Starting phenix.real_space_refine on Tue Feb 13 23:00:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3q_31434/02_2024/7f3q_31434_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3q_31434/02_2024/7f3q_31434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3q_31434/02_2024/7f3q_31434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3q_31434/02_2024/7f3q_31434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3q_31434/02_2024/7f3q_31434_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3q_31434/02_2024/7f3q_31434_updated.pdb" } resolution = 3.3 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 5055 2.51 5 N 1339 2.21 5 O 1578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "H GLU 154": "OE1" <-> "OE2" Residue "H GLU 218": "OE1" <-> "OE2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "L GLU 185": "OE1" <-> "OE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B GLU 122": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8003 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "H" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1594 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain breaks: 1 Chain: "L" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1596 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 195} Chain: "C" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1691 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 215} Chain: "B" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1560 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MES': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.72, per 1000 atoms: 0.59 Number of scatterers: 8003 At special positions: 0 Unit cell: (97.11, 87.98, 146.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1578 8.00 N 1339 7.00 C 5055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 110 " distance=2.05 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.02 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 193 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.5 seconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 20 sheets defined 6.5% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.970A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'L' and resid 27 through 29 No H-bonds generated for 'chain 'L' and resid 27 through 29' Processing helix chain 'L' and resid 124 through 129 Processing helix chain 'L' and resid 184 through 187 No H-bonds generated for 'chain 'L' and resid 184 through 187' Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 121 through 126 Processing sheet with id= A, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.614A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= C, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= D, first strand: chain 'H' and resid 113 through 115 removed outlier: 5.849A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 126 through 130 removed outlier: 4.051A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 157 through 160 removed outlier: 3.698A pdb=" N VAL H 213 " --> pdb=" O VAL H 204 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 9 through 12 removed outlier: 5.902A pdb=" N THR L 104 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL L 12 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR L 106 " --> pdb=" O VAL L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.750A pdb=" N THR L 69 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER L 66 " --> pdb=" O THR L 69 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 96 through 98 removed outlier: 3.561A pdb=" N ILE L 47 " --> pdb=" O TRP L 34 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLN L 36 " --> pdb=" O PRO L 45 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 132 through 134 Processing sheet with id= K, first strand: chain 'L' and resid 147 through 152 removed outlier: 3.720A pdb=" N THR L 147 " --> pdb=" O THR L 198 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 17 through 21 Processing sheet with id= M, first strand: chain 'C' and resid 135 through 137 removed outlier: 6.319A pdb=" N ARG C 52 " --> pdb=" O TRP C 61 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N TRP C 61 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 179 through 182 Processing sheet with id= O, first strand: chain 'C' and resid 191 through 193 removed outlier: 7.299A pdb=" N LEU C 206 " --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS C 171 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER C 208 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU C 169 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL C 210 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLY C 167 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL C 212 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ALA C 165 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.523A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.119A pdb=" N ARG B 102 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ALA B 13 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLU B 104 " --> pdb=" O ALA B 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'B' and resid 85 through 90 removed outlier: 6.356A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 113 through 117 removed outlier: 3.569A pdb=" N ASN B 136 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 176 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR B 172 " --> pdb=" O ASN B 137 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 144 through 149 removed outlier: 3.574A pdb=" N CYS B 193 " --> pdb=" O LYS B 206 " (cutoff:3.500A) 230 hydrogen bonds defined for protein. 591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2497 1.34 - 1.47: 2164 1.47 - 1.59: 3508 1.59 - 1.72: 1 1.72 - 1.85: 35 Bond restraints: 8205 Sorted by residual: bond pdb=" C8 MES H 301 " pdb=" S MES H 301 " ideal model delta sigma weight residual 1.814 1.662 0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" CB ASN B 31 " pdb=" CG ASN B 31 " ideal model delta sigma weight residual 1.516 1.415 0.101 2.50e-02 1.60e+03 1.63e+01 bond pdb=" N TYR L 174 " pdb=" CA TYR L 174 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.22e-02 6.72e+03 7.68e+00 bond pdb=" N LYS C 237 " pdb=" CA LYS C 237 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.26e+00 bond pdb=" N LYS B 45 " pdb=" CA LYS B 45 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 5.76e+00 ... (remaining 8200 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.26: 274 106.26 - 113.23: 4393 113.23 - 120.20: 2749 120.20 - 127.17: 3667 127.17 - 134.13: 101 Bond angle restraints: 11184 Sorted by residual: angle pdb=" N CYS A 379 " pdb=" CA CYS A 379 " pdb=" C CYS A 379 " ideal model delta sigma weight residual 108.60 114.22 -5.62 1.46e+00 4.69e-01 1.48e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 122.28 -7.88 2.30e+00 1.89e-01 1.17e+01 angle pdb=" C ALA B 50 " pdb=" N ALA B 51 " pdb=" CA ALA B 51 " ideal model delta sigma weight residual 121.54 127.09 -5.55 1.91e+00 2.74e-01 8.43e+00 angle pdb=" CA GLN C 53 " pdb=" CB GLN C 53 " pdb=" CG GLN C 53 " ideal model delta sigma weight residual 114.10 108.41 5.69 2.00e+00 2.50e-01 8.08e+00 angle pdb=" C3 MES H 301 " pdb=" N4 MES H 301 " pdb=" C5 MES H 301 " ideal model delta sigma weight residual 109.71 117.80 -8.09 3.00e+00 1.11e-01 7.27e+00 ... (remaining 11179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4472 17.95 - 35.90: 314 35.90 - 53.85: 63 53.85 - 71.80: 27 71.80 - 89.74: 7 Dihedral angle restraints: 4883 sinusoidal: 1859 harmonic: 3024 Sorted by residual: dihedral pdb=" CA TYR L 142 " pdb=" C TYR L 142 " pdb=" N PRO L 143 " pdb=" CA PRO L 143 " ideal model delta harmonic sigma weight residual 180.00 142.62 37.38 0 5.00e+00 4.00e-02 5.59e+01 dihedral pdb=" CB CYS H 146 " pdb=" SG CYS H 146 " pdb=" SG CYS H 202 " pdb=" CB CYS H 202 " ideal model delta sinusoidal sigma weight residual 93.00 147.11 -54.11 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 4880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 1244 0.228 - 0.455: 0 0.455 - 0.683: 0 0.683 - 0.910: 0 0.910 - 1.137: 1 Chirality restraints: 1245 Sorted by residual: chirality pdb=" N4 MES H 301 " pdb=" C3 MES H 301 " pdb=" C5 MES H 301 " pdb=" C7 MES H 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.26 -1.14 2.00e-01 2.50e+01 3.23e+01 chirality pdb=" CG LEU B 33 " pdb=" CB LEU B 33 " pdb=" CD1 LEU B 33 " pdb=" CD2 LEU B 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE C 65 " pdb=" N ILE C 65 " pdb=" C ILE C 65 " pdb=" CB ILE C 65 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1242 not shown) Planarity restraints: 1439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 128 " 0.030 2.00e-02 2.50e+03 1.97e-02 6.81e+00 pdb=" CG PHE C 128 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE C 128 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 128 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 128 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 128 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 128 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR L 142 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.77e+00 pdb=" N PRO L 143 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO L 143 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 143 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 187 " 0.014 2.00e-02 2.50e+03 1.51e-02 5.68e+00 pdb=" CG TRP L 187 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP L 187 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP L 187 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 187 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP L 187 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 187 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 187 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 187 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 187 " 0.001 2.00e-02 2.50e+03 ... (remaining 1436 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 21 2.46 - 3.07: 5126 3.07 - 3.68: 11511 3.68 - 4.29: 17239 4.29 - 4.90: 29284 Nonbonded interactions: 63181 Sorted by model distance: nonbonded pdb=" O ASP L 153 " pdb=" OG SER L 154 " model vdw 1.848 2.440 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.212 2.440 nonbonded pdb=" OD1 ASP B 169 " pdb=" OG1 THR B 171 " model vdw 2.229 2.440 nonbonded pdb=" OG1 THR A 393 " pdb=" O GLU A 516 " model vdw 2.256 2.440 nonbonded pdb=" NH1 ARG B 107 " pdb=" O THR B 108 " model vdw 2.264 2.520 ... (remaining 63176 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.950 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 24.090 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 0.152 8205 Z= 0.381 Angle : 0.809 9.306 11184 Z= 0.442 Chirality : 0.058 1.137 1245 Planarity : 0.005 0.065 1438 Dihedral : 13.817 89.744 2921 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.59 % Favored : 94.32 % Rotamer: Outliers : 2.14 % Allowed : 3.61 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.94 (0.26), residues: 1038 helix: -3.16 (0.55), residues: 57 sheet: 0.48 (0.26), residues: 425 loop : -1.26 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP L 187 HIS 0.006 0.001 HIS C 118 PHE 0.038 0.002 PHE C 128 TYR 0.019 0.003 TYR C 108 ARG 0.006 0.001 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 213 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: H 31 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7512 (mt-10) REVERT: H 207 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8454 (ttmt) REVERT: L 78 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7472 (mt-10) REVERT: L 187 TRP cc_start: 0.7702 (t60) cc_final: 0.7244 (t-100) REVERT: B 17 ASP cc_start: 0.7164 (m-30) cc_final: 0.6837 (m-30) REVERT: B 153 LEU cc_start: 0.8540 (mp) cc_final: 0.8010 (mp) REVERT: B 166 ASP cc_start: 0.8446 (t0) cc_final: 0.8176 (t70) outliers start: 19 outliers final: 5 residues processed: 225 average time/residue: 0.2408 time to fit residues: 69.3232 Evaluate side-chains 161 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 156 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 29 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.7980 chunk 78 optimal weight: 30.0000 chunk 43 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 52 optimal weight: 50.0000 chunk 41 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 60 optimal weight: 30.0000 chunk 93 optimal weight: 7.9990 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 474 GLN L 25 ASN L 169 GLN L 171 ASN L 186 GLN C 228 HIS B 89 GLN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8205 Z= 0.350 Angle : 0.683 10.539 11184 Z= 0.349 Chirality : 0.046 0.185 1245 Planarity : 0.005 0.081 1438 Dihedral : 5.296 33.390 1173 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.82 % Allowed : 11.51 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % 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: -0.79 (0.25), residues: 1038 helix: -3.09 (0.53), residues: 57 sheet: 0.69 (0.25), residues: 422 loop : -1.24 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 103 HIS 0.005 0.001 HIS C 228 PHE 0.026 0.002 PHE C 150 TYR 0.023 0.002 TYR L 142 ARG 0.003 0.001 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 176 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: H 80 TYR cc_start: 0.8835 (m-10) cc_final: 0.8442 (m-10) REVERT: H 123 LYS cc_start: 0.9027 (ttmt) cc_final: 0.8800 (ttmm) REVERT: L 78 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7527 (mt-10) REVERT: C 150 PHE cc_start: 0.8434 (m-10) cc_final: 0.8089 (m-10) REVERT: B 17 ASP cc_start: 0.7931 (m-30) cc_final: 0.7499 (m-30) REVERT: B 121 ASP cc_start: 0.7543 (p0) cc_final: 0.6978 (p0) REVERT: B 168 LYS cc_start: 0.9168 (tppp) cc_final: 0.8962 (tppp) outliers start: 25 outliers final: 16 residues processed: 189 average time/residue: 0.2665 time to fit residues: 63.7017 Evaluate side-chains 155 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 185 SER Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 101 optimal weight: 30.0000 chunk 83 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 75 optimal weight: 40.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8205 Z= 0.243 Angle : 0.590 8.033 11184 Z= 0.301 Chirality : 0.044 0.159 1245 Planarity : 0.004 0.069 1438 Dihedral : 4.805 36.429 1167 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.72 % Allowed : 13.88 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % 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: -0.61 (0.25), residues: 1038 helix: -2.96 (0.55), residues: 57 sheet: 0.86 (0.25), residues: 418 loop : -1.16 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 187 HIS 0.005 0.001 HIS C 228 PHE 0.021 0.001 PHE C 150 TYR 0.025 0.002 TYR L 142 ARG 0.004 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 156 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 80 TYR cc_start: 0.8806 (m-80) cc_final: 0.8413 (m-10) REVERT: H 123 LYS cc_start: 0.8984 (ttmt) cc_final: 0.8758 (ttmm) REVERT: H 214 ASP cc_start: 0.8376 (t0) cc_final: 0.7890 (t0) REVERT: L 78 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7508 (mt-10) REVERT: L 187 TRP cc_start: 0.8626 (t-100) cc_final: 0.7853 (t-100) REVERT: C 210 VAL cc_start: 0.9139 (p) cc_final: 0.8834 (m) REVERT: B 17 ASP cc_start: 0.7888 (m-30) cc_final: 0.7409 (m-30) REVERT: B 125 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7746 (mttp) REVERT: B 187 LYS cc_start: 0.7356 (mmtm) cc_final: 0.7104 (mmtm) REVERT: B 191 TYR cc_start: 0.3629 (p90) cc_final: 0.3405 (p90) outliers start: 33 outliers final: 19 residues processed: 179 average time/residue: 0.2469 time to fit residues: 56.6857 Evaluate side-chains 162 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 176 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 501 ASN B 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8205 Z= 0.415 Angle : 0.652 8.722 11184 Z= 0.338 Chirality : 0.045 0.203 1245 Planarity : 0.005 0.078 1438 Dihedral : 5.172 37.799 1167 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.95 % Allowed : 14.67 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % 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: -0.65 (0.25), residues: 1038 helix: -2.97 (0.56), residues: 57 sheet: 0.92 (0.25), residues: 406 loop : -1.21 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 103 HIS 0.003 0.001 HIS H 35 PHE 0.015 0.002 PHE B 71 TYR 0.029 0.002 TYR L 142 ARG 0.004 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 154 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 123 LYS cc_start: 0.9097 (ttmt) cc_final: 0.8853 (ttmm) REVERT: L 78 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7551 (mt-10) REVERT: B 121 ASP cc_start: 0.7966 (p0) cc_final: 0.7669 (p0) REVERT: B 125 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7548 (mtmm) outliers start: 35 outliers final: 24 residues processed: 178 average time/residue: 0.2402 time to fit residues: 55.8560 Evaluate side-chains 169 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.0970 chunk 56 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 74 optimal weight: 0.0570 chunk 41 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 0 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8205 Z= 0.143 Angle : 0.547 6.827 11184 Z= 0.277 Chirality : 0.043 0.148 1245 Planarity : 0.004 0.065 1438 Dihedral : 4.537 35.890 1167 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.03 % Allowed : 17.95 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.36 (0.25), residues: 1038 helix: -2.87 (0.58), residues: 57 sheet: 1.12 (0.26), residues: 399 loop : -0.97 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.005 0.001 HIS L 199 PHE 0.006 0.001 PHE A 400 TYR 0.028 0.001 TYR L 142 ARG 0.005 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 0.923 Fit side-chains REVERT: H 31 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7600 (mt-10) REVERT: H 80 TYR cc_start: 0.8772 (m-80) cc_final: 0.8361 (m-10) REVERT: H 123 LYS cc_start: 0.8909 (ttmt) cc_final: 0.8693 (ttmm) REVERT: C 210 VAL cc_start: 0.9087 (p) cc_final: 0.8849 (m) REVERT: C 227 ASN cc_start: 0.8098 (m110) cc_final: 0.7038 (m110) REVERT: B 17 ASP cc_start: 0.7954 (m-30) cc_final: 0.7536 (m-30) REVERT: B 42 LYS cc_start: 0.8574 (mmtt) cc_final: 0.8250 (mtpt) REVERT: B 77 SER cc_start: 0.7812 (t) cc_final: 0.7553 (p) REVERT: B 121 ASP cc_start: 0.7863 (p0) cc_final: 0.7565 (p0) REVERT: B 125 LYS cc_start: 0.7831 (mtmm) cc_final: 0.7606 (mtmm) REVERT: B 180 LEU cc_start: 0.8527 (tp) cc_final: 0.8285 (tp) outliers start: 18 outliers final: 11 residues processed: 177 average time/residue: 0.2452 time to fit residues: 55.8561 Evaluate side-chains 162 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 82 optimal weight: 0.3980 chunk 46 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8205 Z= 0.252 Angle : 0.568 6.713 11184 Z= 0.290 Chirality : 0.043 0.161 1245 Planarity : 0.004 0.082 1438 Dihedral : 4.593 40.638 1167 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.60 % Allowed : 17.95 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % 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: -0.34 (0.26), residues: 1038 helix: -2.89 (0.58), residues: 57 sheet: 1.11 (0.25), residues: 406 loop : -0.97 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 103 HIS 0.004 0.001 HIS C 192 PHE 0.011 0.001 PHE B 71 TYR 0.020 0.001 TYR H 151 ARG 0.005 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 149 time to evaluate : 0.859 Fit side-chains REVERT: H 123 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8764 (ttmm) REVERT: L 78 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7450 (mt-10) REVERT: C 234 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8533 (mmmt) REVERT: B 17 ASP cc_start: 0.7983 (m-30) cc_final: 0.7552 (m-30) REVERT: B 77 SER cc_start: 0.7823 (t) cc_final: 0.7569 (p) REVERT: B 121 ASP cc_start: 0.7897 (p0) cc_final: 0.7583 (p0) REVERT: B 125 LYS cc_start: 0.7907 (mtmm) cc_final: 0.7683 (mtmm) REVERT: B 180 LEU cc_start: 0.8555 (tp) cc_final: 0.8303 (tp) REVERT: B 189 LYS cc_start: 0.2789 (mmtt) cc_final: 0.1268 (tptt) outliers start: 23 outliers final: 16 residues processed: 162 average time/residue: 0.2546 time to fit residues: 53.0660 Evaluate side-chains 160 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 55 optimal weight: 40.0000 chunk 99 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 60 optimal weight: 30.0000 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8205 Z= 0.335 Angle : 0.610 9.162 11184 Z= 0.313 Chirality : 0.045 0.210 1245 Planarity : 0.004 0.045 1438 Dihedral : 4.705 36.010 1167 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.62 % Favored : 95.28 % Rotamer: Outliers : 3.05 % Allowed : 18.17 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.37 (0.26), residues: 1038 helix: -2.95 (0.59), residues: 56 sheet: 1.11 (0.25), residues: 401 loop : -0.99 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 131 HIS 0.003 0.001 HIS C 192 PHE 0.013 0.001 PHE B 71 TYR 0.025 0.002 TYR H 80 ARG 0.005 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 0.980 Fit side-chains REVERT: A 487 ASN cc_start: 0.7484 (m-40) cc_final: 0.7220 (m110) REVERT: H 123 LYS cc_start: 0.9077 (ttmt) cc_final: 0.8833 (ttmm) REVERT: L 78 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7492 (mt-10) REVERT: C 234 LYS cc_start: 0.8895 (mtpp) cc_final: 0.8645 (mmmt) REVERT: B 17 ASP cc_start: 0.8022 (m-30) cc_final: 0.7573 (m-30) REVERT: B 77 SER cc_start: 0.7840 (t) cc_final: 0.7593 (p) REVERT: B 180 LEU cc_start: 0.8496 (tp) cc_final: 0.8240 (tp) REVERT: B 189 LYS cc_start: 0.2728 (mmtt) cc_final: 0.1228 (tptt) outliers start: 27 outliers final: 20 residues processed: 165 average time/residue: 0.2415 time to fit residues: 51.7052 Evaluate side-chains 167 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 40.0000 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 0.0270 chunk 49 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8205 Z= 0.179 Angle : 0.559 7.325 11184 Z= 0.285 Chirality : 0.043 0.163 1245 Planarity : 0.004 0.085 1438 Dihedral : 4.516 36.736 1167 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.48 % Allowed : 18.51 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1038 helix: -2.94 (0.59), residues: 56 sheet: 1.15 (0.25), residues: 413 loop : -0.93 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 HIS 0.004 0.001 HIS C 192 PHE 0.006 0.001 PHE H 95 TYR 0.022 0.001 TYR H 151 ARG 0.005 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 0.935 Fit side-chains REVERT: A 487 ASN cc_start: 0.7482 (m-40) cc_final: 0.7195 (m110) REVERT: H 31 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7600 (mt-10) REVERT: H 123 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8743 (ttmm) REVERT: L 78 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7474 (mt-10) REVERT: C 152 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8501 (mm) REVERT: C 234 LYS cc_start: 0.8933 (mtpp) cc_final: 0.8598 (mmmt) REVERT: C 238 LYS cc_start: 0.8210 (tttp) cc_final: 0.7931 (tptm) REVERT: B 17 ASP cc_start: 0.7996 (m-30) cc_final: 0.7706 (m-30) REVERT: B 77 SER cc_start: 0.7813 (t) cc_final: 0.7569 (p) REVERT: B 180 LEU cc_start: 0.8423 (tp) cc_final: 0.8177 (tp) REVERT: B 189 LYS cc_start: 0.2756 (mmtt) cc_final: 0.1278 (tptt) outliers start: 22 outliers final: 19 residues processed: 160 average time/residue: 0.2410 time to fit residues: 50.1438 Evaluate side-chains 168 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 155 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 55 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 60 optimal weight: 40.0000 chunk 97 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8205 Z= 0.259 Angle : 0.579 7.696 11184 Z= 0.297 Chirality : 0.044 0.181 1245 Planarity : 0.004 0.067 1438 Dihedral : 4.560 37.343 1167 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.60 % Allowed : 18.17 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % 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: -0.26 (0.26), residues: 1038 helix: -2.94 (0.58), residues: 56 sheet: 1.21 (0.25), residues: 409 loop : -0.95 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 187 HIS 0.004 0.001 HIS C 192 PHE 0.009 0.001 PHE B 71 TYR 0.022 0.002 TYR H 151 ARG 0.003 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 0.841 Fit side-chains REVERT: A 487 ASN cc_start: 0.7512 (m-40) cc_final: 0.7225 (m110) REVERT: H 123 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8779 (ttmm) REVERT: L 78 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7480 (mt-10) REVERT: C 152 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8488 (mm) REVERT: C 234 LYS cc_start: 0.8917 (mtpp) cc_final: 0.8583 (mmmt) REVERT: C 238 LYS cc_start: 0.8265 (tttp) cc_final: 0.7977 (tptm) REVERT: B 17 ASP cc_start: 0.7984 (m-30) cc_final: 0.7696 (m-30) REVERT: B 77 SER cc_start: 0.7806 (t) cc_final: 0.7561 (p) REVERT: B 180 LEU cc_start: 0.8453 (tp) cc_final: 0.8198 (tp) outliers start: 23 outliers final: 21 residues processed: 159 average time/residue: 0.2333 time to fit residues: 48.2119 Evaluate side-chains 169 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 155 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 40.0000 chunk 46 optimal weight: 30.0000 chunk 68 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 50 optimal weight: 30.0000 chunk 64 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8205 Z= 0.360 Angle : 0.627 8.615 11184 Z= 0.323 Chirality : 0.045 0.212 1245 Planarity : 0.005 0.069 1438 Dihedral : 4.837 40.857 1167 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.82 % Allowed : 18.28 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % 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: -0.38 (0.26), residues: 1038 helix: -2.89 (0.59), residues: 56 sheet: 1.09 (0.25), residues: 411 loop : -1.03 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 187 HIS 0.004 0.001 HIS C 192 PHE 0.013 0.001 PHE B 71 TYR 0.024 0.002 TYR H 151 ARG 0.006 0.001 ARG H 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 0.965 Fit side-chains REVERT: A 487 ASN cc_start: 0.7555 (m-40) cc_final: 0.7275 (m110) REVERT: H 123 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8814 (ttmm) REVERT: H 203 ASN cc_start: 0.7669 (m-40) cc_final: 0.6983 (m-40) REVERT: L 78 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7507 (mt-10) REVERT: C 152 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8447 (mm) REVERT: C 234 LYS cc_start: 0.8919 (mtpp) cc_final: 0.8586 (mmmt) REVERT: C 238 LYS cc_start: 0.8307 (tttp) cc_final: 0.7979 (tptm) REVERT: B 17 ASP cc_start: 0.8037 (m-30) cc_final: 0.7647 (m-30) REVERT: B 77 SER cc_start: 0.7827 (t) cc_final: 0.7586 (p) REVERT: B 180 LEU cc_start: 0.8443 (tp) cc_final: 0.8172 (tp) outliers start: 25 outliers final: 19 residues processed: 163 average time/residue: 0.2507 time to fit residues: 53.3612 Evaluate side-chains 168 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 155 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.123576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.087112 restraints weight = 12268.342| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.67 r_work: 0.2787 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8205 Z= 0.153 Angle : 0.565 8.302 11184 Z= 0.285 Chirality : 0.043 0.153 1245 Planarity : 0.004 0.065 1438 Dihedral : 4.417 33.830 1167 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.69 % Allowed : 19.98 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % 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: -0.14 (0.26), residues: 1038 helix: -2.70 (0.66), residues: 49 sheet: 1.22 (0.25), residues: 421 loop : -0.92 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 187 HIS 0.002 0.001 HIS C 192 PHE 0.005 0.001 PHE B 138 TYR 0.023 0.001 TYR H 151 ARG 0.005 0.000 ARG H 16 =============================================================================== Job complete usr+sys time: 2079.37 seconds wall clock time: 38 minutes 23.00 seconds (2303.00 seconds total)