Starting phenix.real_space_refine on Wed Jan 22 15:28:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cl4_16712/01_2025/8cl4_16712.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cl4_16712/01_2025/8cl4_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/cci-nas-00/data/ceres_data/8cl4_16712/01_2025/8cl4_16712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cl4_16712/01_2025/8cl4_16712.map" model { file = "/net/cci-nas-00/data/ceres_data/8cl4_16712/01_2025/8cl4_16712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cl4_16712/01_2025/8cl4_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-5571/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: 5.94, per 1000 atoms: 0.45 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: 3.21 Conformation dependent library (CDL) restraints added in 1.8 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: 1.23 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: 3.65 Time building geometry restraints manager: 3.75 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' } 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: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.150 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.440 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 681 time to evaluate : 1.483 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: 0.2988 time to fit residues: 277.8477 Evaluate side-chains 491 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 2.053 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.133682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.101375 restraints weight = 22750.211| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.67 r_work: 0.3271 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 to be fit. rotamer outliers: 32 poor density : 558 time to evaluate : 1.555 Fit side-chains REVERT: B 175 GLU cc_start: 0.8513 (tp30) cc_final: 0.8201 (tp30) REVERT: B 195 ASN cc_start: 0.7501 (t0) cc_final: 0.6997 (t0) REVERT: C 166 ASP cc_start: 0.7850 (m-30) cc_final: 0.7494 (m-30) REVERT: C 168 PHE cc_start: 0.8698 (t80) cc_final: 0.8115 (t80) REVERT: C 200 THR cc_start: 0.8771 (m) cc_final: 0.8456 (p) REVERT: C 213 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 192 GLN cc_start: 0.8604 (tm-30) cc_final: 0.7672 (tm-30) REVERT: E 166 ASP cc_start: 0.8082 (m-30) cc_final: 0.7809 (m-30) REVERT: E 171 THR cc_start: 0.8643 (m) cc_final: 0.8265 (p) REVERT: E 200 THR cc_start: 0.8686 (m) cc_final: 0.8458 (p) REVERT: E 213 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7959 (mt-10) REVERT: F 3 VAL cc_start: 0.8859 (t) cc_final: 0.8637 (m) REVERT: F 66 MET cc_start: 0.8946 (tpt) cc_final: 0.8739 (tpt) REVERT: H 183 ASN cc_start: 0.8113 (m-40) cc_final: 0.7907 (m-40) REVERT: H 200 THR cc_start: 0.8731 (m) cc_final: 0.8501 (p) REVERT: H 213 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7904 (mt-10) REVERT: I 183 ASN cc_start: 0.8558 (m-40) cc_final: 0.8312 (m-40) REVERT: J 167 ARG cc_start: 0.8637 (mtm-85) cc_final: 0.8422 (ttp80) REVERT: J 216 THR cc_start: 0.9289 (m) cc_final: 0.9083 (p) REVERT: K 166 ASP cc_start: 0.7884 (m-30) cc_final: 0.7644 (m-30) REVERT: K 167 ARG cc_start: 0.8270 (mtp85) cc_final: 0.8017 (mtp85) REVERT: K 171 THR cc_start: 0.8619 (m) cc_final: 0.8260 (p) REVERT: K 182 LYS cc_start: 0.8381 (mttt) cc_final: 0.8080 (mttp) REVERT: K 200 THR cc_start: 0.8793 (m) cc_final: 0.8550 (p) REVERT: K 213 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8105 (mt-10) REVERT: L 183 ASN cc_start: 0.8495 (m-40) cc_final: 0.8255 (m-40) REVERT: L 192 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8002 (tm-30) REVERT: L 195 ASN cc_start: 0.8184 (p0) cc_final: 0.7920 (p0) REVERT: L 210 THR cc_start: 0.8935 (p) cc_final: 0.8442 (p) REVERT: L 213 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8213 (mp0) REVERT: M 179 GLN cc_start: 0.7000 (mm-40) cc_final: 0.6741 (tt0) REVERT: M 198 CYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8138 (m) REVERT: N 168 PHE cc_start: 0.8841 (t80) cc_final: 0.8629 (t80) REVERT: N 170 LYS cc_start: 0.8533 (ttpp) cc_final: 0.8259 (ttmm) REVERT: N 200 THR cc_start: 0.8774 (m) cc_final: 0.8550 (p) REVERT: N 213 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7913 (mt-10) REVERT: O 195 ASN cc_start: 0.8244 (p0) cc_final: 0.7860 (p0) outliers start: 32 outliers final: 14 residues processed: 579 average time/residue: 0.3024 time to fit residues: 240.0909 Evaluate side-chains 490 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 475 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 M residue 198 CYS 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 156 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN A 50 GLN E 192 GLN I 120 HIS M 219 GLN O 176 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.130371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.097263 restraints weight = 23248.918| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.65 r_work: 0.3200 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13595 Z= 0.307 Angle : 0.621 8.938 18440 Z= 0.324 Chirality : 0.044 0.177 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.851 21.567 1820 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.75 % Allowed : 15.49 % Favored : 81.76 % 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: 1.43 (0.19), residues: 1685 helix: 1.03 (0.14), residues: 1170 sheet: -1.89 (0.64), residues: 45 loop : 1.47 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 184 HIS 0.003 0.001 HIS I 120 PHE 0.021 0.002 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 533 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 494 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8603 (tp30) cc_final: 0.8328 (tp30) REVERT: C 166 ASP cc_start: 0.7869 (m-30) cc_final: 0.7556 (m-30) REVERT: C 168 PHE cc_start: 0.8555 (t80) cc_final: 0.8295 (t80) REVERT: C 200 THR cc_start: 0.8723 (m) cc_final: 0.8442 (p) REVERT: A 192 GLN cc_start: 0.8716 (tm-30) cc_final: 0.7953 (tm-30) REVERT: A 215 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7894 (mtp) REVERT: E 200 THR cc_start: 0.8678 (m) cc_final: 0.8462 (p) REVERT: E 213 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8086 (mp0) REVERT: F 3 VAL cc_start: 0.8848 (t) cc_final: 0.8610 (m) REVERT: F 66 MET cc_start: 0.9009 (tpt) cc_final: 0.8733 (tpt) REVERT: F 82 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7888 (ttp80) REVERT: F 130 TYR cc_start: 0.9124 (t80) cc_final: 0.8824 (t80) REVERT: F 215 MET cc_start: 0.8488 (mtp) cc_final: 0.8111 (mtp) REVERT: H 200 THR cc_start: 0.8761 (m) cc_final: 0.8553 (p) REVERT: H 213 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7952 (mt-10) REVERT: I 183 ASN cc_start: 0.8563 (m-40) cc_final: 0.8285 (m-40) REVERT: K 200 THR cc_start: 0.8798 (m) cc_final: 0.8554 (p) REVERT: K 213 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8028 (mt-10) REVERT: L 183 ASN cc_start: 0.8434 (m-40) cc_final: 0.8166 (m-40) REVERT: L 192 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8078 (tm-30) REVERT: N 170 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8327 (ttmm) REVERT: N 200 THR cc_start: 0.8791 (m) cc_final: 0.8571 (p) REVERT: N 213 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7940 (mt-10) outliers start: 39 outliers final: 27 residues processed: 514 average time/residue: 0.2959 time to fit residues: 209.3029 Evaluate side-chains 479 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 451 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 110 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 215 MET 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 197 ASP Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 189 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 22 optimal weight: 0.0670 chunk 15 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 0.0670 chunk 134 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN A 183 ASN A 195 ASN G 193 ASN H 192 GLN I 195 ASN J 155 GLN M 219 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.135392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.102923 restraints weight = 22620.572| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.66 r_work: 0.3303 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13595 Z= 0.177 Angle : 0.566 8.585 18440 Z= 0.296 Chirality : 0.041 0.168 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.530 20.294 1820 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.17 % Allowed : 16.13 % Favored : 80.70 % 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: 1.60 (0.20), residues: 1685 helix: 1.16 (0.15), residues: 1175 sheet: -1.77 (0.66), residues: 45 loop : 1.50 (0.28), residues: 465 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 0.014 0.001 PHE N 168 TYR 0.008 0.001 TYR E 164 ARG 0.006 0.000 ARG L 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 518 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 473 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8520 (tp30) cc_final: 0.8257 (tp30) REVERT: C 164 TYR cc_start: 0.7582 (t80) cc_final: 0.7358 (t80) REVERT: C 166 ASP cc_start: 0.7823 (m-30) cc_final: 0.7498 (m-30) REVERT: C 168 PHE cc_start: 0.8287 (t80) cc_final: 0.8050 (t80) REVERT: C 200 THR cc_start: 0.8735 (m) cc_final: 0.8466 (p) REVERT: C 213 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8090 (mp0) REVERT: A 167 ARG cc_start: 0.8585 (mtm-85) cc_final: 0.8367 (mtm-85) REVERT: A 176 GLN cc_start: 0.8246 (tt0) cc_final: 0.7878 (tp40) REVERT: A 178 SER cc_start: 0.8474 (OUTLIER) cc_final: 0.8073 (p) REVERT: A 192 GLN cc_start: 0.8714 (tm-30) cc_final: 0.7984 (tm-30) REVERT: D 157 PRO cc_start: 0.8567 (Cg_endo) cc_final: 0.8242 (Cg_exo) REVERT: E 168 PHE cc_start: 0.8773 (t80) cc_final: 0.8517 (t80) REVERT: E 200 THR cc_start: 0.8602 (m) cc_final: 0.8390 (p) REVERT: E 213 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8039 (mp0) REVERT: F 3 VAL cc_start: 0.8852 (t) cc_final: 0.8613 (m) REVERT: F 66 MET cc_start: 0.8924 (tpt) cc_final: 0.8680 (tpt) REVERT: H 168 PHE cc_start: 0.8560 (t80) cc_final: 0.8001 (t80) REVERT: H 213 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7913 (mt-10) REVERT: I 145 TYR cc_start: 0.8978 (m-80) cc_final: 0.8777 (m-80) REVERT: I 183 ASN cc_start: 0.8577 (m-40) cc_final: 0.8328 (m-40) REVERT: J 167 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8202 (ttp-170) REVERT: K 200 THR cc_start: 0.8682 (m) cc_final: 0.8456 (p) REVERT: K 213 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8072 (mt-10) REVERT: L 197 ASP cc_start: 0.8288 (p0) cc_final: 0.7947 (p0) REVERT: N 168 PHE cc_start: 0.8263 (t80) cc_final: 0.8057 (t80) REVERT: N 170 LYS cc_start: 0.8515 (ttpp) cc_final: 0.8284 (ttmm) REVERT: N 213 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7984 (mt-10) REVERT: O 195 ASN cc_start: 0.8369 (p0) cc_final: 0.7960 (p0) REVERT: O 197 ASP cc_start: 0.8312 (p0) cc_final: 0.8088 (p0) outliers start: 45 outliers final: 20 residues processed: 493 average time/residue: 0.2783 time to fit residues: 191.3150 Evaluate side-chains 471 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 450 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain F residue 2 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 210 THR 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 71 GLU Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 2 optimal weight: 0.0070 chunk 141 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 195 ASN M 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.134462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.101606 restraints weight = 22908.103| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.72 r_work: 0.3289 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4466 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= 0.208 Angle : 0.557 8.479 18440 Z= 0.293 Chirality : 0.041 0.160 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.437 22.129 1820 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.03 % Allowed : 16.27 % Favored : 80.70 % 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: 1.65 (0.20), residues: 1685 helix: 1.21 (0.15), residues: 1175 sheet: -1.63 (0.67), residues: 45 loop : 1.48 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 184 HIS 0.001 0.000 HIS F 12 PHE 0.020 0.001 PHE N 168 TYR 0.008 0.001 TYR H 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 501 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 458 time to evaluate : 1.500 Fit side-chains REVERT: B 175 GLU cc_start: 0.8526 (tp30) cc_final: 0.8279 (tp30) REVERT: C 166 ASP cc_start: 0.7538 (m-30) cc_final: 0.7249 (m-30) REVERT: C 213 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8086 (mp0) REVERT: A 192 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8180 (tm-30) REVERT: E 213 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8059 (mp0) REVERT: F 3 VAL cc_start: 0.8852 (t) cc_final: 0.8620 (m) REVERT: F 66 MET cc_start: 0.8941 (tpt) cc_final: 0.8733 (tpt) REVERT: H 213 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7882 (mt-10) REVERT: I 183 ASN cc_start: 0.8541 (m-40) cc_final: 0.8284 (m-40) REVERT: K 213 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8072 (mt-10) REVERT: L 192 GLN cc_start: 0.8540 (tm-30) cc_final: 0.7999 (tm-30) REVERT: L 197 ASP cc_start: 0.8116 (p0) cc_final: 0.7911 (p0) REVERT: M 167 ARG cc_start: 0.8657 (ttp80) cc_final: 0.8421 (ttp-170) REVERT: N 168 PHE cc_start: 0.8202 (t80) cc_final: 0.7753 (t80) REVERT: N 213 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8002 (mt-10) outliers start: 43 outliers final: 26 residues processed: 477 average time/residue: 0.2644 time to fit residues: 177.2058 Evaluate side-chains 459 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 433 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 2 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 I residue 210 THR 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 71 GLU Chi-restraints excluded: chain L residue 149 SER Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 101 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 115 optimal weight: 0.0040 chunk 91 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN M 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.134879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.101901 restraints weight = 22987.170| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.77 r_work: 0.3286 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4703 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= 0.189 Angle : 0.566 10.442 18440 Z= 0.295 Chirality : 0.041 0.163 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.361 24.088 1820 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.46 % Allowed : 18.73 % Favored : 78.80 % 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: 1.25 (0.15), residues: 1170 sheet: -1.35 (0.67), residues: 45 loop : 1.41 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 184 HIS 0.001 0.000 HIS A 12 PHE 0.017 0.001 PHE H 168 TYR 0.006 0.001 TYR H 164 ARG 0.008 0.000 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 486 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 451 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 157 PRO cc_start: 0.8472 (Cg_endo) cc_final: 0.8247 (Cg_exo) REVERT: B 175 GLU cc_start: 0.8540 (tp30) cc_final: 0.8316 (tp30) REVERT: C 166 ASP cc_start: 0.7302 (m-30) cc_final: 0.6983 (m-30) REVERT: C 213 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8058 (mp0) REVERT: E 213 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8038 (mp0) REVERT: H 168 PHE cc_start: 0.8203 (t80) cc_final: 0.7964 (t80) REVERT: I 183 ASN cc_start: 0.8505 (m-40) cc_final: 0.8276 (m-40) REVERT: J 167 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8368 (ttp-170) REVERT: K 213 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8031 (mt-10) REVERT: L 152 ASP cc_start: 0.8848 (m-30) cc_final: 0.8641 (m-30) REVERT: L 192 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8087 (tm-30) REVERT: L 197 ASP cc_start: 0.7928 (p0) cc_final: 0.7616 (p0) REVERT: M 167 ARG cc_start: 0.8686 (ttp80) cc_final: 0.8481 (ttp80) REVERT: N 213 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7949 (mt-10) REVERT: O 192 GLN cc_start: 0.8558 (tm-30) cc_final: 0.7733 (tm-30) outliers start: 35 outliers final: 20 residues processed: 465 average time/residue: 0.2792 time to fit residues: 181.1961 Evaluate side-chains 448 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 428 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain E residue 181 VAL 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 135 ILE Chi-restraints excluded: chain G residue 195 ASN 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 I residue 210 THR Chi-restraints excluded: chain J residue 218 CYS 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 178 SER Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 176 GLN Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 19 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN I 195 ASN ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 GLN O 50 GLN O 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.130056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096728 restraints weight = 23088.721| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.71 r_work: 0.3109 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13595 Z= 0.399 Angle : 0.667 10.933 18440 Z= 0.346 Chirality : 0.046 0.169 2085 Planarity : 0.005 0.043 2390 Dihedral : 4.616 27.065 1820 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.17 % Allowed : 19.93 % Favored : 76.90 % 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: 1.25 (0.20), residues: 1685 helix: 0.90 (0.15), residues: 1175 sheet: -1.38 (0.65), residues: 45 loop : 1.31 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 184 HIS 0.002 0.001 HIS L 62 PHE 0.025 0.002 PHE H 168 TYR 0.011 0.001 TYR H 164 ARG 0.008 0.001 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 483 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 438 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8667 (tp30) cc_final: 0.8370 (tp30) REVERT: C 166 ASP cc_start: 0.7918 (m-30) cc_final: 0.7628 (m-30) REVERT: A 68 MET cc_start: 0.8736 (mtm) cc_final: 0.8514 (mtm) REVERT: E 213 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8076 (mp0) REVERT: F 45 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7648 (mm-30) REVERT: F 111 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8501 (tt) REVERT: F 192 GLN cc_start: 0.8788 (tm-30) cc_final: 0.7799 (tm-30) REVERT: H 175 GLU cc_start: 0.3990 (mt-10) cc_final: 0.3784 (mt-10) REVERT: H 213 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8187 (mp0) REVERT: I 167 ARG cc_start: 0.8595 (mtm-85) cc_final: 0.8367 (mtm-85) REVERT: I 183 ASN cc_start: 0.8530 (m-40) cc_final: 0.8291 (m-40) REVERT: J 203 LYS cc_start: 0.8429 (mtpp) cc_final: 0.8220 (mtmt) REVERT: L 192 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8162 (tm-30) REVERT: L 197 ASP cc_start: 0.8020 (p0) cc_final: 0.7756 (p0) REVERT: L 215 MET cc_start: 0.8530 (mtp) cc_final: 0.8222 (mtt) REVERT: M 203 LYS cc_start: 0.8470 (mtpp) cc_final: 0.8206 (mtmt) REVERT: N 213 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8055 (mp0) REVERT: O 192 GLN cc_start: 0.8781 (tm-30) cc_final: 0.7910 (tm-30) outliers start: 45 outliers final: 32 residues processed: 456 average time/residue: 0.2786 time to fit residues: 177.9772 Evaluate side-chains 450 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 417 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 214 MET 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 18 ARG Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 197 ASP 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 210 THR 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 71 GLU Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 111 LEU Chi-restraints excluded: chain O residue 176 GLN Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.0328 > 50: distance: 23 - 28: 7.548 distance: 28 - 29: 11.288 distance: 29 - 30: 25.347 distance: 29 - 32: 10.875 distance: 30 - 31: 23.225 distance: 30 - 37: 10.354 distance: 32 - 33: 13.676 distance: 33 - 34: 8.622 distance: 34 - 35: 13.254 distance: 35 - 36: 8.884 distance: 37 - 38: 31.369 distance: 38 - 39: 31.534 distance: 38 - 41: 37.229 distance: 39 - 40: 14.372 distance: 39 - 42: 14.344 distance: 42 - 43: 7.943 distance: 43 - 46: 11.615 distance: 44 - 53: 7.107 distance: 46 - 47: 7.518 distance: 47 - 48: 9.676 distance: 47 - 49: 5.368 distance: 48 - 50: 9.205 distance: 49 - 51: 4.755 distance: 50 - 52: 5.069 distance: 51 - 52: 4.150 distance: 53 - 54: 6.966 distance: 54 - 55: 14.856 distance: 54 - 57: 9.082 distance: 55 - 56: 18.330 distance: 55 - 59: 12.735 distance: 57 - 58: 17.827 distance: 59 - 60: 8.983 distance: 59 - 65: 14.165 distance: 60 - 61: 8.618 distance: 60 - 63: 5.880 distance: 61 - 66: 3.671 distance: 63 - 64: 12.755 distance: 64 - 65: 8.962 distance: 66 - 67: 15.517 distance: 67 - 68: 15.062 distance: 67 - 70: 21.607 distance: 68 - 69: 12.901 distance: 68 - 75: 6.318 distance: 69 - 97: 12.413 distance: 70 - 71: 13.791 distance: 71 - 72: 9.444 distance: 72 - 73: 8.104 distance: 72 - 74: 9.976 distance: 75 - 76: 6.998 distance: 76 - 77: 9.781 distance: 76 - 79: 3.401 distance: 77 - 78: 5.102 distance: 77 - 82: 8.727 distance: 78 - 105: 7.870 distance: 79 - 80: 12.393 distance: 79 - 81: 6.363 distance: 82 - 83: 5.462 distance: 83 - 84: 4.980 distance: 84 - 85: 7.784 distance: 84 - 90: 3.058 distance: 85 - 112: 5.681 distance: 86 - 87: 5.813 distance: 86 - 88: 7.447 distance: 87 - 89: 5.221 distance: 90 - 91: 4.995 distance: 90 - 96: 8.931 distance: 91 - 92: 4.807 distance: 92 - 93: 3.952 distance: 92 - 97: 5.763 distance: 93 - 118: 3.221 distance: 94 - 95: 5.747 distance: 95 - 96: 4.414 distance: 97 - 98: 3.422 distance: 98 - 99: 5.186 distance: 98 - 101: 4.514 distance: 100 - 123: 5.822 distance: 101 - 102: 9.231 distance: 102 - 103: 5.426 distance: 103 - 104: 4.823