2.160 2.440 nonbonded pdb=" O ASN K 521 " pdb=" ND2 ASN K 527 " model vdw 2.169 2.520 ... (remaining 135480 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 16 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 16 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 124)) } 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=0.25 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: 2.520 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: 6.380 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 49.450 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16319 Z= 0.322 Angle : 0.793 8.521 23343 Z= 0.468 Chirality : 0.044 0.294 2687 Planarity : 0.006 0.087 1951 Dihedral : 25.084 150.392 6761 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.44 (0.24), residues: 1193 helix: 1.69 (0.19), residues: 712 sheet: -0.08 (0.59), residues: 77 loop : -0.06 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 543 HIS 0.009 0.001 HIS K 363 PHE 0.020 0.002 PHE G 25 TYR 0.016 0.002 TYR H 40 ARG 0.010 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.7663 (mmm) cc_final: 0.7448 (tpt) REVERT: B 91 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8563 (ttpp) REVERT: D 85 LYS cc_start: 0.8834 (mttm) cc_final: 0.8379 (mmtt) REVERT: E 81 ASP cc_start: 0.8162 (p0) cc_final: 0.7955 (p0) REVERT: F 25 ASN cc_start: 0.8340 (m110) cc_final: 0.8067 (m110) REVERT: H 33 ARG cc_start: 0.7305 (mmt90) cc_final: 0.7089 (mtt180) REVERT: H 34 LYS cc_start: 0.8550 (tppt) cc_final: 0.7881 (tptp) REVERT: H 115 THR cc_start: 0.8982 (m) cc_final: 0.8690 (m) REVERT: K 428 SER cc_start: 0.7424 (m) cc_final: 0.6805 (t) REVERT: K 431 THR cc_start: 0.8565 (m) cc_final: 0.8195 (p) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.3167 time to fit residues: 82.1104 Evaluate side-chains 149 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 84 optimal weight: 4.9990 chunk 130 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN B 75 HIS C 73 ASN E 108 ASN G 31 HIS H 82 HIS K 325 GLN K 330 HIS K 363 HIS ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16319 Z= 0.179 Angle : 0.542 7.601 23343 Z= 0.322 Chirality : 0.036 0.150 2687 Planarity : 0.005 0.042 1951 Dihedral : 28.886 151.371 4569 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.83 % Allowed : 6.20 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.79 (0.24), residues: 1193 helix: 1.86 (0.19), residues: 718 sheet: 0.48 (0.58), residues: 85 loop : 0.18 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 182 HIS 0.006 0.001 HIS K 545 PHE 0.009 0.001 PHE G 25 TYR 0.022 0.001 TYR K 315 ARG 0.007 0.000 ARG L 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.7826 (mmm) cc_final: 0.7616 (mmm) REVERT: B 91 LYS cc_start: 0.8802 (ttmm) cc_final: 0.8530 (ttpp) REVERT: D 85 LYS cc_start: 0.8820 (mttm) cc_final: 0.8374 (mmtt) REVERT: D 95 GLN cc_start: 0.8535 (tt0) cc_final: 0.8238 (tt0) REVERT: D 113 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7853 (mm-30) REVERT: E 81 ASP cc_start: 0.8161 (p0) cc_final: 0.7957 (p0) REVERT: F 25 ASN cc_start: 0.8347 (m110) cc_final: 0.8054 (m110) REVERT: H 34 LYS cc_start: 0.8424 (tppt) cc_final: 0.7926 (tttp) REVERT: H 42 TYR cc_start: 0.7429 (t80) cc_final: 0.6626 (t80) REVERT: H 115 THR cc_start: 0.8960 (m) cc_final: 0.8681 (m) REVERT: K 388 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7433 (tm-30) outliers start: 8 outliers final: 4 residues processed: 168 average time/residue: 0.2990 time to fit residues: 72.7554 Evaluate side-chains 152 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 436 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN K 521 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16319 Z= 0.318 Angle : 0.580 5.830 23343 Z= 0.337 Chirality : 0.038 0.146 2687 Planarity : 0.004 0.043 1951 Dihedral : 29.410 146.856 4569 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.55 % Allowed : 8.68 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.48 (0.24), residues: 1193 helix: 1.58 (0.19), residues: 716 sheet: 0.58 (0.59), residues: 85 loop : 0.09 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 182 HIS 0.005 0.001 HIS K 545 PHE 0.019 0.002 PHE G 25 TYR 0.036 0.002 TYR K 315 ARG 0.005 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 162 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8615 (tttt) REVERT: D 85 LYS cc_start: 0.8890 (mttm) cc_final: 0.8359 (mmtt) REVERT: D 95 GLN cc_start: 0.8572 (tt0) cc_final: 0.8250 (tt0) REVERT: D 113 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8039 (mm-30) REVERT: H 34 LYS cc_start: 0.8396 (tppt) cc_final: 0.7904 (tttp) REVERT: H 42 TYR cc_start: 0.7530 (t80) cc_final: 0.6591 (t80) REVERT: H 115 THR cc_start: 0.8987 (m) cc_final: 0.8726 (m) REVERT: K 326 ARG cc_start: 0.7677 (mmm-85) cc_final: 0.7445 (mmt90) REVERT: K 388 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7602 (tm-30) outliers start: 15 outliers final: 10 residues processed: 169 average time/residue: 0.3293 time to fit residues: 78.1427 Evaluate side-chains 160 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain L residue 67 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 109 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16319 Z= 0.283 Angle : 0.557 6.815 23343 Z= 0.325 Chirality : 0.037 0.167 2687 Planarity : 0.004 0.044 1951 Dihedral : 29.368 146.245 4569 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.76 % Allowed : 10.85 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1193 helix: 1.59 (0.19), residues: 716 sheet: 0.70 (0.58), residues: 83 loop : 0.06 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 543 HIS 0.005 0.001 HIS K 545 PHE 0.015 0.002 PHE C 25 TYR 0.029 0.002 TYR K 315 ARG 0.011 0.000 ARG K 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 1.387 Fit side-chains REVERT: B 91 LYS cc_start: 0.8864 (ttmm) cc_final: 0.8626 (tttt) REVERT: D 85 LYS cc_start: 0.8887 (mttm) cc_final: 0.8351 (mmtt) REVERT: D 95 GLN cc_start: 0.8556 (tt0) cc_final: 0.8255 (tt0) REVERT: D 113 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7974 (mm-30) REVERT: F 88 TYR cc_start: 0.8454 (m-10) cc_final: 0.8094 (m-10) REVERT: H 34 LYS cc_start: 0.8334 (tppt) cc_final: 0.7915 (tttp) REVERT: H 42 TYR cc_start: 0.7510 (t80) cc_final: 0.6615 (t80) REVERT: K 388 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7640 (tm-30) outliers start: 17 outliers final: 13 residues processed: 169 average time/residue: 0.3246 time to fit residues: 76.5762 Evaluate side-chains 157 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 502 CYS Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 67 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16319 Z= 0.222 Angle : 0.536 8.149 23343 Z= 0.314 Chirality : 0.035 0.159 2687 Planarity : 0.004 0.042 1951 Dihedral : 29.212 146.356 4569 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.86 % Allowed : 11.67 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.65 (0.24), residues: 1193 helix: 1.73 (0.19), residues: 721 sheet: 0.85 (0.58), residues: 83 loop : 0.04 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 543 HIS 0.004 0.001 HIS K 545 PHE 0.010 0.001 PHE C 25 TYR 0.019 0.001 TYR H 40 ARG 0.011 0.000 ARG K 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 1.357 Fit side-chains REVERT: B 84 MET cc_start: 0.7996 (mmm) cc_final: 0.7678 (mmm) REVERT: B 91 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8594 (tttt) REVERT: D 85 LYS cc_start: 0.8900 (mttm) cc_final: 0.8362 (mmtt) REVERT: D 95 GLN cc_start: 0.8529 (tt0) cc_final: 0.8249 (tt0) REVERT: D 113 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7930 (mm-30) REVERT: E 59 GLU cc_start: 0.7916 (pm20) cc_final: 0.7716 (pm20) REVERT: H 34 LYS cc_start: 0.8387 (tppt) cc_final: 0.7944 (tttp) REVERT: H 115 THR cc_start: 0.8993 (m) cc_final: 0.8740 (m) REVERT: K 200 ARG cc_start: 0.7055 (ttm-80) cc_final: 0.6802 (mmt180) REVERT: K 388 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7597 (tm-30) outliers start: 18 outliers final: 11 residues processed: 167 average time/residue: 0.3443 time to fit residues: 82.8020 Evaluate side-chains 157 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 502 CYS Chi-restraints excluded: chain K residue 522 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 357 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16319 Z= 0.222 Angle : 0.537 10.220 23343 Z= 0.314 Chirality : 0.035 0.155 2687 Planarity : 0.004 0.040 1951 Dihedral : 29.175 146.672 4569 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.38 % Allowed : 11.57 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.61 (0.24), residues: 1193 helix: 1.74 (0.19), residues: 722 sheet: 0.77 (0.56), residues: 93 loop : -0.07 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 543 HIS 0.004 0.001 HIS K 545 PHE 0.011 0.001 PHE C 25 TYR 0.017 0.001 TYR H 40 ARG 0.006 0.000 ARG K 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 1.252 Fit side-chains REVERT: B 91 LYS cc_start: 0.8864 (ttmm) cc_final: 0.8612 (tttt) REVERT: D 80 LEU cc_start: 0.9100 (mp) cc_final: 0.8869 (mp) REVERT: D 85 LYS cc_start: 0.8896 (mttm) cc_final: 0.8354 (mmtt) REVERT: D 95 GLN cc_start: 0.8530 (tt0) cc_final: 0.8232 (tt0) REVERT: D 113 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7857 (mm-30) REVERT: H 34 LYS cc_start: 0.8329 (tppt) cc_final: 0.7935 (tttp) REVERT: H 115 THR cc_start: 0.8973 (m) cc_final: 0.8723 (m) REVERT: K 325 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.6975 (mp10) REVERT: K 388 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7656 (tm-30) outliers start: 23 outliers final: 14 residues processed: 177 average time/residue: 0.3091 time to fit residues: 77.8477 Evaluate side-chains 160 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 325 GLN Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 502 CYS Chi-restraints excluded: chain K residue 522 VAL Chi-restraints excluded: chain L residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 138 optimal weight: 40.0000 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 16319 Z= 0.402 Angle : 0.627 11.399 23343 Z= 0.357 Chirality : 0.040 0.159 2687 Planarity : 0.005 0.042 1951 Dihedral : 29.836 145.673 4569 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.27 % Allowed : 12.81 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.24), residues: 1193 helix: 1.38 (0.19), residues: 720 sheet: 0.80 (0.60), residues: 83 loop : -0.23 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 182 HIS 0.005 0.001 HIS K 545 PHE 0.015 0.002 PHE C 25 TYR 0.018 0.002 TYR K 205 ARG 0.005 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 1.386 Fit side-chains REVERT: B 25 ASN cc_start: 0.8758 (t0) cc_final: 0.8546 (t0) REVERT: B 91 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8661 (tttt) REVERT: D 113 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7752 (mm-30) REVERT: F 88 TYR cc_start: 0.8507 (m-10) cc_final: 0.8207 (m-10) REVERT: H 34 LYS cc_start: 0.8334 (tppt) cc_final: 0.7938 (tttp) REVERT: H 42 TYR cc_start: 0.7656 (t80) cc_final: 0.6652 (t80) REVERT: H 68 ASP cc_start: 0.8152 (t0) cc_final: 0.7937 (t0) REVERT: K 325 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.6942 (mp10) outliers start: 22 outliers final: 15 residues processed: 167 average time/residue: 0.3119 time to fit residues: 73.8918 Evaluate side-chains 166 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 325 GLN Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 502 CYS Chi-restraints excluded: chain K residue 522 VAL Chi-restraints excluded: chain K residue 539 ASP Chi-restraints excluded: chain L residue 67 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 357 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16319 Z= 0.209 Angle : 0.548 12.930 23343 Z= 0.318 Chirality : 0.035 0.170 2687 Planarity : 0.004 0.040 1951 Dihedral : 29.166 145.503 4569 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.65 % Allowed : 13.43 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.54 (0.25), residues: 1193 helix: 1.70 (0.19), residues: 721 sheet: 0.79 (0.57), residues: 93 loop : -0.14 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 543 HIS 0.004 0.001 HIS L 68 PHE 0.010 0.001 PHE C 25 TYR 0.016 0.001 TYR H 40 ARG 0.004 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 1.185 Fit side-chains REVERT: B 84 MET cc_start: 0.8008 (mmm) cc_final: 0.7640 (mmm) REVERT: B 91 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8613 (tttt) REVERT: D 95 GLN cc_start: 0.8579 (tt0) cc_final: 0.8287 (tt0) REVERT: D 113 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7892 (mm-30) REVERT: H 34 LYS cc_start: 0.8280 (tppt) cc_final: 0.7899 (tttp) REVERT: H 115 THR cc_start: 0.8972 (m) cc_final: 0.8723 (m) REVERT: K 325 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.6961 (mp10) REVERT: K 388 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7703 (tm-30) outliers start: 16 outliers final: 12 residues processed: 161 average time/residue: 0.2930 time to fit residues: 68.1442 Evaluate side-chains 159 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 325 GLN Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 495 LEU Chi-restraints excluded: chain L residue 67 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 27 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16319 Z= 0.190 Angle : 0.541 12.858 23343 Z= 0.313 Chirality : 0.035 0.165 2687 Planarity : 0.004 0.041 1951 Dihedral : 29.050 145.317 4569 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.65 % Allowed : 14.05 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.70 (0.25), residues: 1193 helix: 1.84 (0.19), residues: 721 sheet: 0.78 (0.56), residues: 96 loop : -0.10 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 543 HIS 0.003 0.001 HIS K 545 PHE 0.027 0.001 PHE K 367 TYR 0.017 0.001 TYR H 121 ARG 0.005 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 1.343 Fit side-chains REVERT: B 84 MET cc_start: 0.8000 (mmm) cc_final: 0.7695 (mmm) REVERT: B 91 LYS cc_start: 0.8852 (ttmm) cc_final: 0.8581 (tttt) REVERT: D 95 GLN cc_start: 0.8546 (tt0) cc_final: 0.8253 (tt0) REVERT: D 113 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7891 (mm-30) REVERT: E 120 MET cc_start: 0.8491 (mtp) cc_final: 0.8272 (mtt) REVERT: H 34 LYS cc_start: 0.8317 (tppt) cc_final: 0.7915 (tttp) REVERT: H 115 THR cc_start: 0.9009 (m) cc_final: 0.8771 (m) REVERT: K 325 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.6961 (mp10) REVERT: K 388 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7721 (tm-30) outliers start: 16 outliers final: 13 residues processed: 159 average time/residue: 0.2996 time to fit residues: 68.4698 Evaluate side-chains 160 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 325 GLN Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 495 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 40.0000 chunk 132 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 90 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16319 Z= 0.221 Angle : 0.550 12.507 23343 Z= 0.316 Chirality : 0.036 0.181 2687 Planarity : 0.004 0.041 1951 Dihedral : 29.113 144.825 4569 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.76 % Allowed : 14.26 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1193 helix: 1.78 (0.19), residues: 721 sheet: 0.69 (0.55), residues: 96 loop : -0.11 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 543 HIS 0.003 0.001 HIS L 68 PHE 0.021 0.001 PHE K 367 TYR 0.017 0.001 TYR D 40 ARG 0.005 0.000 ARG F 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 1.339 Fit side-chains REVERT: B 84 MET cc_start: 0.8007 (mmm) cc_final: 0.7666 (mmm) REVERT: B 91 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8635 (tttt) REVERT: D 80 LEU cc_start: 0.9070 (mp) cc_final: 0.8862 (mp) REVERT: D 95 GLN cc_start: 0.8578 (tt0) cc_final: 0.8295 (tt0) REVERT: D 113 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7890 (mm-30) REVERT: F 24 ASP cc_start: 0.6413 (p0) cc_final: 0.6189 (p0) REVERT: F 25 ASN cc_start: 0.8158 (m-40) cc_final: 0.7957 (m110) REVERT: H 34 LYS cc_start: 0.8310 (tppt) cc_final: 0.7911 (tttp) REVERT: H 42 TYR cc_start: 0.7516 (t80) cc_final: 0.6584 (t80) REVERT: H 115 THR cc_start: 0.9013 (m) cc_final: 0.8774 (m) REVERT: K 325 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.6963 (mp10) REVERT: K 388 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7735 (tm-30) outliers start: 17 outliers final: 14 residues processed: 159 average time/residue: 0.3192 time to fit residues: 73.2939 Evaluate side-chains 159 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 325 GLN Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 495 LEU Chi-restraints excluded: chain L residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 105 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 246 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 = 0.3852 r_free = 0.3852 target = 0.124753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.092790 restraints weight = 27615.827| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.93 r_work: 0.3190 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16319 Z= 0.173 Angle : 0.533 12.782 23343 Z= 0.307 Chirality : 0.034 0.166 2687 Planarity : 0.004 0.042 1951 Dihedral : 28.854 144.946 4569 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.55 % Allowed : 14.36 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.78 (0.24), residues: 1193 helix: 1.92 (0.19), residues: 721 sheet: 0.70 (0.55), residues: 96 loop : -0.08 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 543 HIS 0.003 0.001 HIS L 68 PHE 0.023 0.001 PHE K 367 TYR 0.017 0.001 TYR H 121 ARG 0.006 0.000 ARG F 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2903.20 seconds wall clock time: 52 minutes 52.38 seconds (3172.38 seconds total)