Starting phenix.real_space_refine on Tue Feb 13 14:00:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8w_29857/02_2024/8g8w_29857_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8w_29857/02_2024/8g8w_29857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8w_29857/02_2024/8g8w_29857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8w_29857/02_2024/8g8w_29857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8w_29857/02_2024/8g8w_29857_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8w_29857/02_2024/8g8w_29857_neut_updated.pdb" } resolution = 3.8 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= 0.012 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 P 8 5.49 5 S 23 5.16 5 C 4165 2.51 5 N 1066 2.21 5 O 1209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 97": "OD1" <-> "OD2" Residue "A ASP 196": "OD1" <-> "OD2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 408": "OD1" <-> "OD2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6471 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2146 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2814 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 24, 'TRANS': 373} Chain breaks: 5 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 10, 'GLU:plan': 16, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 169 Chain: "C" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1349 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 3 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 422 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 179 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 139 Unusual residues: {'CDL': 3, 'GTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 2, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 4.37, per 1000 atoms: 0.68 Number of scatterers: 6471 At special positions: 0 Unit cell: (72.24, 92.02, 203.82, 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) S 23 16.00 P 8 15.00 O 1209 8.00 N 1066 7.00 C 4165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 98 " distance=2.03 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 Links applied ALPHA1-4 " GLC D 1 " - " GLC D 2 " Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.2 seconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 8 sheets defined 41.6% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 13 through 30 Processing helix chain 'A' and resid 32 through 42 Processing helix chain 'A' and resid 58 through 69 Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 89 through 104 removed outlier: 4.341A pdb=" N ASP A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 129 Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 177 through 204 Processing helix chain 'A' and resid 212 through 241 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 271 through 297 Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 138 through 152 Processing helix chain 'B' and resid 164 through 171 Proline residue: B 169 - end of helix Processing helix chain 'B' and resid 186 through 194 removed outlier: 4.362A pdb=" N GLY B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 212 through 218 removed outlier: 4.052A pdb=" N VAL B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 279 through 282 No H-bonds generated for 'chain 'B' and resid 279 through 282' Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 350 through 359 removed outlier: 4.175A pdb=" N SER B 354 " --> pdb=" O TRP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 403 Processing helix chain 'B' and resid 408 through 417 removed outlier: 3.966A pdb=" N ASP B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 434 removed outlier: 3.650A pdb=" N GLU B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS B 434 " --> pdb=" O GLU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 447 removed outlier: 3.518A pdb=" N LYS B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 465 removed outlier: 4.166A pdb=" N SER B 458 " --> pdb=" O PRO B 455 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA B 459 " --> pdb=" O GLN B 456 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 460 " --> pdb=" O MET B 457 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TRP B 461 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL B 464 " --> pdb=" O TRP B 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 142 through 155 Processing helix chain 'C' and resid 168 through 171 No H-bonds generated for 'chain 'C' and resid 168 through 171' Processing helix chain 'C' and resid 398 through 407 Processing sheet with id= A, first strand: chain 'B' and resid 6 through 10 Processing sheet with id= B, first strand: chain 'B' and resid 121 through 123 removed outlier: 3.567A pdb=" N MET B 37 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 52 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG B 41 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE B 50 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 128 through 131 Processing sheet with id= D, first strand: chain 'B' and resid 180 through 183 removed outlier: 6.152A pdb=" N ALA B 385 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 346 through 348 Processing sheet with id= F, first strand: chain 'C' and resid 8 through 10 Processing sheet with id= G, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.036A pdb=" N ARG C 41 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE C 50 " --> pdb=" O ARG C 41 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 184 through 188 removed outlier: 5.877A pdb=" N ALA C 389 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE C 391 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ALA C 230 " --> pdb=" O ILE C 391 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 861 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: 1.95 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1069 1.32 - 1.45: 1808 1.45 - 1.57: 3699 1.57 - 1.69: 15 1.69 - 1.82: 36 Bond restraints: 6627 Sorted by residual: bond pdb=" OA3 CDL A 402 " pdb=" PA1 CDL A 402 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.64e+00 bond pdb=" OB3 CDL A 404 " pdb=" PB2 CDL A 404 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.51e+00 bond pdb=" OB3 CDL A 403 " pdb=" PB2 CDL A 403 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.35e+00 bond pdb=" OA3 CDL A 404 " pdb=" PA1 CDL A 404 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.26e+00 bond pdb=" OA3 CDL A 403 " pdb=" PA1 CDL A 403 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.03e+00 ... (remaining 6622 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.20: 219 106.20 - 113.15: 3547 113.15 - 120.09: 2186 120.09 - 127.04: 3036 127.04 - 133.98: 91 Bond angle restraints: 9079 Sorted by residual: angle pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sigma weight residual 120.50 133.11 -12.61 3.00e+00 1.11e-01 1.77e+01 angle pdb=" C1' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C3' GTP A 401 " ideal model delta sigma weight residual 111.00 99.26 11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O1B GTP A 401 " pdb=" PB GTP A 401 " pdb=" O2B GTP A 401 " ideal model delta sigma weight residual 109.50 119.63 -10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" CB MET B 442 " pdb=" CG MET B 442 " pdb=" SD MET B 442 " ideal model delta sigma weight residual 112.70 122.34 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" PB GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sigma weight residual 120.50 130.08 -9.58 3.00e+00 1.11e-01 1.02e+01 ... (remaining 9074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 3739 35.44 - 70.89: 115 70.89 - 106.33: 5 106.33 - 141.77: 2 141.77 - 177.22: 2 Dihedral angle restraints: 3863 sinusoidal: 1294 harmonic: 2569 Sorted by residual: dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -78.19 -177.22 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual -68.92 83.42 -152.34 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual 303.79 171.36 132.44 1 2.00e+01 2.50e-03 4.02e+01 ... (remaining 3860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 935 0.070 - 0.140: 100 0.140 - 0.210: 4 0.210 - 0.280: 0 0.280 - 0.350: 4 Chirality restraints: 1043 Sorted by residual: chirality pdb=" C1 GLC D 1 " pdb=" C2 GLC D 1 " pdb=" O1 GLC D 1 " pdb=" O5 GLC D 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.39 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" C3' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C4' GTP A 401 " pdb=" O3' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.78 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA4 CDL A 402 " pdb=" CA3 CDL A 402 " pdb=" CA6 CDL A 402 " pdb=" OA6 CDL A 402 " both_signs ideal model delta sigma weight residual False -2.57 -2.27 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 1040 not shown) Planarity restraints: 1152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 89 " 0.043 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO C 90 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 231 " 0.031 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO C 232 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 232 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 232 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 454 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 455 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 455 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 455 " 0.020 5.00e-02 4.00e+02 ... (remaining 1149 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1156 2.77 - 3.30: 5870 3.30 - 3.83: 10211 3.83 - 4.37: 10680 4.37 - 4.90: 19816 Nonbonded interactions: 47733 Sorted by model distance: nonbonded pdb=" OG SER C 55 " pdb=" OH TYR C 112 " model vdw 2.234 2.440 nonbonded pdb=" OD1 ASP B 179 " pdb=" OG SER B 391 " model vdw 2.238 2.440 nonbonded pdb=" NE2 GLN A 42 " pdb=" OD2 ASP A 234 " model vdw 2.309 2.520 nonbonded pdb=" O ASP C 75 " pdb=" N ASN C 79 " model vdw 2.316 2.520 nonbonded pdb=" NZ LYS A 138 " pdb=" O1B GTP A 401 " model vdw 2.324 2.520 ... (remaining 47728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 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: 6.790 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: 0.010 Extract box with map and model: 22.930 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 22.160 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6627 Z= 0.241 Angle : 0.686 12.609 9079 Z= 0.315 Chirality : 0.046 0.350 1043 Planarity : 0.004 0.066 1152 Dihedral : 17.422 177.216 2215 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.18 % Allowed : 19.37 % Favored : 80.44 % 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: 1.75 (0.29), residues: 880 helix: 2.73 (0.28), residues: 344 sheet: 0.79 (0.40), residues: 144 loop : -0.10 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 281 HIS 0.002 0.001 HIS A 146 PHE 0.008 0.001 PHE A 286 TYR 0.011 0.001 TYR C 82 ARG 0.002 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.756 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.1709 time to fit residues: 13.2105 Evaluate side-chains 50 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.0504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6627 Z= 0.232 Angle : 0.517 6.926 9079 Z= 0.254 Chirality : 0.042 0.184 1043 Planarity : 0.004 0.057 1152 Dihedral : 13.776 179.483 1094 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.40 % Allowed : 17.53 % Favored : 80.07 % 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: 1.62 (0.29), residues: 880 helix: 2.50 (0.28), residues: 355 sheet: 0.84 (0.40), residues: 144 loop : -0.20 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 281 HIS 0.002 0.001 HIS B 185 PHE 0.012 0.001 PHE B 206 TYR 0.009 0.001 TYR C 97 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.786 Fit side-chains REVERT: A 292 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8564 (tt) REVERT: B 106 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7548 (t80) outliers start: 13 outliers final: 8 residues processed: 63 average time/residue: 0.1977 time to fit residues: 17.8407 Evaluate side-chains 60 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 79 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN B 207 GLN B 403 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6627 Z= 0.351 Angle : 0.589 6.258 9079 Z= 0.298 Chirality : 0.044 0.176 1043 Planarity : 0.005 0.059 1152 Dihedral : 13.367 179.579 1094 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.87 % Allowed : 18.27 % Favored : 77.86 % 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: 1.17 (0.28), residues: 880 helix: 2.12 (0.28), residues: 352 sheet: 0.69 (0.40), residues: 144 loop : -0.45 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 39 HIS 0.004 0.001 HIS B 160 PHE 0.017 0.002 PHE A 224 TYR 0.014 0.002 TYR C 97 ARG 0.002 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 50 time to evaluate : 0.740 Fit side-chains REVERT: A 155 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8679 (m) REVERT: B 106 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7522 (t80) REVERT: C 85 MET cc_start: 0.9033 (tpp) cc_final: 0.8025 (mmt) REVERT: C 88 LEU cc_start: 0.7801 (tt) cc_final: 0.7587 (tt) outliers start: 21 outliers final: 12 residues processed: 69 average time/residue: 0.1533 time to fit residues: 15.4000 Evaluate side-chains 64 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6627 Z= 0.257 Angle : 0.534 6.432 9079 Z= 0.268 Chirality : 0.042 0.165 1043 Planarity : 0.004 0.056 1152 Dihedral : 13.075 179.505 1094 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.24 % Allowed : 18.63 % Favored : 77.12 % 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: 1.20 (0.29), residues: 880 helix: 2.20 (0.28), residues: 352 sheet: 0.66 (0.40), residues: 144 loop : -0.47 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 281 HIS 0.003 0.001 HIS B 160 PHE 0.015 0.001 PHE C 70 TYR 0.010 0.001 TYR C 97 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 53 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 155 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8624 (m) REVERT: B 30 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7323 (pp) REVERT: C 85 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8034 (mmt) REVERT: C 88 LEU cc_start: 0.7828 (tt) cc_final: 0.7615 (tt) outliers start: 23 outliers final: 14 residues processed: 72 average time/residue: 0.1504 time to fit residues: 15.8947 Evaluate side-chains 68 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 51 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 85 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.0020 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 6627 Z= 0.413 Angle : 0.622 6.335 9079 Z= 0.317 Chirality : 0.044 0.179 1043 Planarity : 0.005 0.058 1152 Dihedral : 13.265 178.658 1094 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 5.35 % Allowed : 18.45 % Favored : 76.20 % 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: 0.75 (0.28), residues: 880 helix: 1.78 (0.28), residues: 352 sheet: 0.52 (0.40), residues: 144 loop : -0.72 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 39 HIS 0.004 0.001 HIS B 160 PHE 0.014 0.002 PHE A 224 TYR 0.014 0.002 TYR C 97 ARG 0.002 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 51 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 155 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8702 (m) REVERT: A 285 MET cc_start: 0.7833 (tmm) cc_final: 0.7417 (tmm) REVERT: B 30 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7423 (pp) outliers start: 29 outliers final: 18 residues processed: 77 average time/residue: 0.1416 time to fit residues: 16.0803 Evaluate side-chains 68 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 48 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6627 Z= 0.257 Angle : 0.546 6.471 9079 Z= 0.273 Chirality : 0.042 0.167 1043 Planarity : 0.005 0.055 1152 Dihedral : 12.831 179.729 1094 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.32 % Allowed : 20.30 % Favored : 76.38 % 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: 1.05 (0.29), residues: 880 helix: 2.09 (0.29), residues: 350 sheet: 0.62 (0.40), residues: 144 loop : -0.58 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 281 HIS 0.003 0.001 HIS B 160 PHE 0.009 0.001 PHE B 182 TYR 0.010 0.001 TYR B 98 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 155 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8633 (m) REVERT: B 30 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7339 (pp) REVERT: B 186 ASP cc_start: 0.8343 (p0) cc_final: 0.8130 (p0) outliers start: 18 outliers final: 11 residues processed: 69 average time/residue: 0.1451 time to fit residues: 14.5937 Evaluate side-chains 65 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 0.0040 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 53 optimal weight: 0.0040 chunk 51 optimal weight: 0.0670 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 overall best weight: 0.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6627 Z= 0.138 Angle : 0.499 6.520 9079 Z= 0.246 Chirality : 0.040 0.148 1043 Planarity : 0.004 0.054 1152 Dihedral : 11.923 177.420 1094 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.21 % Allowed : 22.51 % Favored : 75.28 % 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: 1.42 (0.29), residues: 880 helix: 2.34 (0.29), residues: 354 sheet: 0.84 (0.40), residues: 145 loop : -0.36 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 281 HIS 0.001 0.000 HIS A 146 PHE 0.007 0.001 PHE C 40 TYR 0.009 0.001 TYR B 227 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.635 Fit side-chains REVERT: A 101 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7535 (tm-30) REVERT: A 155 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8481 (m) REVERT: A 285 MET cc_start: 0.7830 (tmm) cc_final: 0.7365 (tmm) outliers start: 12 outliers final: 6 residues processed: 71 average time/residue: 0.1549 time to fit residues: 16.0870 Evaluate side-chains 62 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.0980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.0370 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6627 Z= 0.173 Angle : 0.520 6.490 9079 Z= 0.255 Chirality : 0.041 0.157 1043 Planarity : 0.004 0.051 1152 Dihedral : 11.574 176.929 1094 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.40 % Allowed : 21.77 % Favored : 75.83 % 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: 1.42 (0.29), residues: 880 helix: 2.33 (0.29), residues: 354 sheet: 0.83 (0.40), residues: 144 loop : -0.33 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 39 HIS 0.002 0.001 HIS B 160 PHE 0.008 0.001 PHE B 182 TYR 0.010 0.001 TYR B 227 ARG 0.002 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7517 (tm-30) REVERT: A 155 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8502 (m) REVERT: A 285 MET cc_start: 0.7774 (tmm) cc_final: 0.7430 (tmm) REVERT: C 10 SER cc_start: 0.6577 (m) cc_final: 0.6057 (t) outliers start: 13 outliers final: 11 residues processed: 67 average time/residue: 0.1488 time to fit residues: 14.5321 Evaluate side-chains 64 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 0.0570 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6627 Z= 0.216 Angle : 0.529 6.679 9079 Z= 0.261 Chirality : 0.041 0.162 1043 Planarity : 0.004 0.055 1152 Dihedral : 11.349 178.501 1094 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.58 % Allowed : 21.96 % Favored : 75.46 % 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: 1.37 (0.29), residues: 880 helix: 2.32 (0.29), residues: 352 sheet: 0.83 (0.40), residues: 144 loop : -0.39 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 39 HIS 0.002 0.001 HIS B 160 PHE 0.008 0.001 PHE B 182 TYR 0.010 0.001 TYR B 227 ARG 0.003 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7474 (tm-30) REVERT: A 155 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8564 (m) REVERT: A 285 MET cc_start: 0.7806 (tmm) cc_final: 0.7523 (tmm) outliers start: 14 outliers final: 10 residues processed: 64 average time/residue: 0.1494 time to fit residues: 13.9709 Evaluate side-chains 62 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 42 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6627 Z= 0.235 Angle : 0.553 8.741 9079 Z= 0.271 Chirality : 0.041 0.163 1043 Planarity : 0.004 0.049 1152 Dihedral : 11.158 179.813 1094 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.03 % Allowed : 22.32 % Favored : 75.65 % 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: 1.34 (0.29), residues: 880 helix: 2.29 (0.29), residues: 351 sheet: 0.76 (0.40), residues: 145 loop : -0.36 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 39 HIS 0.002 0.001 HIS B 160 PHE 0.009 0.001 PHE C 70 TYR 0.010 0.001 TYR B 227 ARG 0.002 0.000 ARG A 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 155 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8594 (m) REVERT: A 285 MET cc_start: 0.7786 (tmm) cc_final: 0.7263 (tmm) REVERT: C 10 SER cc_start: 0.6708 (m) cc_final: 0.6336 (t) outliers start: 11 outliers final: 10 residues processed: 63 average time/residue: 0.1461 time to fit residues: 13.4774 Evaluate side-chains 63 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 3 optimal weight: 0.0010 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.151515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.140432 restraints weight = 10675.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.138903 restraints weight = 17731.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137983 restraints weight = 17255.809| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6627 Z= 0.198 Angle : 0.531 9.036 9079 Z= 0.261 Chirality : 0.041 0.159 1043 Planarity : 0.004 0.053 1152 Dihedral : 10.888 179.815 1094 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.03 % Allowed : 22.14 % Favored : 75.83 % 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: 1.40 (0.29), residues: 880 helix: 2.34 (0.29), residues: 351 sheet: 0.82 (0.40), residues: 145 loop : -0.35 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 39 HIS 0.002 0.001 HIS B 160 PHE 0.011 0.001 PHE C 70 TYR 0.010 0.001 TYR B 227 ARG 0.002 0.000 ARG A 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1772.12 seconds wall clock time: 33 minutes 17.64 seconds (1997.64 seconds total)