Starting phenix.real_space_refine on Fri Feb 16 18:54:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieo_35388/02_2024/8ieo_35388_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieo_35388/02_2024/8ieo_35388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieo_35388/02_2024/8ieo_35388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieo_35388/02_2024/8ieo_35388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieo_35388/02_2024/8ieo_35388_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieo_35388/02_2024/8ieo_35388_trim_updated.pdb" } resolution = 3.78 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= 0.031 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 53 5.16 5 C 5156 2.51 5 N 1377 2.21 5 O 1408 1.98 5 F 4 1.80 5 H 8260 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 254": "OD1" <-> "OD2" Residue "P TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 316": "OD1" <-> "OD2" Residue "P GLU 520": "OE1" <-> "OE2" Residue "P ASP 521": "OD1" <-> "OD2" Residue "P GLU 617": "OE1" <-> "OE2" Residue "P GLU 650": "OE1" <-> "OE2" Residue "P GLU 771": "OE1" <-> "OE2" Residue "P PHE 945": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 952": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 967": "OD1" <-> "OD2" Residue "P TYR 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 1128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 1139": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16260 Number of models: 1 Model: "" Number of chains: 2 Chain: "P" Number of atoms: 16240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 16240 Classifications: {'peptide': 1031} Link IDs: {'CIS': 1, 'PTRANS': 68, 'TRANS': 961} Chain breaks: 7 Chain: "P" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {' MG': 1, 'ALF': 1, 'SPM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.64, per 1000 atoms: 0.47 Number of scatterers: 16260 At special positions: 0 Unit cell: (89.79, 119.355, 129.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 53 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1408 8.00 N 1377 7.00 C 5156 6.00 H 8260 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=0, symmetry=0 Time building additional restraints: 13.24 Conformation dependent library (CDL) restraints added in 1.8 seconds 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 6 sheets defined 38.4% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'P' and resid 50 through 59 removed outlier: 3.860A pdb=" N GLY P 59 " --> pdb=" O TRP P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 64 No H-bonds generated for 'chain 'P' and resid 62 through 64' Processing helix chain 'P' and resid 70 through 74 Processing helix chain 'P' and resid 188 through 191 No H-bonds generated for 'chain 'P' and resid 188 through 191' Processing helix chain 'P' and resid 209 through 216 Processing helix chain 'P' and resid 239 through 253 removed outlier: 4.117A pdb=" N PHE P 243 " --> pdb=" O PRO P 239 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLN P 244 " --> pdb=" O TYR P 240 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA P 245 " --> pdb=" O TYR P 241 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU P 252 " --> pdb=" O ILE P 248 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA P 253 " --> pdb=" O ALA P 249 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 288 removed outlier: 3.614A pdb=" N CYS P 262 " --> pdb=" O TRP P 258 " (cutoff:3.500A) Processing helix chain 'P' and resid 399 through 401 No H-bonds generated for 'chain 'P' and resid 399 through 401' Processing helix chain 'P' and resid 403 through 409 removed outlier: 3.506A pdb=" N LEU P 407 " --> pdb=" O ALA P 403 " (cutoff:3.500A) Processing helix chain 'P' and resid 422 through 449 removed outlier: 3.511A pdb=" N GLY P 439 " --> pdb=" O LEU P 435 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE P 441 " --> pdb=" O LEU P 437 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR P 442 " --> pdb=" O LEU P 438 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE P 444 " --> pdb=" O THR P 440 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE P 446 " --> pdb=" O TYR P 442 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LEU P 447 " --> pdb=" O SER P 443 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR P 448 " --> pdb=" O ILE P 444 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG P 449 " --> pdb=" O PHE P 445 " (cutoff:3.500A) Processing helix chain 'P' and resid 457 through 466 Processing helix chain 'P' and resid 473 through 490 removed outlier: 4.074A pdb=" N MET P 477 " --> pdb=" O LEU P 473 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR P 478 " --> pdb=" O PRO P 474 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL P 479 " --> pdb=" O ALA P 475 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N CYS P 480 " --> pdb=" O ALA P 476 " (cutoff:3.500A) Processing helix chain 'P' and resid 550 through 557 Processing helix chain 'P' and resid 572 through 580 Processing helix chain 'P' and resid 657 through 663 Processing helix chain 'P' and resid 675 through 682 Processing helix chain 'P' and resid 697 through 706 Processing helix chain 'P' and resid 730 through 742 removed outlier: 3.511A pdb=" N THR P 733 " --> pdb=" O PRO P 730 " (cutoff:3.500A) Proline residue: P 734 - end of helix Processing helix chain 'P' and resid 754 through 764 removed outlier: 3.520A pdb=" N THR P 759 " --> pdb=" O GLN P 755 " (cutoff:3.500A) Processing helix chain 'P' and resid 827 through 832 Processing helix chain 'P' and resid 841 through 845 removed outlier: 3.903A pdb=" N LEU P 845 " --> pdb=" O LEU P 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 841 through 845' Processing helix chain 'P' and resid 858 through 869 removed outlier: 4.315A pdb=" N LEU P 869 " --> pdb=" O GLU P 865 " (cutoff:3.500A) Processing helix chain 'P' and resid 883 through 888 Processing helix chain 'P' and resid 899 through 903 Processing helix chain 'P' and resid 916 through 953 removed outlier: 3.709A pdb=" N THR P 953 " --> pdb=" O LEU P 949 " (cutoff:3.500A) Processing helix chain 'P' and resid 961 through 975 removed outlier: 3.805A pdb=" N ILE P 970 " --> pdb=" O ILE P 966 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR P 971 " --> pdb=" O ASP P 967 " (cutoff:3.500A) Processing helix chain 'P' and resid 999 through 1025 Processing helix chain 'P' and resid 1045 through 1062 removed outlier: 3.519A pdb=" N VAL P1049 " --> pdb=" O TYR P1045 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL P1050 " --> pdb=" O GLU P1046 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU P1053 " --> pdb=" O VAL P1049 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE P1056 " --> pdb=" O SER P1052 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN P1057 " --> pdb=" O LEU P1053 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR P1058 " --> pdb=" O SER P1054 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU P1059 " --> pdb=" O SER P1055 " (cutoff:3.500A) Processing helix chain 'P' and resid 1080 through 1095 removed outlier: 3.979A pdb=" N ALA P1084 " --> pdb=" O PRO P1080 " (cutoff:3.500A) Processing helix chain 'P' and resid 1116 through 1139 Processing helix chain 'P' and resid 1142 through 1147 removed outlier: 4.044A pdb=" N LEU P1146 " --> pdb=" O LEU P1142 " (cutoff:3.500A) Processing helix chain 'P' and resid 1159 through 1167 removed outlier: 3.503A pdb=" N ARG P1164 " --> pdb=" O LYS P1160 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'P' and resid 174 through 176 removed outlier: 4.374A pdb=" N ILE P 174 " --> pdb=" O TYR P 183 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR P 183 " --> pdb=" O ILE P 174 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE P 176 " --> pdb=" O ALA P 181 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA P 181 " --> pdb=" O ILE P 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'P' and resid 294 through 298 removed outlier: 3.931A pdb=" N VAL P 297 " --> pdb=" O GLU P 305 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU P 305 " --> pdb=" O VAL P 297 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'P' and resid 338 through 340 removed outlier: 3.953A pdb=" N LYS P 354 " --> pdb=" O CYS P 338 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL P 340 " --> pdb=" O VAL P 352 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL P 352 " --> pdb=" O VAL P 340 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'P' and resid 509 through 512 removed outlier: 7.105A pdb=" N ARG P 745 " --> pdb=" O VAL P 510 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N PHE P 512 " --> pdb=" O ARG P 745 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL P 747 " --> pdb=" O PHE P 512 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'P' and resid 689 through 694 removed outlier: 3.569A pdb=" N GLY P 655 " --> pdb=" O ALA P 689 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU P 650 " --> pdb=" O VAL P 641 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL P 641 " --> pdb=" O GLU P 650 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL P 640 " --> pdb=" O HIS P 626 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS P 626 " --> pdb=" O VAL P 640 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'P' and resid 874 through 877 removed outlier: 6.920A pdb=" N VAL P 891 " --> pdb=" O MET P 875 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N GLY P 877 " --> pdb=" O VAL P 891 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE P 893 " --> pdb=" O GLY P 877 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 244 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.57 Time building geometry restraints manager: 13.81 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: 8233 1.03 - 1.23: 28 1.23 - 1.42: 3247 1.42 - 1.62: 4839 1.62 - 1.81: 83 Bond restraints: 16430 Sorted by residual: bond pdb=" F1 ALF P1201 " pdb="AL ALF P1201 " ideal model delta sigma weight residual 1.684 1.800 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" F2 ALF P1201 " pdb="AL ALF P1201 " ideal model delta sigma weight residual 1.685 1.800 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" F4 ALF P1201 " pdb="AL ALF P1201 " ideal model delta sigma weight residual 1.686 1.801 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" F3 ALF P1201 " pdb="AL ALF P1201 " ideal model delta sigma weight residual 1.685 1.799 -0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" N TRP P 608 " pdb=" CA TRP P 608 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 ... (remaining 16425 not shown) Histogram of bond angle deviations from ideal: 89.97 - 107.97: 2825 107.97 - 125.97: 26830 125.97 - 143.98: 181 143.98 - 161.98: 0 161.98 - 179.98: 2 Bond angle restraints: 29838 Sorted by residual: angle pdb=" F1 ALF P1201 " pdb="AL ALF P1201 " pdb=" F2 ALF P1201 " ideal model delta sigma weight residual 108.68 179.96 -71.28 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F3 ALF P1201 " pdb="AL ALF P1201 " pdb=" F4 ALF P1201 " ideal model delta sigma weight residual 109.63 179.98 -70.35 3.00e+00 1.11e-01 5.50e+02 angle pdb=" N PRO P 621 " pdb=" CD PRO P 621 " pdb=" CG PRO P 621 " ideal model delta sigma weight residual 103.20 92.92 10.28 1.50e+00 4.44e-01 4.70e+01 angle pdb=" F2 ALF P1201 " pdb="AL ALF P1201 " pdb=" F4 ALF P1201 " ideal model delta sigma weight residual 110.21 89.99 20.22 3.00e+00 1.11e-01 4.54e+01 angle pdb=" F1 ALF P1201 " pdb="AL ALF P1201 " pdb=" F3 ALF P1201 " ideal model delta sigma weight residual 109.69 90.03 19.66 3.00e+00 1.11e-01 4.29e+01 ... (remaining 29833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6857 17.87 - 35.74: 600 35.74 - 53.61: 192 53.61 - 71.48: 55 71.48 - 89.35: 15 Dihedral angle restraints: 7719 sinusoidal: 4299 harmonic: 3420 Sorted by residual: dihedral pdb=" CB GLU P 139 " pdb=" CG GLU P 139 " pdb=" CD GLU P 139 " pdb=" OE1 GLU P 139 " ideal model delta sinusoidal sigma weight residual 0.00 87.16 -87.16 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" N PRO P 621 " pdb=" CG PRO P 621 " pdb=" CD PRO P 621 " pdb=" CB PRO P 621 " ideal model delta sinusoidal sigma weight residual 30.00 70.06 -40.06 1 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CG ARG P 636 " pdb=" CD ARG P 636 " pdb=" NE ARG P 636 " pdb=" CZ ARG P 636 " ideal model delta sinusoidal sigma weight residual 90.00 131.96 -41.96 2 1.50e+01 4.44e-03 9.54e+00 ... (remaining 7716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 899 0.029 - 0.058: 261 0.058 - 0.087: 84 0.087 - 0.116: 62 0.116 - 0.145: 11 Chirality restraints: 1317 Sorted by residual: chirality pdb=" CA VAL P 767 " pdb=" N VAL P 767 " pdb=" C VAL P 767 " pdb=" CB VAL P 767 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE P 350 " pdb=" N ILE P 350 " pdb=" C ILE P 350 " pdb=" CB ILE P 350 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA VAL P 620 " pdb=" N VAL P 620 " pdb=" C VAL P 620 " pdb=" CB VAL P 620 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1314 not shown) Planarity restraints: 2353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL P1079 " -0.077 5.00e-02 4.00e+02 1.18e-01 2.21e+01 pdb=" N PRO P1080 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO P1080 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO P1080 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG P1073 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO P1074 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO P1074 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO P1074 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN P1026 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO P1027 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO P1027 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO P1027 " -0.023 5.00e-02 4.00e+02 ... (remaining 2350 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1996 2.25 - 2.83: 35405 2.83 - 3.42: 38970 3.42 - 4.01: 50294 4.01 - 4.60: 76673 Nonbonded interactions: 203338 Sorted by model distance: nonbonded pdb="HH12 ARG P 745 " pdb=" O GLY P 848 " model vdw 1.657 1.850 nonbonded pdb=" HZ3 LYS P 514 " pdb=" OD2 ASP P 752 " model vdw 1.681 1.850 nonbonded pdb=" O LYS P 514 " pdb=" HG1 THR P 519 " model vdw 1.701 1.850 nonbonded pdb=" O MET P 477 " pdb=" HG1 THR P 481 " model vdw 1.709 1.850 nonbonded pdb=" OE2 GLU P 337 " pdb=" HE ARG P 384 " model vdw 1.711 1.850 ... (remaining 203333 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.140 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 54.900 Find NCS groups from input model: 0.340 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 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 0.116 8170 Z= 0.241 Angle : 1.197 71.275 11117 Z= 0.471 Chirality : 0.037 0.145 1317 Planarity : 0.004 0.118 1397 Dihedral : 15.040 89.347 3014 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.11 % Allowed : 17.69 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.87 (0.28), residues: 1015 helix: 3.04 (0.29), residues: 386 sheet: -0.34 (0.71), residues: 51 loop : -1.16 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP P 100 HIS 0.006 0.000 HIS P 413 PHE 0.009 0.000 PHE P1081 TYR 0.009 0.000 TYR P 183 ARG 0.004 0.000 ARG P 980 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.3672 time to fit residues: 55.3823 Evaluate side-chains 101 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 207 GLN P 244 GLN P 944 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8170 Z= 0.230 Angle : 0.861 33.103 11117 Z= 0.355 Chirality : 0.040 0.138 1317 Planarity : 0.004 0.082 1397 Dihedral : 3.416 45.224 1128 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.13 % Allowed : 17.35 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.09 (0.27), residues: 1015 helix: 2.24 (0.28), residues: 393 sheet: -0.90 (0.63), residues: 61 loop : -1.54 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 251 HIS 0.006 0.001 HIS P 413 PHE 0.012 0.001 PHE P1081 TYR 0.015 0.001 TYR P 259 ARG 0.004 0.000 ARG P 740 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.735 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: P 213 LYS cc_start: 0.7602 (tptp) cc_final: 0.6864 (mptt) REVERT: P 239 PRO cc_start: 0.6043 (Cg_exo) cc_final: 0.5824 (Cg_endo) outliers start: 10 outliers final: 5 residues processed: 121 average time/residue: 0.3648 time to fit residues: 63.2291 Evaluate side-chains 110 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 513 ASP Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 849 THR Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8170 Z= 0.230 Angle : 0.844 32.226 11117 Z= 0.349 Chirality : 0.039 0.150 1317 Planarity : 0.004 0.050 1397 Dihedral : 3.700 48.762 1128 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.25 % Allowed : 16.78 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.12 (0.27), residues: 1015 helix: 2.17 (0.28), residues: 396 sheet: -0.81 (0.66), residues: 62 loop : -1.81 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 100 HIS 0.007 0.001 HIS P 772 PHE 0.014 0.001 PHE P1081 TYR 0.026 0.001 TYR P 871 ARG 0.002 0.000 ARG P1034 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 239 PRO cc_start: 0.6235 (Cg_exo) cc_final: 0.6018 (Cg_endo) REVERT: P 288 MET cc_start: 0.5321 (ttt) cc_final: 0.5085 (ttt) REVERT: P 311 GLU cc_start: 0.7651 (mp0) cc_final: 0.7254 (mt-10) REVERT: P 771 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7569 (tp30) REVERT: P 946 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8140 (tt) outliers start: 11 outliers final: 6 residues processed: 121 average time/residue: 0.4277 time to fit residues: 71.9671 Evaluate side-chains 107 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 513 ASP Chi-restraints excluded: chain P residue 771 GLU Chi-restraints excluded: chain P residue 844 VAL Chi-restraints excluded: chain P residue 849 THR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 1095 LEU Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 10 optimal weight: 0.0470 chunk 44 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 94 optimal weight: 0.0980 chunk 99 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8170 Z= 0.145 Angle : 0.793 29.766 11117 Z= 0.312 Chirality : 0.037 0.129 1317 Planarity : 0.004 0.066 1397 Dihedral : 3.587 55.916 1128 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.02 % Allowed : 17.57 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.10 (0.28), residues: 1015 helix: 2.34 (0.28), residues: 396 sheet: -0.67 (0.68), residues: 62 loop : -1.67 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 100 HIS 0.005 0.001 HIS P 497 PHE 0.011 0.001 PHE P1081 TYR 0.014 0.001 TYR P 871 ARG 0.004 0.000 ARG P1109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 240 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.7030 (t80) REVERT: P 288 MET cc_start: 0.5304 (ttt) cc_final: 0.5026 (ttt) REVERT: P 311 GLU cc_start: 0.7634 (mp0) cc_final: 0.7266 (mt-10) REVERT: P 771 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7546 (tp30) REVERT: P 963 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8131 (t80) outliers start: 9 outliers final: 5 residues processed: 102 average time/residue: 0.3956 time to fit residues: 57.5225 Evaluate side-chains 100 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 240 TYR Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 513 ASP Chi-restraints excluded: chain P residue 771 GLU Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 963 PHE Chi-restraints excluded: chain P residue 1095 LEU Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8170 Z= 0.226 Angle : 0.844 31.307 11117 Z= 0.351 Chirality : 0.040 0.134 1317 Planarity : 0.004 0.055 1397 Dihedral : 4.109 57.495 1128 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.38 % Allowed : 16.67 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.49 (0.27), residues: 1015 helix: 1.80 (0.28), residues: 404 sheet: -0.90 (0.61), residues: 77 loop : -2.06 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 55 HIS 0.006 0.001 HIS P 413 PHE 0.016 0.002 PHE P 906 TYR 0.035 0.002 TYR P 871 ARG 0.004 0.000 ARG P1158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 240 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.6922 (t80) REVERT: P 288 MET cc_start: 0.5643 (ttt) cc_final: 0.5285 (ttt) REVERT: P 311 GLU cc_start: 0.7619 (mp0) cc_final: 0.7418 (mt-10) REVERT: P 771 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: P 843 LYS cc_start: 0.6969 (tttt) cc_final: 0.6011 (tttm) REVERT: P 871 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.6499 (t80) REVERT: P 946 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8088 (tt) REVERT: P 963 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8286 (t80) REVERT: P 981 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7881 (m) REVERT: P 991 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7739 (mtm110) outliers start: 21 outliers final: 9 residues processed: 105 average time/residue: 0.3970 time to fit residues: 59.0358 Evaluate side-chains 95 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 240 TYR Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 467 VAL Chi-restraints excluded: chain P residue 513 ASP Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 771 GLU Chi-restraints excluded: chain P residue 849 THR Chi-restraints excluded: chain P residue 871 TYR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 963 PHE Chi-restraints excluded: chain P residue 981 THR Chi-restraints excluded: chain P residue 1095 LEU Chi-restraints excluded: chain P residue 1096 VAL Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.0770 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 0.0170 chunk 24 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 46 optimal weight: 0.0170 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 overall best weight: 0.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 207 GLN P 726 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8170 Z= 0.149 Angle : 0.801 29.766 11117 Z= 0.318 Chirality : 0.038 0.129 1317 Planarity : 0.004 0.067 1397 Dihedral : 3.871 57.724 1128 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.04 % Allowed : 17.57 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.23 (0.28), residues: 1015 helix: 2.01 (0.28), residues: 406 sheet: -0.76 (0.63), residues: 77 loop : -1.93 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 251 HIS 0.006 0.001 HIS P 413 PHE 0.012 0.001 PHE P1081 TYR 0.020 0.001 TYR P 871 ARG 0.002 0.000 ARG P 384 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 1.278 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: P 240 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7016 (t80) REVERT: P 288 MET cc_start: 0.5554 (ttt) cc_final: 0.5192 (ttt) REVERT: P 771 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: P 843 LYS cc_start: 0.6803 (tttt) cc_final: 0.5863 (tttm) REVERT: P 871 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.6164 (t80) REVERT: P 946 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8067 (tt) REVERT: P 963 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8292 (t80) REVERT: P 991 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7711 (mtm110) outliers start: 18 outliers final: 9 residues processed: 94 average time/residue: 0.4411 time to fit residues: 58.0648 Evaluate side-chains 93 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 207 GLN Chi-restraints excluded: chain P residue 240 TYR Chi-restraints excluded: chain P residue 241 TYR Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 467 VAL Chi-restraints excluded: chain P residue 513 ASP Chi-restraints excluded: chain P residue 726 ASN Chi-restraints excluded: chain P residue 771 GLU Chi-restraints excluded: chain P residue 871 TYR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 963 PHE Chi-restraints excluded: chain P residue 1095 LEU Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 99 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8170 Z= 0.180 Angle : 0.807 30.133 11117 Z= 0.323 Chirality : 0.038 0.130 1317 Planarity : 0.004 0.062 1397 Dihedral : 3.933 56.814 1128 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.59 % Allowed : 18.59 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.29 (0.27), residues: 1015 helix: 1.93 (0.28), residues: 412 sheet: -0.78 (0.63), residues: 77 loop : -1.98 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 55 HIS 0.006 0.001 HIS P 413 PHE 0.012 0.001 PHE P1081 TYR 0.022 0.001 TYR P 871 ARG 0.003 0.000 ARG P 725 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 1.417 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: P 288 MET cc_start: 0.5686 (ttt) cc_final: 0.5327 (ttt) REVERT: P 771 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: P 843 LYS cc_start: 0.6628 (tttt) cc_final: 0.5900 (tttm) REVERT: P 871 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.6296 (t80) REVERT: P 946 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8091 (tt) REVERT: P 963 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8341 (t80) REVERT: P 991 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7714 (mtm110) outliers start: 14 outliers final: 9 residues processed: 91 average time/residue: 0.3881 time to fit residues: 50.3466 Evaluate side-chains 92 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 241 TYR Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 513 ASP Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 518 LEU Chi-restraints excluded: chain P residue 555 LEU Chi-restraints excluded: chain P residue 771 GLU Chi-restraints excluded: chain P residue 871 TYR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 963 PHE Chi-restraints excluded: chain P residue 1095 LEU Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 90 optimal weight: 0.3980 chunk 95 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 207 GLN P 777 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8170 Z= 0.179 Angle : 0.810 29.991 11117 Z= 0.325 Chirality : 0.038 0.129 1317 Planarity : 0.004 0.069 1397 Dihedral : 3.941 55.959 1128 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.93 % Allowed : 18.37 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: -0.25 (0.28), residues: 1015 helix: 1.94 (0.28), residues: 415 sheet: -0.65 (0.62), residues: 80 loop : -1.97 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 55 HIS 0.006 0.001 HIS P 413 PHE 0.012 0.001 PHE P1081 TYR 0.023 0.001 TYR P 871 ARG 0.003 0.000 ARG P 384 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 1.235 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: P 288 MET cc_start: 0.5805 (ttt) cc_final: 0.5415 (ttt) REVERT: P 771 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: P 843 LYS cc_start: 0.6728 (tttt) cc_final: 0.6048 (tttm) REVERT: P 865 GLU cc_start: 0.8109 (tp30) cc_final: 0.7873 (mm-30) REVERT: P 871 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.6025 (t80) REVERT: P 946 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8007 (tt) REVERT: P 963 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8391 (t80) REVERT: P 981 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.8042 (m) outliers start: 17 outliers final: 9 residues processed: 101 average time/residue: 0.3835 time to fit residues: 55.3159 Evaluate side-chains 95 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 241 TYR Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 401 CYS Chi-restraints excluded: chain P residue 513 ASP Chi-restraints excluded: chain P residue 518 LEU Chi-restraints excluded: chain P residue 771 GLU Chi-restraints excluded: chain P residue 871 TYR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 963 PHE Chi-restraints excluded: chain P residue 981 THR Chi-restraints excluded: chain P residue 1095 LEU Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.1980 chunk 60 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P1057 GLN P1127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8170 Z= 0.185 Angle : 0.817 29.979 11117 Z= 0.327 Chirality : 0.038 0.130 1317 Planarity : 0.004 0.064 1397 Dihedral : 3.972 55.784 1128 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.70 % Allowed : 18.59 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.27 (0.28), residues: 1015 helix: 1.97 (0.28), residues: 412 sheet: -0.65 (0.64), residues: 80 loop : -2.01 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 251 HIS 0.007 0.001 HIS P 772 PHE 0.011 0.001 PHE P1081 TYR 0.024 0.001 TYR P 871 ARG 0.003 0.000 ARG P 384 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 1.160 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: P 288 MET cc_start: 0.5853 (ttt) cc_final: 0.5438 (ttp) REVERT: P 771 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: P 843 LYS cc_start: 0.6733 (tttt) cc_final: 0.6052 (tttm) REVERT: P 865 GLU cc_start: 0.8167 (tp30) cc_final: 0.7919 (mm-30) REVERT: P 871 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.5932 (t80) REVERT: P 946 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7961 (tt) REVERT: P 963 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8404 (t80) REVERT: P 981 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8122 (m) outliers start: 15 outliers final: 9 residues processed: 97 average time/residue: 0.3834 time to fit residues: 53.1741 Evaluate side-chains 95 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 401 CYS Chi-restraints excluded: chain P residue 467 VAL Chi-restraints excluded: chain P residue 513 ASP Chi-restraints excluded: chain P residue 517 THR Chi-restraints excluded: chain P residue 518 LEU Chi-restraints excluded: chain P residue 771 GLU Chi-restraints excluded: chain P residue 849 THR Chi-restraints excluded: chain P residue 871 TYR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 963 PHE Chi-restraints excluded: chain P residue 981 THR Chi-restraints excluded: chain P residue 1095 LEU Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.0060 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 102 optimal weight: 0.3980 chunk 94 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 626 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8170 Z= 0.168 Angle : 0.805 29.820 11117 Z= 0.320 Chirality : 0.038 0.130 1317 Planarity : 0.004 0.072 1397 Dihedral : 3.940 55.438 1128 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.36 % Allowed : 18.93 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: -0.20 (0.28), residues: 1015 helix: 2.02 (0.28), residues: 412 sheet: -0.23 (0.71), residues: 68 loop : -2.00 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 55 HIS 0.005 0.001 HIS P 413 PHE 0.011 0.001 PHE P1081 TYR 0.022 0.001 TYR P 871 ARG 0.002 0.000 ARG P 384 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 1.281 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: P 288 MET cc_start: 0.5852 (ttt) cc_final: 0.5415 (ttp) REVERT: P 771 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: P 843 LYS cc_start: 0.6771 (tttt) cc_final: 0.6057 (tttm) REVERT: P 865 GLU cc_start: 0.8148 (tp30) cc_final: 0.7897 (mm-30) REVERT: P 946 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7940 (tt) REVERT: P 963 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8400 (t80) outliers start: 12 outliers final: 8 residues processed: 93 average time/residue: 0.4131 time to fit residues: 55.3887 Evaluate side-chains 92 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 401 CYS Chi-restraints excluded: chain P residue 513 ASP Chi-restraints excluded: chain P residue 518 LEU Chi-restraints excluded: chain P residue 771 GLU Chi-restraints excluded: chain P residue 849 THR Chi-restraints excluded: chain P residue 871 TYR Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 946 ILE Chi-restraints excluded: chain P residue 963 PHE Chi-restraints excluded: chain P residue 1095 LEU Chi-restraints excluded: chain P residue 1126 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 0.0030 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.191294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.145838 restraints weight = 31640.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.145310 restraints weight = 26563.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.147314 restraints weight = 20797.355| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8170 Z= 0.146 Angle : 0.799 29.846 11117 Z= 0.315 Chirality : 0.037 0.131 1317 Planarity : 0.004 0.064 1397 Dihedral : 3.838 55.163 1128 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.25 % Allowed : 18.82 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.07 (0.28), residues: 1015 helix: 2.11 (0.28), residues: 414 sheet: -0.26 (0.67), residues: 73 loop : -1.93 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 251 HIS 0.005 0.001 HIS P 413 PHE 0.008 0.001 PHE P1081 TYR 0.016 0.001 TYR P 871 ARG 0.003 0.000 ARG P 384 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3536.02 seconds wall clock time: 63 minutes 34.74 seconds (3814.74 seconds total)