Starting phenix.real_space_refine on Sun Jun 15 02:53:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8izy_35877/06_2025/8izy_35877_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8izy_35877/06_2025/8izy_35877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8izy_35877/06_2025/8izy_35877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8izy_35877/06_2025/8izy_35877.map" model { file = "/net/cci-nas-00/data/ceres_data/8izy_35877/06_2025/8izy_35877_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8izy_35877/06_2025/8izy_35877_neut_trim.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 36 5.16 5 C 5616 2.51 5 N 1400 2.21 5 O 1356 1.98 5 F 8 1.80 5 H 8360 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16776 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4144 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 bond proxies already assigned to first conformer: 4167 Chain: "B" Number of atoms: 4144 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 bond proxies already assigned to first conformer: 4167 Chain: "C" Number of atoms: 4144 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 bond proxies already assigned to first conformer: 4167 Chain: "D" Number of atoms: 4144 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 bond proxies already assigned to first conformer: 4167 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {'9MF': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'9MF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'9MF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'9MF': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AVAL A 132 " occ=0.50 ... (30 atoms not shown) pdb="HG23BVAL A 132 " occ=0.50 residue: pdb=" N AVAL B 132 " occ=0.50 ... (30 atoms not shown) pdb="HG23BVAL B 132 " occ=0.50 residue: pdb=" N AVAL C 132 " occ=0.50 ... (30 atoms not shown) pdb="HG23BVAL C 132 " occ=0.50 residue: pdb=" N AVAL D 132 " occ=0.50 ... (30 atoms not shown) pdb="HG23BVAL D 132 " occ=0.50 Time building chain proxies: 14.52, per 1000 atoms: 0.87 Number of scatterers: 16776 At special positions: 0 Unit cell: (128.778, 128.778, 77.064, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 F 8 9.00 O 1356 8.00 N 1400 7.00 C 5616 6.00 H 8360 1.00 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: 4.70 Conformation dependent library (CDL) restraints added in 2.3 seconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1864 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 86.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 71 through 86 Processing helix chain 'A' and resid 92 through 114 removed outlier: 3.783A pdb=" N HIS A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 4.240A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.663A pdb=" N ALA A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 254 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 330 removed outlier: 3.916A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 92 through 114 removed outlier: 3.779A pdb=" N HIS B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 4.170A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 155 through 164 removed outlier: 3.666A pdb=" N ALA B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 184 Processing helix chain 'B' and resid 196 through 211 Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 254 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 287 through 330 removed outlier: 3.920A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 92 through 114 removed outlier: 3.783A pdb=" N HIS C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 removed outlier: 4.238A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 155 through 164 removed outlier: 3.667A pdb=" N ALA C 164 " --> pdb=" O ARG C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 184 Processing helix chain 'C' and resid 196 through 211 Processing helix chain 'C' and resid 215 through 228 Processing helix chain 'C' and resid 228 through 254 Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 287 through 330 removed outlier: 3.922A pdb=" N THR C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Proline residue: C 308 - end of helix Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 92 through 114 removed outlier: 3.779A pdb=" N HIS D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 removed outlier: 4.237A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 155 through 164 removed outlier: 3.733A pdb=" N ALA D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 184 Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 254 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 287 through 330 removed outlier: 3.920A pdb=" N THR D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix 668 hydrogen bonds defined for protein. 2008 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: 5.90 Time building geometry restraints manager: 5.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8336 1.03 - 1.23: 40 1.23 - 1.42: 3860 1.42 - 1.61: 4728 1.61 - 1.81: 48 Bond restraints: 17012 Sorted by residual: bond pdb=" C09 9MF D 801 " pdb=" N08 9MF D 801 " ideal model delta sigma weight residual 1.352 1.452 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C09 9MF C 801 " pdb=" N08 9MF C 801 " ideal model delta sigma weight residual 1.352 1.451 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C09 9MF A 803 " pdb=" N08 9MF A 803 " ideal model delta sigma weight residual 1.352 1.451 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C09 9MF B 801 " pdb=" N08 9MF B 801 " ideal model delta sigma weight residual 1.352 1.451 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C09 9MF A 801 " pdb=" N08 9MF A 801 " ideal model delta sigma weight residual 1.352 1.451 -0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 17007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 30302 2.02 - 4.04: 177 4.04 - 6.06: 29 6.06 - 8.08: 8 8.08 - 10.10: 8 Bond angle restraints: 30524 Sorted by residual: angle pdb=" N08 9MF A 801 " pdb=" C09 9MF A 801 " pdb=" O11 9MF A 801 " ideal model delta sigma weight residual 110.34 120.44 -10.10 3.00e+00 1.11e-01 1.13e+01 angle pdb=" N ARG B 213 " pdb=" CA ARG B 213 " pdb=" CB ARG B 213 " ideal model delta sigma weight residual 114.17 110.33 3.84 1.14e+00 7.69e-01 1.13e+01 angle pdb=" N08 9MF C 802 " pdb=" C09 9MF C 802 " pdb=" O11 9MF C 802 " ideal model delta sigma weight residual 110.34 120.41 -10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" N08 9MF B 802 " pdb=" C09 9MF B 802 " pdb=" O11 9MF B 802 " ideal model delta sigma weight residual 110.34 120.37 -10.03 3.00e+00 1.11e-01 1.12e+01 angle pdb=" N ARG A 213 " pdb=" CA ARG A 213 " pdb=" CB ARG A 213 " ideal model delta sigma weight residual 114.17 110.36 3.81 1.14e+00 7.69e-01 1.11e+01 ... (remaining 30519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6885 17.96 - 35.91: 671 35.91 - 53.87: 250 53.87 - 71.83: 82 71.83 - 89.79: 12 Dihedral angle restraints: 7900 sinusoidal: 4120 harmonic: 3780 Sorted by residual: dihedral pdb=" CA ARG C 207 " pdb=" CB ARG C 207 " pdb=" CG ARG C 207 " pdb=" CD ARG C 207 " ideal model delta sinusoidal sigma weight residual 180.00 121.23 58.77 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ARG B 207 " pdb=" CB ARG B 207 " pdb=" CG ARG B 207 " pdb=" CD ARG B 207 " ideal model delta sinusoidal sigma weight residual 180.00 121.27 58.73 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ARG C 89 " pdb=" CB ARG C 89 " pdb=" CG ARG C 89 " pdb=" CD ARG C 89 " ideal model delta sinusoidal sigma weight residual 180.00 122.13 57.87 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 7897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 816 0.025 - 0.049: 258 0.049 - 0.074: 116 0.074 - 0.099: 52 0.099 - 0.123: 18 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CB THR A 298 " pdb=" CA THR A 298 " pdb=" OG1 THR A 298 " pdb=" CG2 THR A 298 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CB THR D 298 " pdb=" CA THR D 298 " pdb=" OG1 THR D 298 " pdb=" CG2 THR D 298 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CB THR C 298 " pdb=" CA THR C 298 " pdb=" OG1 THR C 298 " pdb=" CG2 THR C 298 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.57e-01 ... (remaining 1257 not shown) Planarity restraints: 2408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 214 " -0.136 9.50e-02 1.11e+02 4.55e-02 2.47e+00 pdb=" NE ARG C 214 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG C 214 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 214 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 214 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 214 " 0.005 2.00e-02 2.50e+03 pdb="HH12 ARG C 214 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C 214 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 214 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 214 " -0.135 9.50e-02 1.11e+02 4.51e-02 2.46e+00 pdb=" NE ARG D 214 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG D 214 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 214 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 214 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG D 214 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG D 214 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 214 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 214 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 214 " -0.135 9.50e-02 1.11e+02 4.51e-02 2.43e+00 pdb=" NE ARG B 214 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 214 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 214 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 214 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 214 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG B 214 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 214 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 214 " -0.000 2.00e-02 2.50e+03 ... (remaining 2405 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 2262 2.26 - 2.84: 36660 2.84 - 3.43: 43923 3.43 - 4.01: 56962 4.01 - 4.60: 87682 Nonbonded interactions: 227489 Sorted by model distance: nonbonded pdb=" OE2 GLU D 254 " pdb=" H GLN D 286 " model vdw 1.671 2.450 nonbonded pdb=" OE2 GLU B 254 " pdb=" H GLN B 286 " model vdw 1.675 2.450 nonbonded pdb=" OE2 GLU A 254 " pdb=" H GLN A 286 " model vdw 1.676 2.450 nonbonded pdb=" OE2 GLU C 254 " pdb=" H GLN C 286 " model vdw 1.677 2.450 nonbonded pdb=" OD2 ASP C 212 " pdb=" HG1 THR C 217 " model vdw 1.718 2.450 ... (remaining 227484 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' and (resid 70 through 131 or resid 133 through 330 or resid 801)) selection = (chain 'B' and (resid 70 through 131 or resid 133 through 330 or resid 801)) selection = (chain 'C' and (resid 70 through 131 or resid 133 through 330 or resid 801)) selection = (chain 'D' and (resid 70 through 131 or resid 133 through 330 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.260 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 45.830 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 8652 Z= 0.285 Angle : 0.648 10.101 11720 Z= 0.310 Chirality : 0.034 0.123 1260 Planarity : 0.004 0.059 1420 Dihedral : 17.996 89.785 3020 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.71 % Allowed : 28.32 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.26), residues: 1000 helix: 2.30 (0.17), residues: 844 sheet: None (None), residues: 0 loop : -1.45 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 269 HIS 0.002 0.001 HIS C 324 PHE 0.009 0.001 PHE D 100 TYR 0.008 0.001 TYR D 74 ARG 0.008 0.000 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.10332 ( 668) hydrogen bonds : angle 4.86329 ( 2008) covalent geometry : bond 0.00580 ( 8652) covalent geometry : angle 0.64798 (11720) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.6919 (tptt) cc_final: 0.6700 (tptp) REVERT: A 214 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.7000 (mtp85) REVERT: A 324 HIS cc_start: 0.7696 (t70) cc_final: 0.7245 (t-90) REVERT: A 327 LYS cc_start: 0.7343 (tppt) cc_final: 0.6662 (tttp) REVERT: B 76 LYS cc_start: 0.6896 (tptt) cc_final: 0.6673 (tptp) REVERT: B 214 ARG cc_start: 0.7240 (ttm-80) cc_final: 0.7004 (mtp85) REVERT: B 324 HIS cc_start: 0.7650 (t70) cc_final: 0.7201 (t-90) REVERT: B 327 LYS cc_start: 0.7339 (tppt) cc_final: 0.6657 (tttp) REVERT: C 76 LYS cc_start: 0.6930 (tptt) cc_final: 0.6709 (tptp) REVERT: C 214 ARG cc_start: 0.7387 (ttm-80) cc_final: 0.7139 (mtp85) REVERT: C 324 HIS cc_start: 0.7711 (t70) cc_final: 0.7265 (t-90) REVERT: C 327 LYS cc_start: 0.7341 (tppt) cc_final: 0.6658 (tttp) REVERT: D 162 LYS cc_start: 0.6336 (pptt) cc_final: 0.5643 (mtmm) REVERT: D 214 ARG cc_start: 0.7393 (ttm-80) cc_final: 0.7143 (mtp85) REVERT: D 324 HIS cc_start: 0.7677 (t70) cc_final: 0.7237 (t-90) outliers start: 6 outliers final: 4 residues processed: 153 average time/residue: 2.3690 time to fit residues: 387.7696 Evaluate side-chains 136 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 135 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 0.0010 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.176711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121369 restraints weight = 67833.459| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.45 r_work: 0.3421 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8652 Z= 0.137 Angle : 0.510 5.924 11720 Z= 0.272 Chirality : 0.034 0.123 1260 Planarity : 0.004 0.044 1420 Dihedral : 9.737 78.319 1208 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.61 % Allowed : 28.32 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.26), residues: 1000 helix: 2.36 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.41 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 269 HIS 0.003 0.001 HIS D 228 PHE 0.012 0.001 PHE A 297 TYR 0.008 0.001 TYR A 82 ARG 0.006 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.05294 ( 668) hydrogen bonds : angle 4.54753 ( 2008) covalent geometry : bond 0.00288 ( 8652) covalent geometry : angle 0.50996 (11720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 1.274 Fit side-chains REVERT: A 76 LYS cc_start: 0.6912 (tptt) cc_final: 0.6699 (tptp) REVERT: A 174 MET cc_start: 0.6932 (ptp) cc_final: 0.6561 (ptm) REVERT: A 214 ARG cc_start: 0.7520 (ttm-80) cc_final: 0.7280 (mtp85) REVERT: A 296 THR cc_start: 0.7947 (OUTLIER) cc_final: 0.7694 (p) REVERT: A 324 HIS cc_start: 0.7846 (t70) cc_final: 0.7416 (t-90) REVERT: B 76 LYS cc_start: 0.6910 (tptt) cc_final: 0.6693 (tptp) REVERT: B 174 MET cc_start: 0.6962 (ptp) cc_final: 0.6583 (ptm) REVERT: B 214 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7277 (mtp85) REVERT: B 296 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7660 (p) REVERT: B 324 HIS cc_start: 0.7850 (t70) cc_final: 0.7420 (t-90) REVERT: C 76 LYS cc_start: 0.6922 (tptt) cc_final: 0.6705 (tptp) REVERT: C 174 MET cc_start: 0.6939 (ptp) cc_final: 0.6566 (ptm) REVERT: C 214 ARG cc_start: 0.7545 (ttm-80) cc_final: 0.7291 (mtp85) REVERT: C 296 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7666 (p) REVERT: C 324 HIS cc_start: 0.7863 (t70) cc_final: 0.7429 (t-90) REVERT: D 162 LYS cc_start: 0.6433 (pptt) cc_final: 0.5902 (mtmm) REVERT: D 174 MET cc_start: 0.6900 (ptp) cc_final: 0.6529 (ptm) REVERT: D 214 ARG cc_start: 0.7526 (ttm-80) cc_final: 0.7267 (mtp85) REVERT: D 296 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7657 (p) REVERT: D 324 HIS cc_start: 0.7854 (t70) cc_final: 0.7422 (t-90) outliers start: 22 outliers final: 7 residues processed: 162 average time/residue: 2.1450 time to fit residues: 374.3766 Evaluate side-chains 144 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.176327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.125087 restraints weight = 70832.513| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.13 r_work: 0.3397 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8652 Z= 0.149 Angle : 0.515 4.812 11720 Z= 0.275 Chirality : 0.034 0.126 1260 Planarity : 0.004 0.034 1420 Dihedral : 9.611 76.235 1208 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.01 % Allowed : 28.91 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.26), residues: 1000 helix: 2.30 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.52 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 269 HIS 0.002 0.001 HIS B 228 PHE 0.013 0.001 PHE A 297 TYR 0.009 0.001 TYR D 74 ARG 0.004 0.000 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.05329 ( 668) hydrogen bonds : angle 4.52084 ( 2008) covalent geometry : bond 0.00320 ( 8652) covalent geometry : angle 0.51456 (11720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.382 Fit side-chains REVERT: A 174 MET cc_start: 0.6814 (ptp) cc_final: 0.6454 (ptm) REVERT: A 214 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.7301 (mtp85) REVERT: A 324 HIS cc_start: 0.7797 (t70) cc_final: 0.7377 (t-90) REVERT: B 174 MET cc_start: 0.6889 (ptp) cc_final: 0.6514 (ptm) REVERT: B 214 ARG cc_start: 0.7526 (ttm-80) cc_final: 0.7300 (mtp85) REVERT: B 324 HIS cc_start: 0.7799 (t70) cc_final: 0.7381 (t-90) REVERT: C 174 MET cc_start: 0.6881 (ptp) cc_final: 0.6511 (ptm) REVERT: C 214 ARG cc_start: 0.7540 (ttm-80) cc_final: 0.7308 (mtp85) REVERT: C 324 HIS cc_start: 0.7813 (t70) cc_final: 0.7391 (t-90) REVERT: D 162 LYS cc_start: 0.6471 (pptt) cc_final: 0.5881 (mtmm) REVERT: D 174 MET cc_start: 0.6840 (ptp) cc_final: 0.6449 (ptm) REVERT: D 214 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7308 (mtp85) REVERT: D 324 HIS cc_start: 0.7801 (t70) cc_final: 0.7379 (t-90) outliers start: 17 outliers final: 8 residues processed: 150 average time/residue: 2.3208 time to fit residues: 373.7106 Evaluate side-chains 142 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.175774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.122707 restraints weight = 71846.482| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.97 r_work: 0.3394 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8652 Z= 0.160 Angle : 0.510 4.660 11720 Z= 0.275 Chirality : 0.035 0.128 1260 Planarity : 0.004 0.030 1420 Dihedral : 9.491 75.305 1208 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.32 % Allowed : 27.61 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.27), residues: 1000 helix: 2.27 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.59 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 269 HIS 0.003 0.001 HIS D 228 PHE 0.013 0.001 PHE A 297 TYR 0.010 0.001 TYR D 74 ARG 0.003 0.000 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.05422 ( 668) hydrogen bonds : angle 4.50795 ( 2008) covalent geometry : bond 0.00351 ( 8652) covalent geometry : angle 0.51022 (11720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7333 (ppt170) REVERT: A 174 MET cc_start: 0.6830 (ptp) cc_final: 0.6465 (ptm) REVERT: A 214 ARG cc_start: 0.7513 (ttm-80) cc_final: 0.7291 (mtp85) REVERT: A 324 HIS cc_start: 0.7822 (t70) cc_final: 0.7405 (t-90) REVERT: B 174 MET cc_start: 0.6808 (ptp) cc_final: 0.6433 (ptm) REVERT: B 214 ARG cc_start: 0.7488 (ttm-80) cc_final: 0.7272 (mtp85) REVERT: B 324 HIS cc_start: 0.7821 (t70) cc_final: 0.7403 (t-90) REVERT: C 87 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7332 (ppt170) REVERT: C 174 MET cc_start: 0.6797 (ptp) cc_final: 0.6424 (ptm) REVERT: C 214 ARG cc_start: 0.7551 (ttm-80) cc_final: 0.7302 (mtp85) REVERT: C 324 HIS cc_start: 0.7840 (t70) cc_final: 0.7419 (t-90) REVERT: D 162 LYS cc_start: 0.6470 (pptt) cc_final: 0.5880 (mtmm) REVERT: D 174 MET cc_start: 0.6804 (ptp) cc_final: 0.6436 (ptm) REVERT: D 214 ARG cc_start: 0.7552 (ttm-80) cc_final: 0.7302 (mtp85) REVERT: D 324 HIS cc_start: 0.7819 (t70) cc_final: 0.7397 (t-90) outliers start: 28 outliers final: 11 residues processed: 163 average time/residue: 2.4747 time to fit residues: 430.8593 Evaluate side-chains 155 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 207 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.175594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.127910 restraints weight = 71075.852| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.13 r_work: 0.3387 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8652 Z= 0.152 Angle : 0.506 4.145 11720 Z= 0.274 Chirality : 0.034 0.126 1260 Planarity : 0.003 0.031 1420 Dihedral : 9.372 73.082 1208 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.90 % Allowed : 28.91 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.26), residues: 1000 helix: 2.27 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.66 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 269 HIS 0.002 0.001 HIS A 228 PHE 0.013 0.001 PHE D 297 TYR 0.010 0.001 TYR D 74 ARG 0.002 0.000 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.05344 ( 668) hydrogen bonds : angle 4.47734 ( 2008) covalent geometry : bond 0.00330 ( 8652) covalent geometry : angle 0.50600 (11720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7337 (ppt170) REVERT: A 174 MET cc_start: 0.6831 (ptp) cc_final: 0.6466 (ptm) REVERT: A 214 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.7277 (mtp85) REVERT: A 324 HIS cc_start: 0.7808 (t70) cc_final: 0.7373 (t-90) REVERT: B 174 MET cc_start: 0.6807 (ptp) cc_final: 0.6428 (ptm) REVERT: B 214 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7272 (mtp85) REVERT: B 324 HIS cc_start: 0.7805 (t70) cc_final: 0.7371 (t-90) REVERT: C 87 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7345 (ppt170) REVERT: C 174 MET cc_start: 0.6812 (ptp) cc_final: 0.6438 (ptm) REVERT: C 214 ARG cc_start: 0.7576 (ttm-80) cc_final: 0.7303 (mtp85) REVERT: C 324 HIS cc_start: 0.7815 (t70) cc_final: 0.7376 (t-90) REVERT: D 162 LYS cc_start: 0.6486 (pptt) cc_final: 0.5873 (mtmm) REVERT: D 174 MET cc_start: 0.6808 (ptp) cc_final: 0.6442 (ptm) REVERT: D 214 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.7308 (mtp85) REVERT: D 324 HIS cc_start: 0.7805 (t70) cc_final: 0.7381 (t-90) outliers start: 16 outliers final: 9 residues processed: 153 average time/residue: 2.5269 time to fit residues: 412.2179 Evaluate side-chains 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 207 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 64.9402 > 50: distance: 305 - 318: 12.214 distance: 318 - 319: 30.041 distance: 318 - 322: 27.316 distance: 319 - 320: 27.002 distance: 319 - 323: 25.379 distance: 319 - 324: 31.949 distance: 325 - 326: 31.207 distance: 325 - 337: 40.819 distance: 326 - 327: 8.607 distance: 326 - 329: 6.891 distance: 326 - 338: 19.821 distance: 327 - 346: 5.371 distance: 329 - 340: 6.537 distance: 335 - 336: 3.719 distance: 346 - 347: 36.069 distance: 346 - 350: 5.019 distance: 347 - 348: 4.541 distance: 348 - 349: 27.066 distance: 353 - 354: 4.618 distance: 354 - 355: 15.218 distance: 354 - 357: 5.066 distance: 355 - 356: 39.390 distance: 357 - 358: 32.511 distance: 357 - 363: 16.446 distance: 357 - 364: 11.397 distance: 358 - 360: 21.564 distance: 365 - 366: 6.719 distance: 365 - 374: 38.409 distance: 366 - 367: 25.279 distance: 366 - 369: 6.497 distance: 366 - 375: 12.801 distance: 367 - 368: 21.595 distance: 367 - 387: 16.431 distance: 369 - 370: 19.834 distance: 369 - 376: 25.313 distance: 369 - 377: 11.324 distance: 370 - 371: 16.742 distance: 370 - 379: 16.576 distance: 371 - 372: 18.271 distance: 371 - 380: 12.642 distance: 371 - 381: 21.665 distance: 372 - 373: 13.139 distance: 372 - 382: 18.873 distance: 372 - 383: 29.936 distance: 373 - 384: 6.328 distance: 373 - 385: 5.672 distance: 373 - 386: 10.531 distance: 387 - 388: 18.533 distance: 387 - 399: 18.351 distance: 388 - 391: 4.632 distance: 388 - 400: 22.215 distance: 389 - 390: 4.234 distance: 389 - 408: 9.519 distance: 391 - 392: 9.083 distance: 391 - 401: 22.396 distance: 391 - 402: 13.894 distance: 393 - 395: 14.389 distance: 393 - 403: 4.132 distance: 394 - 396: 8.400 distance: 394 - 404: 7.494 distance: 395 - 397: 6.646 distance: 395 - 405: 7.253 distance: 396 - 397: 11.420 distance: 397 - 398: 9.936 distance: 398 - 407: 27.874 distance: 408 - 409: 16.527 distance: 408 - 414: 24.951 distance: 409 - 412: 28.714 distance: 409 - 415: 20.836 distance: 410 - 422: 11.113 distance: 412 - 413: 24.363 distance: 412 - 416: 9.316 distance: 412 - 417: 9.252 distance: 413 - 414: 13.812 distance: 413 - 418: 28.803 distance: 413 - 419: 19.730 distance: 414 - 420: 13.795 distance: 414 - 421: 11.645 distance: 422 - 431: 25.537 distance: 423 - 424: 3.250 distance: 423 - 426: 19.402 distance: 423 - 432: 16.034 distance: 424 - 425: 12.142 distance: 424 - 439: 10.152 distance: 426 - 427: 19.200 distance: 426 - 433: 13.193 distance: 426 - 434: 9.909 distance: 427 - 428: 11.605 distance: 427 - 435: 27.378 distance: 427 - 436: 12.215 distance: 428 - 430: 4.217 distance: 430 - 438: 17.166 distance: 439 - 440: 16.413 distance: 440 - 443: 6.092 distance: 440 - 447: 11.419 distance: 441 - 442: 7.599 distance: 441 - 453: 15.939 distance: 442 - 498: 26.328 distance: 443 - 444: 11.805 distance: 443 - 445: 11.253 distance: 443 - 448: 8.632 distance: 445 - 450: 8.686 distance: 445 - 451: 3.454 distance: 445 - 452: 4.067 distance: 453 - 454: 3.491 distance: 454 - 455: 13.708 distance: 454 - 457: 6.004 distance: 454 - 468: 10.660 distance: 455 - 456: 31.335 distance: 455 - 477: 9.632 distance: 456 - 522: 21.205 distance: 457 - 458: 4.069 distance: 457 - 469: 12.331 distance: 457 - 470: 3.981 distance: 458 - 459: 12.764 distance: 458 - 460: 17.411 distance: 459 - 461: 9.879 distance: 459 - 471: 6.484 distance: 460 - 462: 20.293 distance: 460 - 463: 23.784 distance: 461 - 462: 13.222 distance: 461 - 472: 8.152 distance: 462 - 464: 13.531 distance: 463 - 465: 5.308 distance: 463 - 473: 10.331 distance: 464 - 466: 9.571 distance: 464 - 474: 7.381 distance: 465 - 466: 8.943 distance: 465 - 475: 4.950