Starting phenix.real_space_refine on Fri Dec 8 15:19:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukg_26580/12_2023/7ukg_26580.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukg_26580/12_2023/7ukg_26580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukg_26580/12_2023/7ukg_26580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukg_26580/12_2023/7ukg_26580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukg_26580/12_2023/7ukg_26580.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukg_26580/12_2023/7ukg_26580.pdb" } resolution = 2.24 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= -0.003 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 60 5.16 5 C 5704 2.51 5 N 1424 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B ASP 233": "OD1" <-> "OD2" Residue "B TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C ASP 233": "OD1" <-> "OD2" Residue "C TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D ASP 233": "OD1" <-> "OD2" Residue "D TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8652 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 163 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "J" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 163 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "K" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 163 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "L" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 163 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.97, per 1000 atoms: 0.57 Number of scatterers: 8652 At special positions: 0 Unit cell: (99.946, 99.946, 79.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 60 16.00 O 1460 8.00 N 1424 7.00 C 5704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.8 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 85.5% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 181 through 205 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 225 through 250 Processing helix chain 'A' and resid 253 through 259 Processing helix chain 'A' and resid 260 through 279 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 320 Processing helix chain 'A' and resid 320 through 347 Processing helix chain 'A' and resid 356 through 369 removed outlier: 4.012A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 401 through 424 Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 181 through 205 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 225 through 250 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 260 through 279 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 4.011A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 Processing helix chain 'B' and resid 401 through 424 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 225 through 250 Processing helix chain 'C' and resid 253 through 259 Processing helix chain 'C' and resid 260 through 279 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 320 Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 356 through 369 removed outlier: 4.011A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 401 through 424 Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 181 through 205 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 225 through 250 Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 260 through 279 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 320 Processing helix chain 'D' and resid 320 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 4.012A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 Processing helix chain 'D' and resid 401 through 424 Processing helix chain 'I' and resid 96 through 117 Processing helix chain 'J' and resid 96 through 117 Processing helix chain 'K' and resid 96 through 117 Processing helix chain 'L' and resid 96 through 117 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 211 removed outlier: 6.111A pdb=" N LEU A 219 " --> pdb=" O CYS A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 208 through 211 removed outlier: 6.111A pdb=" N LEU B 219 " --> pdb=" O CYS B 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 208 through 211 removed outlier: 6.111A pdb=" N LEU C 219 " --> pdb=" O CYS C 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 208 through 211 removed outlier: 6.111A pdb=" N LEU D 219 " --> pdb=" O CYS D 209 " (cutoff:3.500A) 717 hydrogen bonds defined for protein. 2055 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2616 1.34 - 1.46: 1520 1.46 - 1.57: 4608 1.57 - 1.69: 0 1.69 - 1.80: 92 Bond restraints: 8836 Sorted by residual: bond pdb=" N ARG B 418 " pdb=" CA ARG B 418 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.81e+00 bond pdb=" N ARG C 418 " pdb=" CA ARG C 418 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.79e+00 bond pdb=" N ARG A 418 " pdb=" CA ARG A 418 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.79e+00 bond pdb=" N ARG D 418 " pdb=" CA ARG D 418 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.76e+00 bond pdb=" CB THR B 316 " pdb=" CG2 THR B 316 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.17e+00 ... (remaining 8831 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.41: 188 106.41 - 113.32: 4988 113.32 - 120.24: 3238 120.24 - 127.15: 3532 127.15 - 134.06: 66 Bond angle restraints: 12012 Sorted by residual: angle pdb=" CA TYR A 188 " pdb=" CB TYR A 188 " pdb=" CG TYR A 188 " ideal model delta sigma weight residual 113.90 118.83 -4.93 1.80e+00 3.09e-01 7.49e+00 angle pdb=" CA TYR B 188 " pdb=" CB TYR B 188 " pdb=" CG TYR B 188 " ideal model delta sigma weight residual 113.90 118.82 -4.92 1.80e+00 3.09e-01 7.46e+00 angle pdb=" CA TYR D 188 " pdb=" CB TYR D 188 " pdb=" CG TYR D 188 " ideal model delta sigma weight residual 113.90 118.78 -4.88 1.80e+00 3.09e-01 7.36e+00 angle pdb=" CA TYR C 188 " pdb=" CB TYR C 188 " pdb=" CG TYR C 188 " ideal model delta sigma weight residual 113.90 118.77 -4.87 1.80e+00 3.09e-01 7.31e+00 angle pdb=" CG ARG D 256 " pdb=" CD ARG D 256 " pdb=" NE ARG D 256 " ideal model delta sigma weight residual 112.00 116.92 -4.92 2.20e+00 2.07e-01 4.99e+00 ... (remaining 12007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 4612 15.49 - 30.98: 468 30.98 - 46.47: 84 46.47 - 61.95: 12 61.95 - 77.44: 8 Dihedral angle restraints: 5184 sinusoidal: 1888 harmonic: 3296 Sorted by residual: dihedral pdb=" CG ARG B 411 " pdb=" CD ARG B 411 " pdb=" NE ARG B 411 " pdb=" CZ ARG B 411 " ideal model delta sinusoidal sigma weight residual -90.00 -133.87 43.87 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG C 411 " pdb=" CD ARG C 411 " pdb=" NE ARG C 411 " pdb=" CZ ARG C 411 " ideal model delta sinusoidal sigma weight residual -90.00 -133.87 43.87 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG D 411 " pdb=" CD ARG D 411 " pdb=" NE ARG D 411 " pdb=" CZ ARG D 411 " ideal model delta sinusoidal sigma weight residual -90.00 -133.86 43.86 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 5181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 714 0.027 - 0.054: 486 0.054 - 0.081: 186 0.081 - 0.108: 50 0.108 - 0.136: 40 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA PHE C 194 " pdb=" N PHE C 194 " pdb=" C PHE C 194 " pdb=" CB PHE C 194 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA PHE A 194 " pdb=" N PHE A 194 " pdb=" C PHE A 194 " pdb=" CB PHE A 194 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA PHE B 194 " pdb=" N PHE B 194 " pdb=" C PHE B 194 " pdb=" CB PHE B 194 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1473 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 417 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C GLN C 417 " 0.062 2.00e-02 2.50e+03 pdb=" O GLN C 417 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG C 418 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 417 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C GLN A 417 " -0.062 2.00e-02 2.50e+03 pdb=" O GLN A 417 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG A 418 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 417 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C GLN B 417 " -0.062 2.00e-02 2.50e+03 pdb=" O GLN B 417 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 418 " 0.021 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.79: 2177 2.79 - 3.38: 10535 3.38 - 3.97: 16944 3.97 - 4.55: 24020 4.55 - 5.14: 33707 Nonbonded interactions: 87383 Sorted by model distance: nonbonded pdb=" OG1 THR D 166 " pdb=" NE2 GLN D 169 " model vdw 2.208 2.520 nonbonded pdb=" OG1 THR C 166 " pdb=" NE2 GLN C 169 " model vdw 2.209 2.520 nonbonded pdb=" OG1 THR B 166 " pdb=" OE1 GLN B 169 " model vdw 2.327 2.440 nonbonded pdb=" OG1 THR A 166 " pdb=" OE1 GLN A 169 " model vdw 2.328 2.440 nonbonded pdb=" O THR A 369 " pdb=" OG1 THR A 370 " model vdw 2.393 2.440 ... (remaining 87378 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 166 through 424) selection = (chain 'B' and resid 166 through 424) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 5.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 23.170 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.650 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 0.049 8836 Z= 0.376 Angle : 0.579 5.237 12012 Z= 0.331 Chirality : 0.043 0.136 1476 Planarity : 0.004 0.036 1448 Dihedral : 13.160 77.443 3056 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % 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: 2.95 (0.25), residues: 1112 helix: 2.16 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.32 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 362 HIS 0.002 0.000 HIS C 306 PHE 0.018 0.002 PHE D 194 TYR 0.021 0.002 TYR B 188 ARG 0.009 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 1.2115 time to fit residues: 164.3587 Evaluate side-chains 124 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 169 GLN C 179 HIS D 169 GLN D 179 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.0527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8836 Z= 0.188 Angle : 0.459 5.019 12012 Z= 0.254 Chirality : 0.039 0.123 1476 Planarity : 0.004 0.031 1448 Dihedral : 3.545 11.890 1236 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.54 % Allowed : 10.61 % Favored : 88.85 % 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: 3.48 (0.25), residues: 1112 helix: 2.55 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.40 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 362 HIS 0.002 0.001 HIS C 306 PHE 0.016 0.002 PHE D 194 TYR 0.020 0.002 TYR C 188 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 0.913 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 138 average time/residue: 1.1468 time to fit residues: 169.2718 Evaluate side-chains 125 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.2272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.0370 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.0970 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 0.0270 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8836 Z= 0.131 Angle : 0.414 4.996 12012 Z= 0.227 Chirality : 0.037 0.113 1476 Planarity : 0.004 0.031 1448 Dihedral : 3.382 11.605 1236 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.97 % Allowed : 10.61 % Favored : 88.42 % 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: 3.90 (0.25), residues: 1112 helix: 2.83 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.60 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 362 HIS 0.003 0.001 HIS A 306 PHE 0.012 0.001 PHE D 194 TYR 0.016 0.001 TYR A 188 ARG 0.005 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 0.930 Fit side-chains outliers start: 9 outliers final: 1 residues processed: 141 average time/residue: 1.1584 time to fit residues: 174.8175 Evaluate side-chains 127 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.4427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.0570 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8836 Z= 0.202 Angle : 0.470 5.022 12012 Z= 0.255 Chirality : 0.039 0.118 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.456 11.608 1236 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.54 % Allowed : 12.66 % Favored : 86.80 % 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: 3.85 (0.25), residues: 1112 helix: 2.79 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.59 (0.47), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 362 HIS 0.002 0.001 HIS C 306 PHE 0.018 0.002 PHE C 289 TYR 0.022 0.002 TYR A 188 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 138 time to evaluate : 1.049 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 143 average time/residue: 1.1017 time to fit residues: 168.7528 Evaluate side-chains 131 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.4231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0040 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 0.0010 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8836 Z= 0.137 Angle : 0.423 4.972 12012 Z= 0.230 Chirality : 0.037 0.112 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.338 11.103 1236 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.97 % Allowed : 12.12 % Favored : 86.90 % 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: 4.10 (0.25), residues: 1112 helix: 2.96 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.69 (0.47), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 362 HIS 0.003 0.001 HIS A 306 PHE 0.014 0.001 PHE C 289 TYR 0.016 0.002 TYR C 188 ARG 0.005 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 1.018 Fit side-chains outliers start: 9 outliers final: 1 residues processed: 135 average time/residue: 1.1970 time to fit residues: 172.6853 Evaluate side-chains 127 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.1976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8836 Z= 0.234 Angle : 0.485 5.035 12012 Z= 0.264 Chirality : 0.040 0.121 1476 Planarity : 0.004 0.031 1448 Dihedral : 3.488 11.042 1236 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.97 % Allowed : 12.77 % Favored : 86.26 % 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: 3.84 (0.25), residues: 1112 helix: 2.79 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.57 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 362 HIS 0.002 0.001 HIS C 306 PHE 0.016 0.002 PHE A 194 TYR 0.022 0.002 TYR A 188 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 1.268 Fit side-chains outliers start: 9 outliers final: 1 residues processed: 136 average time/residue: 1.1943 time to fit residues: 174.1679 Evaluate side-chains 128 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.3220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 0.0970 chunk 65 optimal weight: 0.4980 chunk 63 optimal weight: 0.6980 chunk 48 optimal weight: 0.2980 chunk 64 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8836 Z= 0.139 Angle : 0.429 4.967 12012 Z= 0.232 Chirality : 0.037 0.113 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.345 10.750 1236 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.54 % Allowed : 12.88 % Favored : 86.58 % 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: 4.06 (0.25), residues: 1112 helix: 2.97 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.52 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 362 HIS 0.003 0.001 HIS A 306 PHE 0.012 0.001 PHE C 289 TYR 0.016 0.002 TYR A 188 ARG 0.005 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 0.934 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 132 average time/residue: 1.2101 time to fit residues: 170.2950 Evaluate side-chains 126 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.2209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8836 Z= 0.232 Angle : 0.482 5.033 12012 Z= 0.263 Chirality : 0.040 0.120 1476 Planarity : 0.004 0.031 1448 Dihedral : 3.471 11.270 1236 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.65 % Allowed : 12.99 % Favored : 86.36 % 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: 3.85 (0.25), residues: 1112 helix: 2.81 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.50 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 362 HIS 0.002 0.001 HIS B 306 PHE 0.016 0.002 PHE A 194 TYR 0.022 0.002 TYR A 188 ARG 0.005 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 0.982 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 143 average time/residue: 1.1536 time to fit residues: 176.6359 Evaluate side-chains 134 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.4234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8836 Z= 0.211 Angle : 0.477 5.015 12012 Z= 0.259 Chirality : 0.039 0.118 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.480 11.837 1236 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.43 % Allowed : 13.10 % Favored : 86.47 % 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: 3.78 (0.25), residues: 1112 helix: 2.77 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.43 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 362 HIS 0.002 0.001 HIS B 306 PHE 0.015 0.002 PHE B 194 TYR 0.022 0.002 TYR A 188 ARG 0.005 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 0.968 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 138 average time/residue: 1.2041 time to fit residues: 177.3422 Evaluate side-chains 131 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.3952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 0.0030 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8836 Z= 0.165 Angle : 0.453 5.744 12012 Z= 0.245 Chirality : 0.038 0.113 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.399 11.749 1236 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.11 % Allowed : 13.20 % Favored : 86.69 % 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: 3.91 (0.25), residues: 1112 helix: 2.88 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.40 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 362 HIS 0.002 0.001 HIS D 306 PHE 0.012 0.001 PHE B 194 TYR 0.017 0.002 TYR A 188 ARG 0.005 0.000 ARG D 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.011 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 1.2631 time to fit residues: 172.2650 Evaluate side-chains 125 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.3347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.151012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103238 restraints weight = 8963.882| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.63 r_work: 0.3102 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8836 Z= 0.189 Angle : 0.471 5.678 12012 Z= 0.254 Chirality : 0.039 0.114 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.422 12.032 1236 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.32 % Allowed : 13.20 % Favored : 86.47 % 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: 3.84 (0.25), residues: 1112 helix: 2.82 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.43 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 362 HIS 0.002 0.001 HIS A 306 PHE 0.014 0.002 PHE C 194 TYR 0.021 0.002 TYR A 188 ARG 0.002 0.000 ARG A 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3622.52 seconds wall clock time: 65 minutes 15.00 seconds (3915.00 seconds total)