Starting phenix.real_space_refine on Mon Dec 11 16:22:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2023/7una_26618_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2023/7una_26618.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2023/7una_26618_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2023/7una_26618_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2023/7una_26618_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2023/7una_26618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2023/7una_26618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2023/7una_26618_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7una_26618/12_2023/7una_26618_trim_updated.pdb" } resolution = 4.0 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= 0.002 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 P 8 5.49 5 S 40 5.16 5 C 5918 2.51 5 N 1521 2.21 5 O 1724 1.98 5 H 9203 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 172": "OE1" <-> "OE2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 254": "OD1" <-> "OD2" Residue "E TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F ASP 203": "OD1" <-> "OD2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "H GLU 180": "OE1" <-> "OE2" Residue "H ASP 194": "OD1" <-> "OD2" Residue "H PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 293": "OE1" <-> "OE2" Residue "H GLU 295": "OE1" <-> "OE2" Residue "H TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 18414 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2286 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain breaks: 4 Chain: "B" Number of atoms: 2266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2266 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 4 Chain: "C" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2306 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain breaks: 4 Chain: "D" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2298 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain breaks: 3 Chain: "E" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2249 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 4 Chain: "F" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2277 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 4 Chain: "G" Number of atoms: 2271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2271 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain breaks: 4 Chain: "H" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2281 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 4 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1' 4BW A 401 " occ=0.47 ... (43 atoms not shown) pdb=" PBS 4BW A 401 " occ=0.47 residue: pdb=" C1' 4BW C 401 " occ=0.47 ... (43 atoms not shown) pdb=" PBS 4BW C 401 " occ=0.47 residue: pdb=" C1' 4BW F 401 " occ=0.47 ... (43 atoms not shown) pdb=" PBS 4BW F 401 " occ=0.47 residue: pdb=" C1' 4BW H 401 " occ=0.47 ... (43 atoms not shown) pdb=" PBS 4BW H 401 " occ=0.47 Time building chain proxies: 7.71, per 1000 atoms: 0.42 Number of scatterers: 18414 At special positions: 0 Unit cell: (134.2, 126.5, 171.6, 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 40 16.00 P 8 15.00 O 1724 8.00 N 1521 7.00 C 5918 6.00 H 9203 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 - 3.50 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.57 Conformation dependent library (CDL) restraints added in 1.4 seconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 16 sheets defined 48.3% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 193.48 Creating SS restraints... Processing helix chain 'A' and resid 155 through 176 Processing helix chain 'A' and resid 207 through 217 Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 286 through 307 Processing helix chain 'B' and resid 154 through 176 Processing helix chain 'B' and resid 207 through 217 Processing helix chain 'B' and resid 262 through 274 removed outlier: 3.740A pdb=" N TYR B 274 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 307 Processing helix chain 'C' and resid 155 through 176 Processing helix chain 'C' and resid 207 through 217 Processing helix chain 'C' and resid 262 through 273 Processing helix chain 'C' and resid 285 through 307 Processing helix chain 'D' and resid 154 through 176 Processing helix chain 'D' and resid 207 through 217 Processing helix chain 'D' and resid 262 through 273 Processing helix chain 'D' and resid 286 through 307 Processing helix chain 'E' and resid 153 through 176 Processing helix chain 'E' and resid 207 through 217 Processing helix chain 'E' and resid 262 through 274 Processing helix chain 'E' and resid 286 through 307 Processing helix chain 'F' and resid 154 through 176 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 262 through 273 Processing helix chain 'F' and resid 285 through 307 Processing helix chain 'G' and resid 153 through 176 Processing helix chain 'G' and resid 207 through 217 Processing helix chain 'G' and resid 262 through 273 Processing helix chain 'G' and resid 286 through 307 removed outlier: 3.861A pdb=" N ARG G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 176 Processing helix chain 'H' and resid 207 through 217 removed outlier: 3.593A pdb=" N TYR H 217 " --> pdb=" O TYR H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 274 Processing helix chain 'H' and resid 286 through 306 Processing sheet with id= A, first strand: chain 'A' and resid 257 through 260 Processing sheet with id= B, first strand: chain 'A' and resid 220 through 222 Processing sheet with id= C, first strand: chain 'B' and resid 193 through 196 Processing sheet with id= D, first strand: chain 'B' and resid 220 through 222 Processing sheet with id= E, first strand: chain 'C' and resid 255 through 260 Processing sheet with id= F, first strand: chain 'C' and resid 220 through 222 Processing sheet with id= G, first strand: chain 'D' and resid 257 through 259 Processing sheet with id= H, first strand: chain 'D' and resid 220 through 222 Processing sheet with id= I, first strand: chain 'E' and resid 257 through 260 removed outlier: 3.703A pdb=" N ASP E 259 " --> pdb=" O ASP E 194 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 220 through 222 Processing sheet with id= K, first strand: chain 'F' and resid 315 through 318 removed outlier: 6.082A pdb=" N VAL F 193 " --> pdb=" O ASN F 316 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU F 318 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL F 195 " --> pdb=" O LEU F 318 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 220 through 222 Processing sheet with id= M, first strand: chain 'G' and resid 220 through 222 Processing sheet with id= N, first strand: chain 'G' and resid 193 through 198 Processing sheet with id= O, first strand: chain 'H' and resid 257 through 259 Processing sheet with id= P, first strand: chain 'H' and resid 220 through 222 497 hydrogen bonds defined for protein. 1221 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: 6.38 Time building geometry restraints manager: 15.06 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: 9179 1.03 - 1.23: 27 1.23 - 1.42: 3844 1.42 - 1.61: 5454 1.61 - 1.81: 80 Bond restraints: 18584 Sorted by residual: bond pdb=" C4' 4BW C 401 " pdb=" O4' 4BW C 401 " ideal model delta sigma weight residual 1.304 1.656 -0.352 2.00e-02 2.50e+03 3.10e+02 bond pdb=" CBI 4BW F 401 " pdb=" CBO 4BW F 401 " ideal model delta sigma weight residual 1.303 1.653 -0.350 2.00e-02 2.50e+03 3.07e+02 bond pdb=" CBI 4BW C 401 " pdb=" CBO 4BW C 401 " ideal model delta sigma weight residual 1.303 1.653 -0.350 2.00e-02 2.50e+03 3.06e+02 bond pdb=" CBI 4BW H 401 " pdb=" CBO 4BW H 401 " ideal model delta sigma weight residual 1.303 1.652 -0.349 2.00e-02 2.50e+03 3.04e+02 bond pdb=" CBI 4BW A 401 " pdb=" CBO 4BW A 401 " ideal model delta sigma weight residual 1.303 1.651 -0.348 2.00e-02 2.50e+03 3.02e+02 ... (remaining 18579 not shown) Histogram of bond angle deviations from ideal: 100.13 - 107.17: 470 107.17 - 114.21: 22829 114.21 - 121.25: 6900 121.25 - 128.29: 3339 128.29 - 135.34: 51 Bond angle restraints: 33589 Sorted by residual: angle pdb=" CA PRO A 237 " pdb=" N PRO A 237 " pdb=" CD PRO A 237 " ideal model delta sigma weight residual 112.00 103.69 8.31 1.40e+00 5.10e-01 3.52e+01 angle pdb=" O3' 4BW F 401 " pdb=" PBR 4BW F 401 " pdb=" OAV 4BW F 401 " ideal model delta sigma weight residual 100.13 113.57 -13.44 3.00e+00 1.11e-01 2.01e+01 angle pdb=" O3' 4BW H 401 " pdb=" PBR 4BW H 401 " pdb=" OAV 4BW H 401 " ideal model delta sigma weight residual 100.13 113.38 -13.25 3.00e+00 1.11e-01 1.95e+01 angle pdb=" O3' 4BW C 401 " pdb=" PBR 4BW C 401 " pdb=" OAV 4BW C 401 " ideal model delta sigma weight residual 100.13 113.33 -13.20 3.00e+00 1.11e-01 1.93e+01 angle pdb=" O3' 4BW A 401 " pdb=" PBR 4BW A 401 " pdb=" OAV 4BW A 401 " ideal model delta sigma weight residual 100.13 113.23 -13.10 3.00e+00 1.11e-01 1.91e+01 ... (remaining 33584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.97: 8208 30.97 - 61.94: 221 61.94 - 92.91: 13 92.91 - 123.88: 0 123.88 - 154.85: 8 Dihedral angle restraints: 8450 sinusoidal: 4539 harmonic: 3911 Sorted by residual: dihedral pdb=" OAV 4BW F 401 " pdb=" CAN 4BW F 401 " pdb=" CBK 4BW F 401 " pdb=" OAX 4BW F 401 " ideal model delta sinusoidal sigma weight residual 179.16 -25.99 -154.85 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" OAV 4BW A 401 " pdb=" CAN 4BW A 401 " pdb=" CBK 4BW A 401 " pdb=" OAX 4BW A 401 " ideal model delta sinusoidal sigma weight residual 179.16 -27.91 -152.93 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" OAV 4BW H 401 " pdb=" CAN 4BW H 401 " pdb=" CBK 4BW H 401 " pdb=" OAX 4BW H 401 " ideal model delta sinusoidal sigma weight residual 179.16 -36.81 -144.03 1 3.00e+01 1.11e-03 1.93e+01 ... (remaining 8447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1192 0.045 - 0.090: 182 0.090 - 0.135: 89 0.135 - 0.180: 20 0.180 - 0.225: 4 Chirality restraints: 1487 Sorted by residual: chirality pdb=" C2' 4BW C 401 " pdb=" C1' 4BW C 401 " pdb=" C3' 4BW C 401 " pdb=" O2' 4BW C 401 " both_signs ideal model delta sigma weight residual False -2.41 -2.63 0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C2' 4BW H 401 " pdb=" C1' 4BW H 401 " pdb=" C3' 4BW H 401 " pdb=" O2' 4BW H 401 " both_signs ideal model delta sigma weight residual False -2.41 -2.62 0.21 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C2' 4BW A 401 " pdb=" C1' 4BW A 401 " pdb=" C3' 4BW A 401 " pdb=" O2' 4BW A 401 " both_signs ideal model delta sigma weight residual False -2.41 -2.61 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1484 not shown) Planarity restraints: 2581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 236 " 0.077 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO A 237 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 163 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.63e+00 pdb=" C ASN A 163 " -0.051 2.00e-02 2.50e+03 pdb=" O ASN A 163 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 164 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 163 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C ASN C 163 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN C 163 " 0.017 2.00e-02 2.50e+03 pdb=" N SER C 164 " 0.015 2.00e-02 2.50e+03 ... (remaining 2578 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1128 2.19 - 2.79: 37776 2.79 - 3.40: 49819 3.40 - 4.00: 62060 4.00 - 4.60: 96007 Nonbonded interactions: 246790 Sorted by model distance: nonbonded pdb=" O SER F 270 " pdb=" H TYR F 274 " model vdw 1.591 1.850 nonbonded pdb=" HG1 THR H 263 " pdb=" O3' 4BW H 401 " model vdw 1.594 1.850 nonbonded pdb=" O GLU F 172 " pdb=" HG SER F 176 " model vdw 1.596 1.850 nonbonded pdb=" OD1 ASN D 308 " pdb=" H ALA D 310 " model vdw 1.599 1.850 nonbonded pdb=" O GLU H 172 " pdb=" HG SER H 176 " model vdw 1.601 1.850 ... (remaining 246785 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 153 through 225 or (resid 235 and (name N or name CA or na \ me C or name O or name HA2 or name HA3)) or resid 236 through 241 or (resid 253 \ and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or \ name HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name \ HG22 or name HG23)) or resid 254 through 274 or resid 285 through 321)) selection = (chain 'B' and (resid 153 through 184 or resid 186 through 225 or resid 235 thro \ ugh 241 or (resid 253 and (name N or name CA or name C or name O or name CB or n \ ame CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 \ or name HG21 or name HG22 or name HG23)) or resid 254 through 274 or resid 285 \ through 321)) selection = (chain 'C' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 225 \ or (resid 235 and (name N or name CA or name C or name O or name HA2 or name HA3 \ )) or resid 236 through 241 or (resid 253 and (name N or name CA or name C or na \ me O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or na \ me HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 254 throu \ gh 274 or (resid 285 and (name N or name CA or name C or name O or name CB or na \ me CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid 286 \ through 321)) selection = (chain 'D' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 225 \ or (resid 235 and (name N or name CA or name C or name O or name HA2 or name HA3 \ )) or resid 236 through 321)) selection = (chain 'E' and (resid 153 through 225 or resid 235 through 241 or (resid 253 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG2 \ 2 or name HG23)) or resid 254 through 255 or (resid 256 and (name N or name CA o \ r name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or \ name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or \ name HE2)) or resid 257 through 274 or resid 285 through 321)) selection = (chain 'F' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 241 \ or (resid 253 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name \ HG21 or name HG22 or name HG23)) or resid 254 through 274 or (resid 285 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name OD \ 2 or name HA or name HB2 or name HB3)) or resid 286 through 321)) selection = (chain 'G' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 225 \ or resid 235 through 241 or (resid 253 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 254 through \ 255 or (resid 256 and (name N or name CA or name C or name O or name CB or name \ CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name \ HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 257 through 321)) \ selection = (chain 'H' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 225 \ or (resid 235 and (name N or name CA or name C or name O or name HA2 or name HA3 \ )) or resid 236 through 241 or (resid 253 and (name N or name CA or name C or na \ me O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or na \ me HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 254 throu \ gh 274 or resid 285 through 321)) } 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=0.47 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.760 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: 0.290 Extract box with map and model: 5.890 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 56.650 Find NCS groups from input model: 0.930 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 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 : 0.020 0.352 9381 Z= 1.395 Angle : 0.865 13.442 12670 Z= 0.406 Chirality : 0.044 0.225 1487 Planarity : 0.006 0.111 1516 Dihedral : 15.468 154.852 3439 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.95 (0.26), residues: 1054 helix: 0.94 (0.22), residues: 519 sheet: -2.23 (0.33), residues: 211 loop : -1.96 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 174 PHE 0.019 0.001 PHE C 191 TYR 0.018 0.001 TYR F 162 ARG 0.008 0.001 ARG D 292 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.4726 time to fit residues: 151.7845 Evaluate side-chains 178 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.576 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 0.4980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9381 Z= 0.203 Angle : 0.542 5.143 12670 Z= 0.290 Chirality : 0.040 0.173 1487 Planarity : 0.004 0.053 1516 Dihedral : 9.246 103.627 1261 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.06 % Allowed : 8.64 % Favored : 89.30 % 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: -0.76 (0.26), residues: 1054 helix: 1.13 (0.22), residues: 515 sheet: -2.19 (0.35), residues: 201 loop : -1.89 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 174 PHE 0.016 0.001 PHE C 191 TYR 0.022 0.001 TYR F 303 ARG 0.004 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 17 residues processed: 197 average time/residue: 0.4514 time to fit residues: 124.2536 Evaluate side-chains 188 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 1.633 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1967 time to fit residues: 8.1197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 320 ASN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9381 Z= 0.336 Angle : 0.621 5.814 12670 Z= 0.338 Chirality : 0.043 0.188 1487 Planarity : 0.005 0.039 1516 Dihedral : 7.291 69.985 1261 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 1.57 % Allowed : 13.44 % Favored : 84.99 % 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: -0.93 (0.25), residues: 1054 helix: 1.00 (0.22), residues: 518 sheet: -2.04 (0.33), residues: 233 loop : -2.16 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 174 PHE 0.017 0.002 PHE C 191 TYR 0.015 0.002 TYR F 303 ARG 0.004 0.001 ARG G 292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 187 average time/residue: 0.4303 time to fit residues: 114.8777 Evaluate side-chains 172 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 163 time to evaluate : 1.678 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2087 time to fit residues: 5.2104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9381 Z= 0.216 Angle : 0.552 5.910 12670 Z= 0.296 Chirality : 0.040 0.179 1487 Planarity : 0.004 0.033 1516 Dihedral : 6.973 64.564 1261 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.86 % Allowed : 14.52 % Favored : 83.61 % 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: -0.76 (0.26), residues: 1054 helix: 1.17 (0.22), residues: 516 sheet: -1.99 (0.33), residues: 234 loop : -2.07 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 256 PHE 0.012 0.001 PHE A 238 TYR 0.019 0.001 TYR F 162 ARG 0.007 0.000 ARG D 292 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 186 average time/residue: 0.4342 time to fit residues: 115.3587 Evaluate side-chains 170 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 1.632 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2141 time to fit residues: 4.8284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9381 Z= 0.203 Angle : 0.543 6.049 12670 Z= 0.291 Chirality : 0.040 0.174 1487 Planarity : 0.004 0.031 1516 Dihedral : 6.676 59.288 1261 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.37 % Allowed : 15.70 % Favored : 82.92 % 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: -0.67 (0.26), residues: 1054 helix: 1.23 (0.22), residues: 517 sheet: -1.96 (0.33), residues: 234 loop : -1.99 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 174 PHE 0.011 0.001 PHE F 297 TYR 0.021 0.001 TYR F 303 ARG 0.006 0.000 ARG G 292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 185 average time/residue: 0.4445 time to fit residues: 115.3165 Evaluate side-chains 172 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 164 time to evaluate : 1.529 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1975 time to fit residues: 4.9237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9381 Z= 0.315 Angle : 0.615 6.300 12670 Z= 0.334 Chirality : 0.042 0.179 1487 Planarity : 0.005 0.043 1516 Dihedral : 6.836 61.779 1261 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.06 % Allowed : 17.27 % Favored : 80.67 % 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: -0.84 (0.25), residues: 1054 helix: 1.07 (0.22), residues: 519 sheet: -1.99 (0.33), residues: 241 loop : -2.08 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 174 PHE 0.015 0.002 PHE D 297 TYR 0.025 0.002 TYR F 303 ARG 0.006 0.001 ARG G 292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 179 average time/residue: 0.4499 time to fit residues: 115.9964 Evaluate side-chains 175 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 1.562 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2684 time to fit residues: 7.7588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 91 optimal weight: 0.2980 chunk 60 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 HIS B 320 ASN C 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9381 Z= 0.164 Angle : 0.531 6.318 12670 Z= 0.282 Chirality : 0.040 0.185 1487 Planarity : 0.004 0.045 1516 Dihedral : 6.572 54.738 1261 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.98 % Allowed : 18.16 % Favored : 80.86 % 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: -0.50 (0.26), residues: 1054 helix: 1.34 (0.22), residues: 516 sheet: -1.87 (0.34), residues: 230 loop : -1.88 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 256 PHE 0.011 0.001 PHE A 238 TYR 0.023 0.001 TYR F 303 ARG 0.006 0.000 ARG G 292 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 179 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 184 average time/residue: 0.4536 time to fit residues: 116.7999 Evaluate side-chains 174 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 1.443 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3521 time to fit residues: 5.6173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9381 Z= 0.202 Angle : 0.544 6.378 12670 Z= 0.290 Chirality : 0.040 0.178 1487 Planarity : 0.004 0.048 1516 Dihedral : 6.479 55.250 1261 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.08 % Allowed : 18.94 % Favored : 79.98 % 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: -0.45 (0.26), residues: 1054 helix: 1.38 (0.22), residues: 515 sheet: -1.85 (0.34), residues: 229 loop : -1.85 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 174 PHE 0.011 0.001 PHE A 238 TYR 0.029 0.001 TYR F 303 ARG 0.010 0.000 ARG D 292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 174 average time/residue: 0.4510 time to fit residues: 110.4754 Evaluate side-chains 172 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 166 time to evaluate : 1.608 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2162 time to fit residues: 4.4129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 ASN C 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9381 Z= 0.165 Angle : 0.533 6.094 12670 Z= 0.281 Chirality : 0.040 0.190 1487 Planarity : 0.004 0.051 1516 Dihedral : 6.392 54.581 1261 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.98 % Allowed : 19.04 % Favored : 79.98 % 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: -0.30 (0.26), residues: 1054 helix: 1.46 (0.22), residues: 516 sheet: -1.80 (0.35), residues: 230 loop : -1.69 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 174 PHE 0.016 0.001 PHE E 240 TYR 0.021 0.001 TYR F 303 ARG 0.014 0.001 ARG D 292 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 176 average time/residue: 0.4415 time to fit residues: 110.2077 Evaluate side-chains 171 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 166 time to evaluate : 1.555 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2122 time to fit residues: 3.8586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9381 Z= 0.175 Angle : 0.533 6.815 12670 Z= 0.281 Chirality : 0.039 0.165 1487 Planarity : 0.004 0.046 1516 Dihedral : 6.325 54.924 1261 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.49 % Allowed : 19.82 % Favored : 79.69 % 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: -0.18 (0.26), residues: 1054 helix: 1.51 (0.22), residues: 517 sheet: -1.71 (0.35), residues: 229 loop : -1.56 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 239 PHE 0.015 0.001 PHE G 191 TYR 0.022 0.001 TYR F 303 ARG 0.010 0.001 ARG D 292 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 173 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 174 average time/residue: 0.4810 time to fit residues: 116.8686 Evaluate side-chains 171 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 168 time to evaluate : 1.530 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2523 time to fit residues: 3.2470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.109490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.096256 restraints weight = 68926.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.099340 restraints weight = 34451.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.101464 restraints weight = 20709.586| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9381 Z= 0.259 Angle : 0.587 6.662 12670 Z= 0.313 Chirality : 0.041 0.177 1487 Planarity : 0.005 0.043 1516 Dihedral : 6.558 57.444 1261 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.59 % Allowed : 19.63 % Favored : 79.78 % 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: -0.37 (0.26), residues: 1054 helix: 1.37 (0.22), residues: 519 sheet: -1.80 (0.35), residues: 231 loop : -1.69 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 174 PHE 0.015 0.002 PHE A 238 TYR 0.021 0.001 TYR F 303 ARG 0.007 0.001 ARG A 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4055.88 seconds wall clock time: 77 minutes 18.93 seconds (4638.93 seconds total)