Starting phenix.real_space_refine on Sat Sep 28 08:30:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl4_16712/09_2024/8cl4_16712.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl4_16712/09_2024/8cl4_16712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl4_16712/09_2024/8cl4_16712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl4_16712/09_2024/8cl4_16712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl4_16712/09_2024/8cl4_16712.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl4_16712/09_2024/8cl4_16712.cif" } resolution = 3.14 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= 0.002 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6995 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 8400 2.51 5 N 2285 2.21 5 O 2535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13335 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 527 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "A" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 38 Restraints were copied for chains: F, I, L, O, E, H, K, N, D, G, J, M Time building chain proxies: 6.29, per 1000 atoms: 0.47 Number of scatterers: 13335 At special positions: 0 Unit cell: (159.96, 155.31, 93.93, 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 115 16.00 O 2535 8.00 N 2285 7.00 C 8400 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 - 3.00 Amino acid : True - 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: 3.62 Conformation dependent library (CDL) restraints added in 1.9 seconds 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 5 sheets defined 75.4% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.855A pdb=" N ALA B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.035A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.559A pdb=" N ALA B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.748A pdb=" N ALA C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.245A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 removed outlier: 3.807A pdb=" N ALA C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'A' and resid 16 through 30 removed outlier: 3.576A pdb=" N LYS A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 removed outlier: 4.027A pdb=" N ARG A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.564A pdb=" N ALA A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.702A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.724A pdb=" N LEU A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.855A pdb=" N ALA D 174 " --> pdb=" O LYS D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.036A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.559A pdb=" N ALA D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'E' and resid 160 through 175 removed outlier: 3.749A pdb=" N ALA E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.245A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 204 removed outlier: 3.807A pdb=" N ALA E 204 " --> pdb=" O THR E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'F' and resid 16 through 30 removed outlier: 3.577A pdb=" N LYS F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 120 Processing helix chain 'F' and resid 125 through 145 removed outlier: 4.028A pdb=" N ARG F 132 " --> pdb=" O GLU F 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP F 133 " --> pdb=" O ILE F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 175 removed outlier: 3.565A pdb=" N ALA F 174 " --> pdb=" O LYS F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 193 removed outlier: 3.702A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.724A pdb=" N LEU F 205 " --> pdb=" O ILE F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'G' and resid 160 through 175 removed outlier: 3.855A pdb=" N ALA G 174 " --> pdb=" O LYS G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.036A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.559A pdb=" N ALA G 204 " --> pdb=" O THR G 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 205 " --> pdb=" O ILE G 201 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 219 Processing helix chain 'H' and resid 160 through 175 removed outlier: 3.748A pdb=" N ALA H 174 " --> pdb=" O LYS H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 193 removed outlier: 4.245A pdb=" N VAL H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 204 removed outlier: 3.807A pdb=" N ALA H 204 " --> pdb=" O THR H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 219 Processing helix chain 'I' and resid 16 through 30 removed outlier: 3.576A pdb=" N LYS I 30 " --> pdb=" O VAL I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 62 through 84 Processing helix chain 'I' and resid 100 through 105 Processing helix chain 'I' and resid 110 through 120 Processing helix chain 'I' and resid 125 through 145 removed outlier: 4.028A pdb=" N ARG I 132 " --> pdb=" O GLU I 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP I 133 " --> pdb=" O ILE I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'I' and resid 160 through 175 removed outlier: 3.564A pdb=" N ALA I 174 " --> pdb=" O LYS I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 193 removed outlier: 3.703A pdb=" N VAL I 191 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 3.724A pdb=" N LEU I 205 " --> pdb=" O ILE I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 219 Processing helix chain 'J' and resid 160 through 175 removed outlier: 3.855A pdb=" N ALA J 174 " --> pdb=" O LYS J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 193 removed outlier: 4.035A pdb=" N LEU J 190 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL J 191 " --> pdb=" O GLU J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 206 removed outlier: 3.559A pdb=" N ALA J 204 " --> pdb=" O THR J 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU J 205 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 219 Processing helix chain 'K' and resid 160 through 175 removed outlier: 3.748A pdb=" N ALA K 174 " --> pdb=" O LYS K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 193 removed outlier: 4.246A pdb=" N VAL K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 204 removed outlier: 3.807A pdb=" N ALA K 204 " --> pdb=" O THR K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 219 Processing helix chain 'L' and resid 16 through 30 removed outlier: 3.576A pdb=" N LYS L 30 " --> pdb=" O VAL L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 44 Processing helix chain 'L' and resid 48 through 57 Processing helix chain 'L' and resid 62 through 84 Processing helix chain 'L' and resid 100 through 105 Processing helix chain 'L' and resid 110 through 120 Processing helix chain 'L' and resid 125 through 145 removed outlier: 4.027A pdb=" N ARG L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP L 133 " --> pdb=" O ILE L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 153 Processing helix chain 'L' and resid 160 through 175 removed outlier: 3.565A pdb=" N ALA L 174 " --> pdb=" O LYS L 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 193 removed outlier: 3.703A pdb=" N VAL L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 205 removed outlier: 3.724A pdb=" N LEU L 205 " --> pdb=" O ILE L 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 219 Processing helix chain 'M' and resid 160 through 175 removed outlier: 3.855A pdb=" N ALA M 174 " --> pdb=" O LYS M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 193 removed outlier: 4.036A pdb=" N LEU M 190 " --> pdb=" O THR M 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL M 191 " --> pdb=" O GLU M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 206 removed outlier: 3.559A pdb=" N ALA M 204 " --> pdb=" O THR M 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY M 206 " --> pdb=" O LEU M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 219 Processing helix chain 'N' and resid 160 through 175 removed outlier: 3.748A pdb=" N ALA N 174 " --> pdb=" O LYS N 170 " (cutoff:3.500A) Processing helix chain 'N' and resid 178 through 193 removed outlier: 4.245A pdb=" N VAL N 191 " --> pdb=" O GLU N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 204 removed outlier: 3.807A pdb=" N ALA N 204 " --> pdb=" O THR N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 219 Processing helix chain 'O' and resid 16 through 30 removed outlier: 3.576A pdb=" N LYS O 30 " --> pdb=" O VAL O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 44 Processing helix chain 'O' and resid 48 through 57 Processing helix chain 'O' and resid 62 through 84 Processing helix chain 'O' and resid 100 through 105 Processing helix chain 'O' and resid 110 through 120 Processing helix chain 'O' and resid 125 through 145 removed outlier: 4.027A pdb=" N ARG O 132 " --> pdb=" O GLU O 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP O 133 " --> pdb=" O ILE O 129 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 153 Processing helix chain 'O' and resid 160 through 175 removed outlier: 3.565A pdb=" N ALA O 174 " --> pdb=" O LYS O 170 " (cutoff:3.500A) Processing helix chain 'O' and resid 178 through 193 removed outlier: 3.703A pdb=" N VAL O 191 " --> pdb=" O GLU O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 205 removed outlier: 3.724A pdb=" N LEU O 205 " --> pdb=" O ILE O 201 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 219 Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=2, first strand: chain 'F' and resid 2 through 4 Processing sheet with id=3, first strand: chain 'I' and resid 2 through 4 Processing sheet with id=4, first strand: chain 'L' and resid 2 through 4 Processing sheet with id=5, first strand: chain 'O' and resid 2 through 4 840 hydrogen bonds defined for protein. 2490 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: 3.89 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4410 1.34 - 1.46: 1422 1.46 - 1.57: 7563 1.57 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 13595 Sorted by residual: bond pdb=" CB PRO I 1 " pdb=" CG PRO I 1 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.58e+00 bond pdb=" CB PRO O 1 " pdb=" CG PRO O 1 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.57e+00 bond pdb=" CB PRO F 1 " pdb=" CG PRO F 1 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.57e+00 bond pdb=" CB PRO L 1 " pdb=" CG PRO L 1 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.57e+00 bond pdb=" CB PRO A 1 " pdb=" CG PRO A 1 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.56e+00 ... (remaining 13590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 15646 1.03 - 2.06: 2240 2.06 - 3.09: 384 3.09 - 4.12: 140 4.12 - 5.14: 30 Bond angle restraints: 18440 Sorted by residual: angle pdb=" N ALA O 177 " pdb=" CA ALA O 177 " pdb=" C ALA O 177 " ideal model delta sigma weight residual 110.24 114.10 -3.86 1.47e+00 4.63e-01 6.89e+00 angle pdb=" N ALA A 177 " pdb=" CA ALA A 177 " pdb=" C ALA A 177 " ideal model delta sigma weight residual 110.24 114.08 -3.84 1.47e+00 4.63e-01 6.84e+00 angle pdb=" N ALA I 177 " pdb=" CA ALA I 177 " pdb=" C ALA I 177 " ideal model delta sigma weight residual 110.24 114.08 -3.84 1.47e+00 4.63e-01 6.84e+00 angle pdb=" N ALA F 177 " pdb=" CA ALA F 177 " pdb=" C ALA F 177 " ideal model delta sigma weight residual 110.24 114.08 -3.84 1.47e+00 4.63e-01 6.81e+00 angle pdb=" N ALA L 177 " pdb=" CA ALA L 177 " pdb=" C ALA L 177 " ideal model delta sigma weight residual 110.24 114.07 -3.83 1.47e+00 4.63e-01 6.78e+00 ... (remaining 18435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 7740 15.68 - 31.37: 450 31.37 - 47.05: 120 47.05 - 62.74: 30 62.74 - 78.42: 20 Dihedral angle restraints: 8360 sinusoidal: 3365 harmonic: 4995 Sorted by residual: dihedral pdb=" CA GLU H 175 " pdb=" C GLU H 175 " pdb=" N GLN H 176 " pdb=" CA GLN H 176 " ideal model delta harmonic sigma weight residual -180.00 -150.43 -29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA GLU E 175 " pdb=" C GLU E 175 " pdb=" N GLN E 176 " pdb=" CA GLN E 176 " ideal model delta harmonic sigma weight residual -180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA GLU C 175 " pdb=" C GLU C 175 " pdb=" N GLN C 176 " pdb=" CA GLN C 176 " ideal model delta harmonic sigma weight residual -180.00 -150.45 -29.55 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 8357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1129 0.033 - 0.065: 610 0.065 - 0.098: 226 0.098 - 0.131: 97 0.131 - 0.164: 23 Chirality restraints: 2085 Sorted by residual: chirality pdb=" CA LYS I 30 " pdb=" N LYS I 30 " pdb=" C LYS I 30 " pdb=" CB LYS I 30 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA LYS A 30 " pdb=" N LYS A 30 " pdb=" C LYS A 30 " pdb=" CB LYS A 30 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CA LYS L 30 " pdb=" N LYS L 30 " pdb=" C LYS L 30 " pdb=" CB LYS L 30 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 2082 not shown) Planarity restraints: 2390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR L 186 " 0.024 2.00e-02 2.50e+03 4.74e-02 2.25e+01 pdb=" C THR L 186 " -0.082 2.00e-02 2.50e+03 pdb=" O THR L 186 " 0.031 2.00e-02 2.50e+03 pdb=" N GLU L 187 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 186 " 0.024 2.00e-02 2.50e+03 4.74e-02 2.24e+01 pdb=" C THR I 186 " -0.082 2.00e-02 2.50e+03 pdb=" O THR I 186 " 0.031 2.00e-02 2.50e+03 pdb=" N GLU I 187 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 186 " -0.024 2.00e-02 2.50e+03 4.74e-02 2.24e+01 pdb=" C THR A 186 " 0.082 2.00e-02 2.50e+03 pdb=" O THR A 186 " -0.031 2.00e-02 2.50e+03 pdb=" N GLU A 187 " -0.028 2.00e-02 2.50e+03 ... (remaining 2387 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 788 2.73 - 3.28: 14664 3.28 - 3.82: 21424 3.82 - 4.36: 26734 4.36 - 4.90: 43361 Nonbonded interactions: 106971 Sorted by model distance: nonbonded pdb=" NH1 ARG I 173 " pdb=" OE1 GLU L 28 " model vdw 2.192 3.120 nonbonded pdb=" NH1 ARG F 173 " pdb=" OE1 GLU I 28 " model vdw 2.193 3.120 nonbonded pdb=" NH1 ARG A 173 " pdb=" OE1 GLU F 28 " model vdw 2.193 3.120 nonbonded pdb=" OE1 GLU A 28 " pdb=" NH1 ARG O 173 " model vdw 2.193 3.120 nonbonded pdb=" NH1 ARG L 173 " pdb=" OE1 GLU O 28 " model vdw 2.193 3.120 ... (remaining 106966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = (chain 'B' and resid 157 through 221) selection = chain 'C' selection = (chain 'D' and resid 157 through 221) selection = chain 'E' selection = (chain 'G' and resid 157 through 221) selection = chain 'H' selection = (chain 'J' and resid 157 through 221) selection = chain 'K' selection = (chain 'M' and resid 157 through 221) selection = chain 'N' } 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.280 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 : 0.004 0.080 13595 Z= 0.287 Angle : 0.824 5.144 18440 Z= 0.497 Chirality : 0.048 0.164 2085 Planarity : 0.009 0.086 2390 Dihedral : 12.071 78.424 5110 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 1685 helix: -0.79 (0.13), residues: 1145 sheet: -2.23 (0.57), residues: 45 loop : 0.82 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP O 117 HIS 0.007 0.003 HIS A 12 PHE 0.024 0.003 PHE A 40 TYR 0.014 0.004 TYR O 169 ARG 0.011 0.002 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 681 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 166 ASP cc_start: 0.7780 (m-30) cc_final: 0.7438 (m-30) REVERT: C 183 ASN cc_start: 0.8263 (m-40) cc_final: 0.8010 (m-40) REVERT: C 213 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7316 (mt-10) REVERT: A 41 SER cc_start: 0.8854 (t) cc_final: 0.8203 (p) REVERT: A 117 TRP cc_start: 0.7838 (m-10) cc_final: 0.7626 (m-90) REVERT: A 183 ASN cc_start: 0.8226 (m-40) cc_final: 0.8026 (m-40) REVERT: D 159 GLU cc_start: 0.8455 (tt0) cc_final: 0.8138 (tt0) REVERT: E 166 ASP cc_start: 0.7808 (m-30) cc_final: 0.7544 (m-30) REVERT: E 168 PHE cc_start: 0.8860 (t80) cc_final: 0.8620 (t80) REVERT: E 213 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7367 (mt-10) REVERT: F 41 SER cc_start: 0.9051 (t) cc_final: 0.8514 (p) REVERT: I 25 LYS cc_start: 0.8235 (mttt) cc_final: 0.8009 (mtmt) REVERT: I 41 SER cc_start: 0.9003 (t) cc_final: 0.8500 (p) REVERT: I 68 MET cc_start: 0.8488 (mtp) cc_final: 0.7987 (mtp) REVERT: I 183 ASN cc_start: 0.8099 (m-40) cc_final: 0.7892 (m-40) REVERT: J 159 GLU cc_start: 0.8496 (tt0) cc_final: 0.8203 (tt0) REVERT: K 182 LYS cc_start: 0.8377 (mttt) cc_final: 0.8091 (mttp) REVERT: K 183 ASN cc_start: 0.8252 (m-40) cc_final: 0.7885 (m-40) REVERT: K 213 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7342 (mt-10) REVERT: L 25 LYS cc_start: 0.8204 (mttt) cc_final: 0.7974 (mtmt) REVERT: L 41 SER cc_start: 0.8927 (t) cc_final: 0.8401 (p) REVERT: L 183 ASN cc_start: 0.8055 (m-40) cc_final: 0.7679 (m-40) REVERT: L 195 ASN cc_start: 0.8189 (p0) cc_final: 0.7778 (p0) REVERT: N 213 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7350 (mt-10) REVERT: O 41 SER cc_start: 0.8938 (t) cc_final: 0.8359 (p) REVERT: O 117 TRP cc_start: 0.7806 (m-10) cc_final: 0.7417 (m-90) REVERT: O 183 ASN cc_start: 0.8214 (m-40) cc_final: 0.7989 (m-40) outliers start: 0 outliers final: 0 residues processed: 681 average time/residue: 0.2979 time to fit residues: 277.8056 Evaluate side-chains 491 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 491 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.3980 chunk 125 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.0170 chunk 96 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN F 50 GLN I 120 HIS J 219 GLN M 179 GLN M 219 GLN O 50 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13595 Z= 0.199 Angle : 0.611 9.655 18440 Z= 0.319 Chirality : 0.041 0.154 2085 Planarity : 0.005 0.039 2390 Dihedral : 5.058 25.145 1820 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Rotamer: Outliers : 2.25 % Allowed : 11.55 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.41 (0.20), residues: 1685 helix: 0.96 (0.14), residues: 1175 sheet: -1.89 (0.64), residues: 45 loop : 1.62 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 184 HIS 0.003 0.000 HIS I 120 PHE 0.013 0.001 PHE F 40 TYR 0.016 0.002 TYR H 164 ARG 0.005 0.000 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 558 time to evaluate : 1.684 Fit side-chains REVERT: B 175 GLU cc_start: 0.8136 (tp30) cc_final: 0.7845 (tp30) REVERT: B 195 ASN cc_start: 0.7228 (t0) cc_final: 0.6564 (t0) REVERT: C 166 ASP cc_start: 0.7622 (m-30) cc_final: 0.7281 (m-30) REVERT: C 168 PHE cc_start: 0.8617 (t80) cc_final: 0.8171 (t80) REVERT: C 200 THR cc_start: 0.8616 (m) cc_final: 0.8382 (p) REVERT: A 192 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7630 (tm-30) REVERT: E 166 ASP cc_start: 0.7863 (m-30) cc_final: 0.7603 (m-30) REVERT: E 171 THR cc_start: 0.8662 (m) cc_final: 0.8437 (p) REVERT: H 213 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7353 (mt-10) REVERT: I 210 THR cc_start: 0.9301 (p) cc_final: 0.9049 (p) REVERT: K 166 ASP cc_start: 0.7660 (m-30) cc_final: 0.7425 (m-30) REVERT: K 167 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7968 (mtp85) REVERT: K 182 LYS cc_start: 0.8497 (mttt) cc_final: 0.8222 (mttp) REVERT: L 192 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7877 (tm-30) REVERT: L 195 ASN cc_start: 0.8254 (p0) cc_final: 0.8000 (p0) REVERT: L 210 THR cc_start: 0.9086 (p) cc_final: 0.8348 (p) REVERT: N 170 LYS cc_start: 0.8505 (ttpp) cc_final: 0.8266 (ttmm) REVERT: N 213 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7392 (mt-10) REVERT: O 195 ASN cc_start: 0.8227 (p0) cc_final: 0.7885 (p0) REVERT: O 210 THR cc_start: 0.9259 (p) cc_final: 0.9059 (p) outliers start: 32 outliers final: 14 residues processed: 579 average time/residue: 0.3048 time to fit residues: 244.7899 Evaluate side-chains 489 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 475 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 149 SER Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 188 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 150 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 133 optimal weight: 0.3980 chunk 148 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN A 50 GLN E 192 GLN M 219 GLN O 176 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13595 Z= 0.190 Angle : 0.577 9.786 18440 Z= 0.301 Chirality : 0.041 0.170 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.677 19.760 1820 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.75 % Allowed : 15.00 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.20), residues: 1685 helix: 1.04 (0.15), residues: 1190 sheet: -1.92 (0.64), residues: 45 loop : 1.61 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 184 HIS 0.003 0.000 HIS I 120 PHE 0.021 0.001 PHE H 168 TYR 0.008 0.001 TYR H 164 ARG 0.006 0.000 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 491 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8140 (tp30) cc_final: 0.7864 (tp30) REVERT: C 166 ASP cc_start: 0.7605 (m-30) cc_final: 0.7258 (m-30) REVERT: C 168 PHE cc_start: 0.8426 (t80) cc_final: 0.8164 (t80) REVERT: C 200 THR cc_start: 0.8585 (m) cc_final: 0.8374 (p) REVERT: E 166 ASP cc_start: 0.7609 (m-30) cc_final: 0.7365 (m-30) REVERT: E 168 PHE cc_start: 0.8766 (t80) cc_final: 0.8469 (t80) REVERT: F 203 LYS cc_start: 0.8507 (mmtm) cc_final: 0.8291 (mmtt) REVERT: H 213 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7426 (mt-10) REVERT: L 192 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7887 (tm-30) REVERT: N 170 LYS cc_start: 0.8495 (ttpp) cc_final: 0.8290 (ttmm) outliers start: 39 outliers final: 22 residues processed: 510 average time/residue: 0.2821 time to fit residues: 198.5455 Evaluate side-chains 470 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 448 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 178 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 0.0070 chunk 16 optimal weight: 0.7980 chunk 71 optimal weight: 0.0770 chunk 100 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 195 ASN D 183 ASN I 195 ASN M 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13595 Z= 0.178 Angle : 0.570 10.087 18440 Z= 0.298 Chirality : 0.041 0.183 2085 Planarity : 0.005 0.040 2390 Dihedral : 4.517 20.244 1820 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.39 % Allowed : 16.62 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.77 (0.20), residues: 1685 helix: 1.14 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : 1.65 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 184 HIS 0.001 0.000 HIS F 12 PHE 0.016 0.001 PHE H 168 TYR 0.008 0.001 TYR E 164 ARG 0.008 0.000 ARG I 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 478 time to evaluate : 1.644 Fit side-chains revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8127 (tp30) cc_final: 0.7846 (tp30) REVERT: C 166 ASP cc_start: 0.7083 (m-30) cc_final: 0.6750 (m-30) REVERT: A 192 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8053 (tm-30) REVERT: E 166 ASP cc_start: 0.7407 (m-30) cc_final: 0.7160 (m-30) REVERT: H 168 PHE cc_start: 0.8297 (t80) cc_final: 0.7828 (t80) REVERT: H 213 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7314 (mt-10) REVERT: I 195 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.8083 (p0) REVERT: L 192 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7929 (tm-30) REVERT: L 197 ASP cc_start: 0.7386 (p0) cc_final: 0.7080 (p0) outliers start: 34 outliers final: 19 residues processed: 492 average time/residue: 0.2876 time to fit residues: 194.4426 Evaluate side-chains 473 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 453 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 195 ASN Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 124 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 110 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.0980 chunk 143 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 ASN H 192 GLN L 195 ASN M 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13595 Z= 0.181 Angle : 0.582 10.005 18440 Z= 0.303 Chirality : 0.041 0.162 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.434 20.801 1820 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.18 % Allowed : 17.25 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.20), residues: 1685 helix: 1.17 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : 1.58 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 184 HIS 0.001 0.000 HIS F 12 PHE 0.018 0.001 PHE N 168 TYR 0.008 0.001 TYR E 164 ARG 0.008 0.000 ARG I 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 472 time to evaluate : 1.523 Fit side-chains revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8112 (tp30) cc_final: 0.7866 (tp30) REVERT: C 166 ASP cc_start: 0.7041 (m-30) cc_final: 0.6742 (m-30) REVERT: C 213 GLU cc_start: 0.7852 (pm20) cc_final: 0.7564 (pm20) REVERT: A 192 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8034 (tm-30) REVERT: E 166 ASP cc_start: 0.7412 (m-30) cc_final: 0.7175 (m-30) REVERT: E 213 GLU cc_start: 0.7982 (pm20) cc_final: 0.7678 (pm20) REVERT: F 192 GLN cc_start: 0.8406 (tm-30) cc_final: 0.7712 (tm-30) REVERT: H 213 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7301 (mt-10) REVERT: K 213 GLU cc_start: 0.8021 (pm20) cc_final: 0.7785 (pm20) REVERT: L 192 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7831 (tm-30) REVERT: L 197 ASP cc_start: 0.7097 (p0) cc_final: 0.6811 (p0) REVERT: M 167 ARG cc_start: 0.8238 (ttp80) cc_final: 0.8029 (ttp-170) REVERT: N 167 ARG cc_start: 0.7885 (mtp180) cc_final: 0.7651 (mtp180) REVERT: N 213 GLU cc_start: 0.7699 (mp0) cc_final: 0.7427 (pm20) REVERT: O 192 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7628 (tm-30) outliers start: 31 outliers final: 16 residues processed: 482 average time/residue: 0.2896 time to fit residues: 197.2113 Evaluate side-chains 458 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 442 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain H residue 215 MET Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 71 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 ASN ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 GLN O 179 GLN O 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13595 Z= 0.273 Angle : 0.623 11.132 18440 Z= 0.323 Chirality : 0.043 0.170 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.531 22.841 1820 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.89 % Allowed : 18.10 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.43 (0.20), residues: 1685 helix: 1.00 (0.15), residues: 1185 sheet: -1.52 (0.63), residues: 45 loop : 1.50 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 184 HIS 0.001 0.000 HIS A 12 PHE 0.030 0.002 PHE H 168 TYR 0.010 0.001 TYR C 164 ARG 0.009 0.001 ARG I 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 453 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8218 (tp30) cc_final: 0.7970 (tp30) REVERT: B 199 LYS cc_start: 0.9017 (ttmm) cc_final: 0.8790 (ttmt) REVERT: C 166 ASP cc_start: 0.7352 (m-30) cc_final: 0.7052 (m-30) REVERT: C 203 LYS cc_start: 0.8429 (mmtt) cc_final: 0.8100 (mmtp) REVERT: C 213 GLU cc_start: 0.8006 (pm20) cc_final: 0.7684 (pm20) REVERT: D 210 THR cc_start: 0.8904 (p) cc_final: 0.8669 (p) REVERT: E 213 GLU cc_start: 0.8142 (pm20) cc_final: 0.7861 (pm20) REVERT: F 192 GLN cc_start: 0.8519 (tm-30) cc_final: 0.7758 (tm-30) REVERT: H 213 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7277 (mt-10) REVERT: K 213 GLU cc_start: 0.7950 (pm20) cc_final: 0.7714 (pm20) REVERT: L 192 GLN cc_start: 0.8412 (tm-30) cc_final: 0.7909 (tm-30) REVERT: L 197 ASP cc_start: 0.7028 (p0) cc_final: 0.6789 (p0) REVERT: O 192 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7686 (tm-30) outliers start: 41 outliers final: 27 residues processed: 469 average time/residue: 0.2679 time to fit residues: 176.4619 Evaluate side-chains 453 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 426 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 185 MET Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 63 GLN Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain M residue 218 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 124 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 96 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 192 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 GLN I 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13595 Z= 0.177 Angle : 0.581 11.216 18440 Z= 0.302 Chirality : 0.041 0.169 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.359 22.262 1820 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.25 % Allowed : 20.00 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.55 (0.20), residues: 1685 helix: 1.09 (0.15), residues: 1175 sheet: -1.17 (0.65), residues: 45 loop : 1.52 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 184 HIS 0.001 0.000 HIS A 12 PHE 0.025 0.001 PHE N 168 TYR 0.008 0.001 TYR C 169 ARG 0.008 0.000 ARG I 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 456 time to evaluate : 1.487 Fit side-chains revert: symmetry clash REVERT: C 166 ASP cc_start: 0.7081 (m-30) cc_final: 0.6790 (m-30) REVERT: C 213 GLU cc_start: 0.7983 (pm20) cc_final: 0.7722 (pm20) REVERT: A 39 MET cc_start: 0.8281 (mtm) cc_final: 0.8024 (mtt) REVERT: D 210 THR cc_start: 0.8818 (p) cc_final: 0.8595 (p) REVERT: E 213 GLU cc_start: 0.8142 (pm20) cc_final: 0.7856 (pm20) REVERT: F 192 GLN cc_start: 0.8522 (tm-30) cc_final: 0.7725 (tm-30) REVERT: H 213 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7271 (mt-10) REVERT: I 192 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8091 (tm-30) REVERT: L 192 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7813 (tm-30) REVERT: M 199 LYS cc_start: 0.8799 (ttmm) cc_final: 0.8547 (ttmt) REVERT: N 213 GLU cc_start: 0.7820 (mp0) cc_final: 0.7583 (mp0) REVERT: O 192 GLN cc_start: 0.8429 (tm-30) cc_final: 0.7525 (tm-30) outliers start: 32 outliers final: 21 residues processed: 469 average time/residue: 0.2703 time to fit residues: 176.6185 Evaluate side-chains 441 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 420 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain O residue 178 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 0.0570 chunk 30 optimal weight: 3.9990 chunk 101 optimal weight: 0.0970 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 63 GLN O 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13595 Z= 0.182 Angle : 0.612 10.456 18440 Z= 0.315 Chirality : 0.041 0.169 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.353 21.845 1820 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.54 % Allowed : 20.70 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.69 (0.20), residues: 1685 helix: 1.17 (0.15), residues: 1170 sheet: -0.95 (0.64), residues: 45 loop : 1.60 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 184 HIS 0.001 0.000 HIS I 62 PHE 0.009 0.001 PHE L 40 TYR 0.007 0.001 TYR N 164 ARG 0.008 0.000 ARG I 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 448 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 166 ASP cc_start: 0.7138 (m-30) cc_final: 0.6851 (m-30) REVERT: A 39 MET cc_start: 0.8269 (mtm) cc_final: 0.8009 (mtt) REVERT: A 192 GLN cc_start: 0.8451 (tm-30) cc_final: 0.7915 (tm-30) REVERT: D 210 THR cc_start: 0.8761 (p) cc_final: 0.8552 (p) REVERT: E 213 GLU cc_start: 0.8151 (pm20) cc_final: 0.7858 (pm20) REVERT: F 192 GLN cc_start: 0.8473 (tm-30) cc_final: 0.7651 (tm-30) REVERT: I 192 GLN cc_start: 0.8382 (tm-30) cc_final: 0.8065 (tm-30) REVERT: K 167 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7679 (mtp-110) REVERT: K 205 LEU cc_start: 0.7435 (pp) cc_final: 0.7180 (pp) REVERT: K 213 GLU cc_start: 0.7810 (pm20) cc_final: 0.7328 (pm20) REVERT: K 215 MET cc_start: 0.8350 (mtp) cc_final: 0.8147 (mtp) REVERT: L 192 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7812 (tm-30) REVERT: O 50 GLN cc_start: 0.7788 (tt0) cc_final: 0.7567 (tt0) outliers start: 36 outliers final: 27 residues processed: 463 average time/residue: 0.2712 time to fit residues: 175.5112 Evaluate side-chains 451 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 424 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain M residue 218 CYS Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 191 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 148 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 45 optimal weight: 0.0670 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13595 Z= 0.233 Angle : 0.643 10.965 18440 Z= 0.332 Chirality : 0.043 0.172 2085 Planarity : 0.005 0.043 2390 Dihedral : 4.432 22.777 1820 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.25 % Allowed : 21.34 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.56 (0.20), residues: 1685 helix: 1.06 (0.15), residues: 1170 sheet: -0.87 (0.64), residues: 45 loop : 1.57 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 184 HIS 0.001 0.000 HIS A 12 PHE 0.009 0.001 PHE H 168 TYR 0.019 0.001 TYR H 164 ARG 0.009 0.001 ARG O 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 429 time to evaluate : 1.603 Fit side-chains revert: symmetry clash REVERT: C 166 ASP cc_start: 0.7151 (m-30) cc_final: 0.6855 (m-30) REVERT: A 39 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7989 (mtt) REVERT: D 210 THR cc_start: 0.8792 (p) cc_final: 0.8582 (p) REVERT: E 213 GLU cc_start: 0.8156 (pm20) cc_final: 0.7859 (pm20) REVERT: F 192 GLN cc_start: 0.8475 (tm-30) cc_final: 0.7619 (tm-30) REVERT: I 182 LYS cc_start: 0.8727 (mttt) cc_final: 0.8457 (mmmm) REVERT: I 192 GLN cc_start: 0.8385 (tm-30) cc_final: 0.8007 (tm-30) REVERT: K 213 GLU cc_start: 0.7855 (pm20) cc_final: 0.7341 (pm20) REVERT: K 215 MET cc_start: 0.8337 (mtp) cc_final: 0.8127 (mtp) REVERT: N 167 ARG cc_start: 0.8095 (mtp180) cc_final: 0.7820 (mtp180) REVERT: O 39 MET cc_start: 0.8114 (mtp) cc_final: 0.7861 (mtm) REVERT: O 192 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8128 (tm-30) outliers start: 32 outliers final: 28 residues processed: 442 average time/residue: 0.2657 time to fit residues: 165.2193 Evaluate side-chains 448 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 419 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 103 optimal weight: 0.0970 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 ASN O 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13595 Z= 0.208 Angle : 0.644 10.673 18440 Z= 0.335 Chirality : 0.043 0.172 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.403 22.388 1820 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.18 % Allowed : 21.90 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.51 (0.20), residues: 1685 helix: 1.03 (0.15), residues: 1170 sheet: -0.72 (0.65), residues: 45 loop : 1.52 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 184 HIS 0.001 0.000 HIS A 12 PHE 0.044 0.001 PHE H 168 TYR 0.010 0.001 TYR F 130 ARG 0.009 0.001 ARG O 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 420 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 166 ASP cc_start: 0.7146 (m-30) cc_final: 0.6848 (m-30) REVERT: A 39 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.8015 (mtt) REVERT: D 210 THR cc_start: 0.8772 (p) cc_final: 0.8565 (p) REVERT: E 213 GLU cc_start: 0.8188 (pm20) cc_final: 0.7932 (pm20) REVERT: F 192 GLN cc_start: 0.8477 (tm-30) cc_final: 0.7608 (tm-30) REVERT: I 192 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7995 (tm-30) REVERT: K 192 GLN cc_start: 0.7220 (tt0) cc_final: 0.6983 (tt0) REVERT: K 215 MET cc_start: 0.8416 (mtp) cc_final: 0.8198 (mtp) REVERT: L 192 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7840 (tm-30) REVERT: O 39 MET cc_start: 0.8096 (mtp) cc_final: 0.7870 (mtm) REVERT: O 192 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8108 (tm-30) outliers start: 31 outliers final: 26 residues processed: 432 average time/residue: 0.2569 time to fit residues: 157.0915 Evaluate side-chains 438 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 411 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 185 MET Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 191 VAL Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 0.0000 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 115 optimal weight: 0.0470 overall best weight: 0.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 63 GLN O 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.136554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101245 restraints weight = 22185.693| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.76 r_work: 0.3213 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13595 Z= 0.181 Angle : 0.626 10.202 18440 Z= 0.326 Chirality : 0.042 0.172 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.344 21.503 1820 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.62 % Allowed : 22.11 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.55 (0.20), residues: 1685 helix: 1.07 (0.15), residues: 1170 sheet: -0.60 (0.66), residues: 45 loop : 1.49 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 184 HIS 0.001 0.000 HIS F 62 PHE 0.042 0.001 PHE H 168 TYR 0.010 0.001 TYR N 164 ARG 0.009 0.001 ARG O 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4327.44 seconds wall clock time: 77 minutes 56.67 seconds (4676.67 seconds total)