Starting phenix.real_space_refine on Wed Feb 14 11:02:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd2_31904/02_2024/7vd2_31904_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd2_31904/02_2024/7vd2_31904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd2_31904/02_2024/7vd2_31904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd2_31904/02_2024/7vd2_31904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd2_31904/02_2024/7vd2_31904_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd2_31904/02_2024/7vd2_31904_neut_updated.pdb" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 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 27 5.49 5 S 34 5.16 5 C 6179 2.51 5 N 1322 2.21 5 O 1555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 33": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F ARG 42": "NH1" <-> "NH2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H ARG 117": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "J ARG 24": "NH1" <-> "NH2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 85": "OE1" <-> "OE2" Residue "I GLU 193": "OE1" <-> "OE2" Residue "I GLU 234": "OE1" <-> "OE2" Residue "I GLU 244": "OE1" <-> "OE2" Residue "I GLU 287": "OE1" <-> "OE2" Residue "I GLU 329": "OE1" <-> "OE2" Residue "I PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9117 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 354 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "D" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 304 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "F" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 354 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 433 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 304 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 458 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 463 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "J" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 433 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "B" Number of atoms: 2190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2190 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 272} Chain: "I" Number of atoms: 2190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2190 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 272} Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 130 Unusual residues: {'PC1': 2, 'UND': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {'PC1': 1, 'UND': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 227 Unusual residues: {'PC1': 4, 'UND': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 173 Unusual residues: {'PC1': 3, 'UND': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 119 Unusual residues: {'PC1': 2, 'UND': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 227 Unusual residues: {'PC1': 4, 'UND': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 314 Unusual residues: {'PC1': 5, 'UND': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 368 Unusual residues: {'PC1': 6, 'UND': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 5.20, per 1000 atoms: 0.57 Number of scatterers: 9117 At special positions: 0 Unit cell: (132.398, 113.845, 95.2929, 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 34 16.00 P 27 15.00 O 1555 8.00 N 1322 7.00 C 6179 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: 3.37 Conformation dependent library (CDL) restraints added in 1.4 seconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 2 sheets defined 34.9% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 27 through 36 removed outlier: 3.596A pdb=" N ARG A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 61 Processing helix chain 'D' and resid 14 through 47 Proline residue: D 42 - end of helix Processing helix chain 'F' and resid 26 through 35 removed outlier: 3.506A pdb=" N ARG F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE F 34 " --> pdb=" O GLY F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 61 Processing helix chain 'G' and resid 6 through 38 removed outlier: 3.914A pdb=" N GLN G 10 " --> pdb=" O LYS G 6 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG G 11 " --> pdb=" O GLU G 7 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ILE G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) Proline residue: G 29 - end of helix Processing helix chain 'G' and resid 49 through 52 Processing helix chain 'E' and resid 16 through 47 removed outlier: 3.553A pdb=" N MET E 20 " --> pdb=" O MET E 16 " (cutoff:3.500A) Proline residue: E 42 - end of helix Processing helix chain 'H' and resid 64 through 95 removed outlier: 3.871A pdb=" N ASP H 68 " --> pdb=" O GLY H 64 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 117 removed outlier: 4.000A pdb=" N GLN H 115 " --> pdb=" O GLN H 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN H 116 " --> pdb=" O GLN H 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 95 Processing helix chain 'C' and resid 97 through 117 Processing helix chain 'J' and resid 7 through 38 removed outlier: 3.514A pdb=" N GLN J 14 " --> pdb=" O GLN J 10 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE J 28 " --> pdb=" O ARG J 24 " (cutoff:3.500A) Proline residue: J 29 - end of helix Processing helix chain 'J' and resid 49 through 52 Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 88 through 93 removed outlier: 4.070A pdb=" N LEU B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'I' and resid 83 through 85 No H-bonds generated for 'chain 'I' and resid 83 through 85' Processing helix chain 'I' and resid 88 through 93 removed outlier: 4.054A pdb=" N LEU I 93 " --> pdb=" O LYS I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 310 No H-bonds generated for 'chain 'I' and resid 308 through 310' Processing sheet with id= A, first strand: chain 'B' and resid 355 through 359 removed outlier: 5.956A pdb=" N GLY B 100 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU B 358 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS B 102 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 160 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 175 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 251 " --> pdb=" O GLY B 232 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 100 through 105 removed outlier: 3.751A pdb=" N ILE I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA I 251 " --> pdb=" O GLY I 232 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN I 179 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TRP I 188 " --> pdb=" O ALA I 177 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA I 177 " --> pdb=" O TRP I 188 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL I 190 " --> pdb=" O LYS I 175 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS I 175 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY I 192 " --> pdb=" O ARG I 173 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG I 173 " --> pdb=" O GLY I 192 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE I 113 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL I 115 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLY I 108 " --> pdb=" O VAL I 115 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N HIS I 117 " --> pdb=" O ASN I 106 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN I 106 " --> pdb=" O HIS I 117 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL I 119 " --> pdb=" O THR I 104 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR I 104 " --> pdb=" O VAL I 119 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU I 121 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LYS I 102 " --> pdb=" O LEU I 121 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1455 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: 2.51 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1294 1.32 - 1.44: 2079 1.44 - 1.56: 5751 1.56 - 1.69: 54 1.69 - 1.81: 58 Bond restraints: 9236 Sorted by residual: bond pdb=" CA SER I 183 " pdb=" CB SER I 183 " ideal model delta sigma weight residual 1.532 1.486 0.046 1.74e-02 3.30e+03 7.06e+00 bond pdb=" O13 PC1 I 402 " pdb=" P PC1 I 402 " ideal model delta sigma weight residual 1.652 1.601 0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" O13 PC1 H 203 " pdb=" P PC1 H 203 " ideal model delta sigma weight residual 1.652 1.601 0.051 2.00e-02 2.50e+03 6.41e+00 bond pdb=" C11 PC1 A 104 " pdb=" O13 PC1 A 104 " ideal model delta sigma weight residual 1.407 1.457 -0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" C11 PC1 F 102 " pdb=" O13 PC1 F 102 " ideal model delta sigma weight residual 1.407 1.457 -0.050 2.00e-02 2.50e+03 6.23e+00 ... (remaining 9231 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.74: 264 106.74 - 113.56: 4870 113.56 - 120.37: 3899 120.37 - 127.19: 3011 127.19 - 134.00: 84 Bond angle restraints: 12128 Sorted by residual: angle pdb=" C SER I 183 " pdb=" N LYS I 184 " pdb=" CA LYS I 184 " ideal model delta sigma weight residual 122.72 115.96 6.76 1.38e+00 5.25e-01 2.40e+01 angle pdb=" N GLU B 85 " pdb=" CA GLU B 85 " pdb=" C GLU B 85 " ideal model delta sigma weight residual 112.93 108.24 4.69 1.12e+00 7.97e-01 1.75e+01 angle pdb=" CA GLU G 46 " pdb=" C GLU G 46 " pdb=" N PRO G 47 " ideal model delta sigma weight residual 118.87 122.18 -3.31 9.00e-01 1.23e+00 1.35e+01 angle pdb=" CA CYS B 86 " pdb=" C CYS B 86 " pdb=" O CYS B 86 " ideal model delta sigma weight residual 121.07 117.56 3.51 1.10e+00 8.26e-01 1.02e+01 angle pdb=" CA THR I 180 " pdb=" C THR I 180 " pdb=" O THR I 180 " ideal model delta sigma weight residual 120.70 117.37 3.33 1.08e+00 8.57e-01 9.53e+00 ... (remaining 12123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5008 17.99 - 35.97: 641 35.97 - 53.96: 214 53.96 - 71.94: 68 71.94 - 89.93: 20 Dihedral angle restraints: 5951 sinusoidal: 3250 harmonic: 2701 Sorted by residual: dihedral pdb=" CA THR B 180 " pdb=" C THR B 180 " pdb=" N GLN B 181 " pdb=" CA GLN B 181 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA LEU B 256 " pdb=" C LEU B 256 " pdb=" N ASN B 257 " pdb=" CA ASN B 257 " ideal model delta harmonic sigma weight residual 180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA GLN J 13 " pdb=" C GLN J 13 " pdb=" N GLN J 14 " pdb=" CA GLN J 14 " ideal model delta harmonic sigma weight residual 180.00 163.89 16.11 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 5948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 763 0.035 - 0.069: 293 0.069 - 0.104: 83 0.104 - 0.139: 37 0.139 - 0.174: 6 Chirality restraints: 1182 Sorted by residual: chirality pdb=" CA ASN I 258 " pdb=" N ASN I 258 " pdb=" C ASN I 258 " pdb=" CB ASN I 258 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CA GLN I 179 " pdb=" N GLN I 179 " pdb=" C GLN I 179 " pdb=" CB GLN I 179 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" C2 PC1 B 408 " pdb=" C1 PC1 B 408 " pdb=" C3 PC1 B 408 " pdb=" O21 PC1 B 408 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 1179 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR I 180 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C THR I 180 " -0.032 2.00e-02 2.50e+03 pdb=" O THR I 180 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN I 181 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 41 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO D 42 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 42 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 42 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 85 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C GLU B 85 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU B 85 " 0.010 2.00e-02 2.50e+03 pdb=" N CYS B 86 " 0.009 2.00e-02 2.50e+03 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1036 2.74 - 3.28: 7954 3.28 - 3.82: 13248 3.82 - 4.36: 16869 4.36 - 4.90: 29901 Nonbonded interactions: 69008 Sorted by model distance: nonbonded pdb=" O LEU J 12 " pdb=" N LEU J 15 " model vdw 2.196 2.520 nonbonded pdb=" O SER G 5 " pdb=" N ALA G 8 " model vdw 2.197 2.520 nonbonded pdb=" OH TYR E 34 " pdb=" O GLY B 232 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR D 34 " pdb=" O GLY I 232 " model vdw 2.218 2.440 nonbonded pdb=" NZ LYS I 91 " pdb=" OE2 GLU I 287 " model vdw 2.255 2.520 ... (remaining 69003 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 25 through 67 or resid 101 through 103)) selection = chain 'F' } ncs_group { reference = (chain 'B' and (resid 76 through 361 or resid 401 through 402 or resid 405 throu \ gh 407)) selection = (chain 'I' and (resid 76 through 361 or resid 401 through 402 or resid 405 throu \ gh 407)) } ncs_group { reference = (chain 'C' and (resid 63 through 118 or resid 201 through 202)) selection = (chain 'H' and (resid 63 through 118 or resid 201 through 202)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'J' } 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: 1.540 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: 6.990 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.070 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 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 : 0.011 0.051 9236 Z= 0.686 Angle : 0.907 9.108 12128 Z= 0.418 Chirality : 0.044 0.174 1182 Planarity : 0.003 0.042 1371 Dihedral : 18.201 89.928 4217 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.50 % Allowed : 0.37 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 1.47 (0.28), residues: 931 helix: 2.37 (0.29), residues: 312 sheet: 0.70 (0.26), residues: 398 loop : -0.48 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 188 HIS 0.008 0.001 HIS B 271 PHE 0.012 0.001 PHE G 27 TYR 0.008 0.001 TYR D 34 ARG 0.006 0.001 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 211 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 19 LYS cc_start: 0.9251 (tptp) cc_final: 0.8764 (tppp) REVERT: D 22 GLU cc_start: 0.8278 (pp20) cc_final: 0.7708 (pp20) REVERT: G 9 LYS cc_start: 0.8581 (pttm) cc_final: 0.8375 (pttm) REVERT: G 41 ASP cc_start: 0.8818 (m-30) cc_final: 0.8541 (m-30) REVERT: E 19 LYS cc_start: 0.8235 (mppt) cc_final: 0.7555 (mptt) REVERT: E 22 GLU cc_start: 0.8341 (pp20) cc_final: 0.8081 (pp20) REVERT: H 67 PHE cc_start: 0.8848 (t80) cc_final: 0.8535 (t80) REVERT: H 104 GLU cc_start: 0.8772 (tp30) cc_final: 0.8541 (mm-30) REVERT: H 111 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8686 (tm-30) REVERT: C 75 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8567 (tm-30) REVERT: C 104 GLU cc_start: 0.8772 (tp30) cc_final: 0.8552 (mm-30) REVERT: J 15 LEU cc_start: 0.9222 (tp) cc_final: 0.8984 (tt) REVERT: B 76 CYS cc_start: 0.8486 (m) cc_final: 0.7972 (t) REVERT: B 294 MET cc_start: 0.8754 (mpp) cc_final: 0.8309 (mpp) REVERT: B 296 ASP cc_start: 0.7970 (m-30) cc_final: 0.7672 (m-30) REVERT: I 294 MET cc_start: 0.8740 (mpp) cc_final: 0.8509 (mpp) outliers start: 4 outliers final: 1 residues processed: 212 average time/residue: 1.3616 time to fit residues: 305.2062 Evaluate side-chains 182 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7038 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9236 Z= 0.189 Angle : 0.644 8.589 12128 Z= 0.317 Chirality : 0.042 0.179 1182 Planarity : 0.004 0.047 1371 Dihedral : 19.797 108.205 2441 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.36 % Allowed : 13.93 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.29), residues: 931 helix: 3.33 (0.29), residues: 318 sheet: 1.22 (0.26), residues: 388 loop : -0.13 (0.47), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 27 HIS 0.003 0.001 HIS I 271 PHE 0.021 0.001 PHE C 67 TYR 0.008 0.001 TYR A 32 ARG 0.007 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 216 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9049 (t0) cc_final: 0.8803 (t0) REVERT: D 18 ARG cc_start: 0.8816 (ttp80) cc_final: 0.8576 (ttp80) REVERT: D 19 LYS cc_start: 0.9254 (tptp) cc_final: 0.8559 (tppp) REVERT: D 22 GLU cc_start: 0.8443 (pp20) cc_final: 0.8064 (pp20) REVERT: G 15 LEU cc_start: 0.9299 (tt) cc_final: 0.8938 (tm) REVERT: E 19 LYS cc_start: 0.8458 (mppt) cc_final: 0.8107 (mptt) REVERT: E 22 GLU cc_start: 0.8336 (pp20) cc_final: 0.8122 (pp20) REVERT: H 67 PHE cc_start: 0.8844 (t80) cc_final: 0.8503 (t80) REVERT: H 72 PHE cc_start: 0.9069 (t80) cc_final: 0.8768 (t80) REVERT: H 75 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8442 (tm-30) REVERT: H 104 GLU cc_start: 0.8715 (tp30) cc_final: 0.8494 (mm-30) REVERT: H 107 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8276 (tm-30) REVERT: H 111 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8655 (tm-30) REVERT: H 112 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8559 (tm-30) REVERT: C 75 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8352 (tm-30) REVERT: C 76 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8258 (mptm) REVERT: C 102 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: C 104 GLU cc_start: 0.8735 (tp30) cc_final: 0.8522 (mm-30) REVERT: C 107 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8141 (tm-30) REVERT: C 110 GLN cc_start: 0.8608 (pp30) cc_final: 0.8379 (pp30) REVERT: J 9 LYS cc_start: 0.8992 (mptt) cc_final: 0.8651 (mptt) REVERT: J 14 GLN cc_start: 0.8883 (mt0) cc_final: 0.8594 (tt0) REVERT: B 76 CYS cc_start: 0.8383 (m) cc_final: 0.7942 (t) REVERT: B 163 GLN cc_start: 0.8445 (mt0) cc_final: 0.8052 (mt0) REVERT: B 294 MET cc_start: 0.8611 (mpp) cc_final: 0.8404 (mpt) REVERT: B 296 ASP cc_start: 0.7947 (m-30) cc_final: 0.7661 (m-30) REVERT: I 163 GLN cc_start: 0.8291 (mt0) cc_final: 0.7970 (mt0) REVERT: I 176 MET cc_start: 0.8170 (mtt) cc_final: 0.7969 (mtm) REVERT: I 240 ARG cc_start: 0.7983 (mtm110) cc_final: 0.7746 (mtm110) outliers start: 19 outliers final: 4 residues processed: 216 average time/residue: 1.2671 time to fit residues: 290.6826 Evaluate side-chains 203 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 197 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain I residue 280 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 0.0040 chunk 80 optimal weight: 1.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS I 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9236 Z= 0.255 Angle : 0.613 8.728 12128 Z= 0.298 Chirality : 0.041 0.192 1182 Planarity : 0.004 0.042 1371 Dihedral : 19.057 89.900 2439 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.10 % Allowed : 15.05 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.29), residues: 931 helix: 3.27 (0.29), residues: 318 sheet: 1.40 (0.26), residues: 388 loop : -0.19 (0.46), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 27 HIS 0.005 0.001 HIS I 271 PHE 0.014 0.001 PHE I 356 TYR 0.006 0.001 TYR C 78 ARG 0.006 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 206 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9165 (t0) cc_final: 0.8793 (t0) REVERT: D 15 GLU cc_start: 0.8863 (pm20) cc_final: 0.7930 (pm20) REVERT: D 18 ARG cc_start: 0.8761 (ttp80) cc_final: 0.8371 (ttp80) REVERT: D 19 LYS cc_start: 0.9284 (tptp) cc_final: 0.8523 (tppp) REVERT: D 20 MET cc_start: 0.8668 (mtp) cc_final: 0.8435 (mtm) REVERT: D 22 GLU cc_start: 0.8456 (pp20) cc_final: 0.8052 (pp20) REVERT: G 9 LYS cc_start: 0.8884 (pttm) cc_final: 0.8648 (pttm) REVERT: E 29 ARG cc_start: 0.8888 (ttp-110) cc_final: 0.8632 (ttp80) REVERT: H 67 PHE cc_start: 0.8787 (t80) cc_final: 0.8435 (t80) REVERT: H 75 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8401 (tm-30) REVERT: H 104 GLU cc_start: 0.8730 (tp30) cc_final: 0.8502 (mm-30) REVERT: H 107 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8246 (tm-30) REVERT: H 111 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8672 (tm-30) REVERT: H 112 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8510 (tm-30) REVERT: C 75 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8413 (tm-30) REVERT: C 102 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: C 104 GLU cc_start: 0.8731 (tp30) cc_final: 0.8523 (mm-30) REVERT: C 107 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7965 (tm-30) REVERT: C 110 GLN cc_start: 0.8547 (pp30) cc_final: 0.8328 (pp30) REVERT: J 9 LYS cc_start: 0.8996 (mptt) cc_final: 0.8689 (mptt) REVERT: B 76 CYS cc_start: 0.8371 (m) cc_final: 0.7956 (t) REVERT: B 96 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9164 (pp) REVERT: B 163 GLN cc_start: 0.8415 (mt0) cc_final: 0.7988 (mt0) REVERT: B 195 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8565 (mtm-85) REVERT: B 294 MET cc_start: 0.8779 (mpp) cc_final: 0.8526 (mmm) REVERT: B 296 ASP cc_start: 0.7993 (m-30) cc_final: 0.7674 (m-30) REVERT: I 96 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9197 (pp) REVERT: I 163 GLN cc_start: 0.8288 (mt0) cc_final: 0.8074 (mt0) REVERT: I 176 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.8013 (mtm) outliers start: 33 outliers final: 15 residues processed: 209 average time/residue: 1.2630 time to fit residues: 280.2253 Evaluate side-chains 215 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 195 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 176 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN I 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9236 Z= 0.177 Angle : 0.597 8.768 12128 Z= 0.288 Chirality : 0.040 0.186 1182 Planarity : 0.004 0.038 1371 Dihedral : 18.691 88.133 2439 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.61 % Allowed : 16.67 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.29), residues: 931 helix: 3.21 (0.29), residues: 318 sheet: 1.50 (0.26), residues: 388 loop : -0.23 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 27 HIS 0.003 0.001 HIS I 220 PHE 0.020 0.001 PHE C 67 TYR 0.007 0.001 TYR H 78 ARG 0.008 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 203 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9208 (t0) cc_final: 0.8783 (t0) REVERT: D 18 ARG cc_start: 0.8733 (ttp80) cc_final: 0.8472 (ttp80) REVERT: D 19 LYS cc_start: 0.9236 (tptp) cc_final: 0.8355 (tppp) REVERT: D 20 MET cc_start: 0.8662 (mtp) cc_final: 0.8404 (mtm) REVERT: D 22 GLU cc_start: 0.8438 (pp20) cc_final: 0.7993 (pp20) REVERT: D 38 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8802 (mp) REVERT: G 13 GLN cc_start: 0.8316 (mt0) cc_final: 0.8094 (mt0) REVERT: E 19 LYS cc_start: 0.8232 (mppt) cc_final: 0.7842 (mptt) REVERT: E 23 ASP cc_start: 0.8772 (m-30) cc_final: 0.8519 (m-30) REVERT: H 67 PHE cc_start: 0.8779 (t80) cc_final: 0.8437 (t80) REVERT: H 75 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8294 (tm-30) REVERT: H 104 GLU cc_start: 0.8715 (tp30) cc_final: 0.8495 (mm-30) REVERT: H 107 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8184 (tm-30) REVERT: H 111 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8615 (tm-30) REVERT: C 75 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8332 (tm-30) REVERT: C 102 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: C 104 GLU cc_start: 0.8689 (tp30) cc_final: 0.8241 (tp30) REVERT: C 107 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8024 (tm-30) REVERT: C 110 GLN cc_start: 0.8477 (pp30) cc_final: 0.8252 (pp30) REVERT: J 9 LYS cc_start: 0.8988 (mptt) cc_final: 0.8649 (mptt) REVERT: J 13 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7975 (pm20) REVERT: B 76 CYS cc_start: 0.8352 (m) cc_final: 0.7977 (t) REVERT: B 163 GLN cc_start: 0.8331 (mt0) cc_final: 0.8063 (mt0) REVERT: B 195 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8556 (mtm-85) REVERT: B 296 ASP cc_start: 0.7992 (m-30) cc_final: 0.7611 (m-30) REVERT: I 96 ILE cc_start: 0.9479 (OUTLIER) cc_final: 0.9202 (pp) outliers start: 29 outliers final: 12 residues processed: 208 average time/residue: 1.2822 time to fit residues: 282.8829 Evaluate side-chains 210 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 280 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.0020 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 chunk 74 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9236 Z= 0.150 Angle : 0.594 9.598 12128 Z= 0.285 Chirality : 0.039 0.183 1182 Planarity : 0.004 0.050 1371 Dihedral : 18.336 87.065 2439 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.11 % Allowed : 19.40 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.29), residues: 931 helix: 3.20 (0.29), residues: 319 sheet: 1.62 (0.25), residues: 386 loop : -0.25 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 259 HIS 0.003 0.001 HIS I 220 PHE 0.012 0.001 PHE I 356 TYR 0.007 0.001 TYR H 78 ARG 0.009 0.001 ARG I 240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 209 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9211 (t0) cc_final: 0.8820 (t0) REVERT: D 19 LYS cc_start: 0.9186 (tptp) cc_final: 0.8781 (tppp) REVERT: D 20 MET cc_start: 0.8580 (mtp) cc_final: 0.8349 (mtm) REVERT: D 22 GLU cc_start: 0.8418 (pp20) cc_final: 0.8023 (pp20) REVERT: D 38 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8792 (mp) REVERT: G 13 GLN cc_start: 0.8312 (mt0) cc_final: 0.8037 (mt0) REVERT: E 19 LYS cc_start: 0.8236 (mppt) cc_final: 0.7811 (tppp) REVERT: E 22 GLU cc_start: 0.8033 (pp20) cc_final: 0.7376 (pp20) REVERT: E 23 ASP cc_start: 0.8772 (m-30) cc_final: 0.8389 (m-30) REVERT: H 67 PHE cc_start: 0.8775 (t80) cc_final: 0.8416 (t80) REVERT: H 75 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8288 (tm-30) REVERT: H 104 GLU cc_start: 0.8701 (tp30) cc_final: 0.8242 (tp30) REVERT: H 107 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8093 (tm-30) REVERT: H 111 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8456 (tm-30) REVERT: H 115 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8294 (mm-40) REVERT: C 75 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8398 (tm-30) REVERT: C 102 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: C 104 GLU cc_start: 0.8668 (tp30) cc_final: 0.8223 (tp30) REVERT: C 107 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7951 (tm-30) REVERT: J 9 LYS cc_start: 0.9027 (mptt) cc_final: 0.8804 (mptt) REVERT: B 76 CYS cc_start: 0.8334 (m) cc_final: 0.8001 (t) REVERT: B 96 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9159 (pp) REVERT: B 195 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8539 (mtm-85) REVERT: B 296 ASP cc_start: 0.8021 (m-30) cc_final: 0.7643 (m-30) REVERT: I 163 GLN cc_start: 0.8169 (mt0) cc_final: 0.7935 (tt0) REVERT: I 293 ARG cc_start: 0.8748 (mtp-110) cc_final: 0.8528 (ttm110) outliers start: 25 outliers final: 9 residues processed: 214 average time/residue: 1.2128 time to fit residues: 276.0625 Evaluate side-chains 207 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 194 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 280 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.7092 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9236 Z= 0.353 Angle : 0.671 8.902 12128 Z= 0.324 Chirality : 0.042 0.195 1182 Planarity : 0.004 0.047 1371 Dihedral : 18.526 88.656 2439 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.98 % Allowed : 19.53 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.29), residues: 931 helix: 3.16 (0.29), residues: 319 sheet: 1.54 (0.26), residues: 388 loop : -0.33 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 25 HIS 0.005 0.001 HIS I 220 PHE 0.022 0.001 PHE C 67 TYR 0.009 0.001 TYR E 34 ARG 0.010 0.001 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 198 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9201 (t0) cc_final: 0.8881 (t0) REVERT: D 19 LYS cc_start: 0.9225 (tptp) cc_final: 0.8813 (tppp) REVERT: D 22 GLU cc_start: 0.8446 (pp20) cc_final: 0.8082 (pp20) REVERT: D 38 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8837 (mp) REVERT: G 13 GLN cc_start: 0.8367 (mt0) cc_final: 0.8099 (mt0) REVERT: E 19 LYS cc_start: 0.8339 (mppt) cc_final: 0.7824 (tppp) REVERT: E 22 GLU cc_start: 0.8122 (pp20) cc_final: 0.7465 (pp20) REVERT: E 23 ASP cc_start: 0.8842 (m-30) cc_final: 0.8510 (m-30) REVERT: H 67 PHE cc_start: 0.8782 (t80) cc_final: 0.8433 (t80) REVERT: H 75 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8303 (tm-30) REVERT: H 104 GLU cc_start: 0.8703 (tp30) cc_final: 0.8253 (tp30) REVERT: H 107 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8181 (tm-30) REVERT: H 111 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8428 (tm-30) REVERT: H 115 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8397 (mm110) REVERT: C 75 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8405 (tm-30) REVERT: C 102 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: C 104 GLU cc_start: 0.8714 (tp30) cc_final: 0.8272 (tp30) REVERT: C 107 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8064 (tm-30) REVERT: J 9 LYS cc_start: 0.9054 (mptt) cc_final: 0.8816 (mptt) REVERT: B 76 CYS cc_start: 0.8410 (m) cc_final: 0.8039 (t) REVERT: B 163 GLN cc_start: 0.8424 (mt0) cc_final: 0.8120 (tt0) REVERT: B 195 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8550 (mtm-85) REVERT: B 296 ASP cc_start: 0.7973 (m-30) cc_final: 0.7544 (m-30) REVERT: I 163 GLN cc_start: 0.8351 (mt0) cc_final: 0.7986 (tt0) REVERT: I 293 ARG cc_start: 0.8797 (mtp-110) cc_final: 0.8535 (ttm110) outliers start: 32 outliers final: 17 residues processed: 203 average time/residue: 1.2436 time to fit residues: 268.0664 Evaluate side-chains 213 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 280 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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: 0.7069 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9236 Z= 0.222 Angle : 0.647 9.044 12128 Z= 0.311 Chirality : 0.040 0.189 1182 Planarity : 0.004 0.054 1371 Dihedral : 18.136 87.853 2439 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.74 % Allowed : 22.14 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.29), residues: 931 helix: 3.12 (0.29), residues: 319 sheet: 1.54 (0.26), residues: 388 loop : -0.32 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 259 HIS 0.004 0.001 HIS B 220 PHE 0.014 0.001 PHE I 356 TYR 0.006 0.001 TYR H 78 ARG 0.014 0.001 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 202 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9239 (t0) cc_final: 0.8907 (t0) REVERT: D 18 ARG cc_start: 0.8705 (ttp80) cc_final: 0.8406 (ttp80) REVERT: D 19 LYS cc_start: 0.9225 (tptp) cc_final: 0.8533 (tppp) REVERT: D 22 GLU cc_start: 0.8404 (pp20) cc_final: 0.7989 (pp20) REVERT: D 23 ASP cc_start: 0.8791 (m-30) cc_final: 0.8226 (m-30) REVERT: D 38 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8761 (mp) REVERT: G 13 GLN cc_start: 0.8312 (mt0) cc_final: 0.8108 (mt0) REVERT: E 19 LYS cc_start: 0.8408 (mppt) cc_final: 0.8149 (ptpt) REVERT: E 22 GLU cc_start: 0.8208 (pp20) cc_final: 0.7988 (pp20) REVERT: E 23 ASP cc_start: 0.8854 (m-30) cc_final: 0.8586 (m-30) REVERT: H 67 PHE cc_start: 0.8781 (t80) cc_final: 0.8423 (t80) REVERT: H 75 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8305 (tm-30) REVERT: H 104 GLU cc_start: 0.8696 (tp30) cc_final: 0.8249 (tp30) REVERT: H 107 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8136 (tm-30) REVERT: H 111 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8487 (tm-30) REVERT: H 115 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8424 (mm110) REVERT: C 75 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8340 (tm-30) REVERT: C 102 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: C 104 GLU cc_start: 0.8706 (tp30) cc_final: 0.8262 (tp30) REVERT: C 107 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8032 (tm-30) REVERT: J 9 LYS cc_start: 0.9015 (mptt) cc_final: 0.8793 (mptt) REVERT: B 76 CYS cc_start: 0.8354 (m) cc_final: 0.7971 (t) REVERT: B 163 GLN cc_start: 0.8353 (mt0) cc_final: 0.8076 (tt0) REVERT: B 195 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8537 (mtm-85) REVERT: B 293 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8058 (ptm-80) REVERT: B 296 ASP cc_start: 0.7867 (m-30) cc_final: 0.7504 (m-30) REVERT: I 163 GLN cc_start: 0.8253 (mt0) cc_final: 0.7950 (tt0) outliers start: 22 outliers final: 12 residues processed: 207 average time/residue: 1.3123 time to fit residues: 288.4608 Evaluate side-chains 212 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 196 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 280 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 0.0770 chunk 68 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 75 optimal weight: 0.0040 overall best weight: 0.7952 ------------------------------------------------------------------------------- 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: 0.7055 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 : 0.003 0.039 9236 Z= 0.192 Angle : 0.659 9.700 12128 Z= 0.318 Chirality : 0.040 0.186 1182 Planarity : 0.004 0.074 1371 Dihedral : 17.788 89.917 2439 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.11 % Allowed : 22.39 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.29), residues: 931 helix: 3.17 (0.29), residues: 319 sheet: 1.59 (0.26), residues: 388 loop : -0.35 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 259 HIS 0.003 0.001 HIS I 220 PHE 0.026 0.001 PHE C 67 TYR 0.006 0.001 TYR H 78 ARG 0.020 0.001 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 202 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8391 (ptp-170) cc_final: 0.8189 (ptt-90) REVERT: A 37 ASP cc_start: 0.9245 (t0) cc_final: 0.8951 (t0) REVERT: D 19 LYS cc_start: 0.9227 (tptp) cc_final: 0.8753 (tppp) REVERT: D 22 GLU cc_start: 0.8405 (pp20) cc_final: 0.8060 (pp20) REVERT: D 38 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8766 (mp) REVERT: G 13 GLN cc_start: 0.8274 (mt0) cc_final: 0.8024 (mt0) REVERT: G 14 GLN cc_start: 0.8731 (mt0) cc_final: 0.8109 (mm-40) REVERT: E 19 LYS cc_start: 0.8322 (mppt) cc_final: 0.7943 (ptpt) REVERT: E 22 GLU cc_start: 0.8235 (pp20) cc_final: 0.7973 (pp20) REVERT: E 23 ASP cc_start: 0.8902 (m-30) cc_final: 0.8616 (m-30) REVERT: H 67 PHE cc_start: 0.8779 (t80) cc_final: 0.8425 (t80) REVERT: H 75 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8280 (tm-30) REVERT: H 104 GLU cc_start: 0.8690 (tp30) cc_final: 0.8246 (tp30) REVERT: H 107 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8095 (tm-30) REVERT: H 111 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8466 (tm-30) REVERT: H 112 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8530 (pp30) REVERT: H 115 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8440 (mm110) REVERT: C 75 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8359 (tm-30) REVERT: C 102 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: C 104 GLU cc_start: 0.8698 (tp30) cc_final: 0.8262 (tp30) REVERT: C 107 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8006 (tm-30) REVERT: C 115 GLN cc_start: 0.9469 (tm-30) cc_final: 0.9259 (pp30) REVERT: J 9 LYS cc_start: 0.8999 (mptt) cc_final: 0.8792 (mptt) REVERT: B 76 CYS cc_start: 0.8345 (m) cc_final: 0.7978 (t) REVERT: B 96 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.9181 (pp) REVERT: B 163 GLN cc_start: 0.8275 (mt0) cc_final: 0.8008 (tt0) REVERT: B 195 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8531 (mtm-85) REVERT: B 296 ASP cc_start: 0.7787 (m-30) cc_final: 0.7434 (m-30) REVERT: I 96 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.9208 (pp) REVERT: I 163 GLN cc_start: 0.8214 (mt0) cc_final: 0.7974 (tt0) outliers start: 25 outliers final: 11 residues processed: 208 average time/residue: 1.2140 time to fit residues: 268.7116 Evaluate side-chains 211 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 195 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 280 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 0.0670 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9236 Z= 0.187 Angle : 0.677 10.594 12128 Z= 0.324 Chirality : 0.040 0.185 1182 Planarity : 0.005 0.061 1371 Dihedral : 17.485 87.378 2439 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.86 % Allowed : 22.76 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.29), residues: 931 helix: 3.31 (0.29), residues: 316 sheet: 1.66 (0.26), residues: 388 loop : -0.36 (0.45), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 259 HIS 0.003 0.001 HIS I 220 PHE 0.012 0.001 PHE I 356 TYR 0.006 0.001 TYR H 78 ARG 0.015 0.001 ARG I 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9243 (t0) cc_final: 0.9004 (t0) REVERT: D 18 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8326 (ttp80) REVERT: D 19 LYS cc_start: 0.9216 (tptp) cc_final: 0.8446 (tppp) REVERT: D 22 GLU cc_start: 0.8408 (pp20) cc_final: 0.7971 (pp20) REVERT: D 23 ASP cc_start: 0.8795 (m-30) cc_final: 0.8184 (m-30) REVERT: D 38 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8739 (mp) REVERT: G 13 GLN cc_start: 0.8307 (mt0) cc_final: 0.7966 (mt0) REVERT: G 14 GLN cc_start: 0.8748 (mt0) cc_final: 0.8078 (mm-40) REVERT: G 41 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8342 (m-30) REVERT: E 19 LYS cc_start: 0.8397 (mppt) cc_final: 0.7799 (ptpt) REVERT: E 23 ASP cc_start: 0.8925 (m-30) cc_final: 0.8632 (m-30) REVERT: H 67 PHE cc_start: 0.8776 (t80) cc_final: 0.8425 (t80) REVERT: H 75 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8261 (tm-30) REVERT: H 104 GLU cc_start: 0.8672 (tp30) cc_final: 0.8243 (tp30) REVERT: H 107 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8025 (tm-30) REVERT: H 111 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8424 (tm-30) REVERT: H 112 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8477 (pp30) REVERT: H 115 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8522 (mm110) REVERT: C 75 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8344 (tm-30) REVERT: C 102 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: C 104 GLU cc_start: 0.8696 (tp30) cc_final: 0.8266 (tp30) REVERT: C 107 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8000 (tm-30) REVERT: C 115 GLN cc_start: 0.9452 (tm-30) cc_final: 0.9226 (pp30) REVERT: J 9 LYS cc_start: 0.8946 (mptt) cc_final: 0.8525 (mptt) REVERT: J 13 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7939 (pm20) REVERT: B 76 CYS cc_start: 0.8327 (m) cc_final: 0.7982 (t) REVERT: B 96 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9186 (pp) REVERT: B 163 GLN cc_start: 0.8217 (mt0) cc_final: 0.7945 (tt0) REVERT: B 195 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8517 (mtm-85) REVERT: I 96 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9214 (pp) REVERT: I 293 ARG cc_start: 0.8719 (mtp-110) cc_final: 0.8408 (ttm110) outliers start: 23 outliers final: 10 residues processed: 207 average time/residue: 1.2049 time to fit residues: 265.2678 Evaluate side-chains 213 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 196 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 280 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.7061 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9236 Z= 0.243 Angle : 0.700 9.819 12128 Z= 0.338 Chirality : 0.041 0.188 1182 Planarity : 0.005 0.071 1371 Dihedral : 17.472 89.824 2439 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.49 % Allowed : 24.25 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.29), residues: 931 helix: 3.29 (0.29), residues: 316 sheet: 1.67 (0.26), residues: 388 loop : -0.44 (0.44), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 259 HIS 0.004 0.001 HIS I 220 PHE 0.027 0.001 PHE C 67 TYR 0.006 0.001 TYR E 34 ARG 0.016 0.001 ARG B 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8410 (ptp-170) cc_final: 0.8202 (ptt-90) REVERT: A 37 ASP cc_start: 0.9249 (t0) cc_final: 0.9019 (t0) REVERT: D 18 ARG cc_start: 0.8678 (ttp80) cc_final: 0.8339 (ttp80) REVERT: D 19 LYS cc_start: 0.9218 (tptp) cc_final: 0.8463 (tppp) REVERT: D 22 GLU cc_start: 0.8405 (pp20) cc_final: 0.7956 (pp20) REVERT: D 23 ASP cc_start: 0.8760 (m-30) cc_final: 0.8123 (m-30) REVERT: D 38 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8790 (mp) REVERT: G 13 GLN cc_start: 0.8274 (mt0) cc_final: 0.7930 (mp10) REVERT: G 14 GLN cc_start: 0.8770 (mt0) cc_final: 0.8111 (mm-40) REVERT: E 22 GLU cc_start: 0.8246 (pp20) cc_final: 0.8004 (pp20) REVERT: E 23 ASP cc_start: 0.8973 (m-30) cc_final: 0.8669 (m-30) REVERT: H 67 PHE cc_start: 0.8768 (t80) cc_final: 0.8419 (t80) REVERT: H 75 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8261 (tm-30) REVERT: H 104 GLU cc_start: 0.8654 (tp30) cc_final: 0.8083 (tp30) REVERT: H 107 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8101 (tm-30) REVERT: H 111 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8409 (tm-30) REVERT: H 115 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8484 (mm110) REVERT: C 75 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8353 (tm-30) REVERT: C 102 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: C 104 GLU cc_start: 0.8704 (tp30) cc_final: 0.8076 (tp30) REVERT: C 107 GLN cc_start: 0.8447 (tm-30) cc_final: 0.8029 (tm-30) REVERT: J 9 LYS cc_start: 0.8964 (mptt) cc_final: 0.8586 (mptt) REVERT: J 13 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7995 (pm20) REVERT: B 76 CYS cc_start: 0.8325 (m) cc_final: 0.7972 (t) REVERT: B 96 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9191 (pp) REVERT: B 163 GLN cc_start: 0.8269 (mt0) cc_final: 0.7984 (tt0) REVERT: B 195 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8574 (mtm-85) REVERT: B 296 ASP cc_start: 0.7621 (p0) cc_final: 0.7221 (p0) REVERT: I 96 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9216 (pp) REVERT: I 293 ARG cc_start: 0.8740 (mtp-110) cc_final: 0.8428 (ttm110) outliers start: 20 outliers final: 11 residues processed: 204 average time/residue: 1.2307 time to fit residues: 266.8169 Evaluate side-chains 210 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 280 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.099224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.067188 restraints weight = 16534.295| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.52 r_work: 0.2772 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9236 Z= 0.250 Angle : 0.708 9.565 12128 Z= 0.343 Chirality : 0.041 0.189 1182 Planarity : 0.005 0.064 1371 Dihedral : 17.415 88.060 2439 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.86 % Allowed : 24.13 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.29), residues: 931 helix: 3.27 (0.29), residues: 316 sheet: 1.64 (0.26), residues: 388 loop : -0.42 (0.44), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 259 HIS 0.004 0.001 HIS I 220 PHE 0.022 0.001 PHE H 72 TYR 0.006 0.001 TYR E 34 ARG 0.020 0.001 ARG B 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4617.67 seconds wall clock time: 81 minutes 58.81 seconds (4918.81 seconds total)