Starting phenix.real_space_refine on Sat Jan 20 02:52:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si6_25138/01_2024/7si6_25138_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si6_25138/01_2024/7si6_25138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si6_25138/01_2024/7si6_25138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si6_25138/01_2024/7si6_25138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si6_25138/01_2024/7si6_25138_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si6_25138/01_2024/7si6_25138_updated.pdb" } resolution = 3.32 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 ------------------------------------------------------------------------------- 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= 1.000 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 49 5.16 5 C 4239 2.51 5 N 1109 2.21 5 O 1202 1.98 5 F 4 1.80 5 H 6910 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 642": "OE1" <-> "OE2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A GLU 902": "OE1" <-> "OE2" Residue "A ASP 1228": "OD1" <-> "OD2" Residue "A ASP 1264": "OD1" <-> "OD2" Residue "A ASP 1309": "OD1" <-> "OD2" Residue "A ASP 1312": "OD1" <-> "OD2" Residue "A TYR 1337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13515 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 13515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 875, 13515 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'peptide': 873, 'undetermined': 2} Link IDs: {'PTRANS': 34, 'TRANS': 838, None: 2} Not linked: pdbres="ARG A1417 " pdbres=" MG A1501 " Not linked: pdbres=" MG A1501 " pdbres="ALF A1502 " Chain breaks: 5 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 6.09, per 1000 atoms: 0.45 Number of scatterers: 13515 At special positions: 0 Unit cell: (90.95, 93.5, 141.1, 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 49 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1202 8.00 N 1109 7.00 C 4239 6.00 H 6910 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS A 499 " 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 Time building additional restraints: 10.51 Conformation dependent library (CDL) restraints added in 1.5 seconds 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 7 sheets defined 48.8% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 497 through 509 Processing helix chain 'A' and resid 536 through 546 Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 641 through 656 Processing helix chain 'A' and resid 659 through 670 Processing helix chain 'A' and resid 691 through 706 Processing helix chain 'A' and resid 708 through 720 Processing helix chain 'A' and resid 726 through 751 Processing helix chain 'A' and resid 761 through 782 Proline residue: A 765 - end of helix Processing helix chain 'A' and resid 788 through 795 Processing helix chain 'A' and resid 888 through 890 No H-bonds generated for 'chain 'A' and resid 888 through 890' Processing helix chain 'A' and resid 892 through 906 Processing helix chain 'A' and resid 913 through 942 removed outlier: 3.528A pdb=" N TYR A 920 " --> pdb=" O LYS A 916 " (cutoff:3.500A) Proline residue: A 923 - end of helix Processing helix chain 'A' and resid 945 through 950 Processing helix chain 'A' and resid 953 through 955 No H-bonds generated for 'chain 'A' and resid 953 through 955' Processing helix chain 'A' and resid 960 through 979 Processing helix chain 'A' and resid 986 through 1002 removed outlier: 3.555A pdb=" N ALA A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1017 removed outlier: 5.035A pdb=" N HIS A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1060 Processing helix chain 'A' and resid 1067 through 1079 Processing helix chain 'A' and resid 1106 through 1111 Processing helix chain 'A' and resid 1157 through 1163 Processing helix chain 'A' and resid 1169 through 1181 Processing helix chain 'A' and resid 1208 through 1217 Processing helix chain 'A' and resid 1230 through 1240 Processing helix chain 'A' and resid 1251 through 1263 Processing helix chain 'A' and resid 1278 through 1283 Processing helix chain 'A' and resid 1295 through 1300 Processing helix chain 'A' and resid 1310 through 1345 removed outlier: 4.316A pdb=" N LEU A1319 " --> pdb=" O SER A1316 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG A1325 " --> pdb=" O ARG A1322 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE A1336 " --> pdb=" O PHE A1333 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N TYR A1337 " --> pdb=" O ALA A1334 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1340 " --> pdb=" O TYR A1337 " (cutoff:3.500A) Proline residue: A1343 - end of helix Processing helix chain 'A' and resid 1358 through 1381 removed outlier: 4.098A pdb=" N SER A1362 " --> pdb=" O PRO A1358 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A1365 " --> pdb=" O GLY A1361 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A1379 " --> pdb=" O SER A1375 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS A1380 " --> pdb=" O SER A1376 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N CYS A1381 " --> pdb=" O LEU A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1393 Processing sheet with id= A, first strand: chain 'A' and resid 549 through 552 Processing sheet with id= B, first strand: chain 'A' and resid 626 through 628 Processing sheet with id= C, first strand: chain 'A' and resid 799 through 803 Processing sheet with id= D, first strand: chain 'A' and resid 827 through 830 removed outlier: 7.138A pdb=" N ASP A 839 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 861 through 863 Processing sheet with id= F, first strand: chain 'A' and resid 1004 through 1006 removed outlier: 3.708A pdb=" N ILE A1290 " --> pdb=" O GLY A1272 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA A1020 " --> pdb=" O ALA A1269 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL A1271 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N MET A1022 " --> pdb=" O VAL A1271 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASP A1221 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N PHE A1023 " --> pdb=" O ASP A1221 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL A1223 " --> pdb=" O PHE A1023 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS A1244 " --> pdb=" O LEU A1224 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER A1407 " --> pdb=" O VAL A1245 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA A1247 " --> pdb=" O SER A1407 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N HIS A1409 " --> pdb=" O ALA A1247 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1090 through 1094 removed outlier: 3.544A pdb=" N GLY A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE A1190 " --> pdb=" O LEU A1194 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU A1194 " --> pdb=" O ILE A1190 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG A1038 " --> pdb=" O ALA A1199 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA A1201 " --> pdb=" O VAL A1036 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL A1036 " --> pdb=" O ALA A1201 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 948 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: 5.16 Time building geometry restraints manager: 10.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6895 1.04 - 1.23: 78 1.23 - 1.43: 2504 1.43 - 1.62: 4050 1.62 - 1.82: 87 Bond restraints: 13614 Sorted by residual: bond pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" F3 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" F4 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.686 1.785 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" CA VAL A 686 " pdb=" CB VAL A 686 " ideal model delta sigma weight residual 1.546 1.538 0.008 8.80e-03 1.29e+04 9.14e-01 ... (remaining 13609 not shown) Histogram of bond angle deviations from ideal: 89.92 - 107.92: 1803 107.92 - 125.92: 22895 125.92 - 143.92: 110 143.92 - 161.92: 0 161.92 - 179.92: 2 Bond angle restraints: 24810 Sorted by residual: angle pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " pdb=" F2 ALF A1502 " ideal model delta sigma weight residual 108.68 179.87 -71.19 3.00e+00 1.11e-01 5.63e+02 angle pdb=" F3 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 109.63 179.92 -70.29 3.00e+00 1.11e-01 5.49e+02 angle pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 110.21 90.05 20.16 3.00e+00 1.11e-01 4.52e+01 angle pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " pdb=" F3 ALF A1502 " ideal model delta sigma weight residual 109.69 89.99 19.70 3.00e+00 1.11e-01 4.31e+01 angle pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " pdb=" F3 ALF A1502 " ideal model delta sigma weight residual 109.59 89.92 19.67 3.00e+00 1.11e-01 4.30e+01 ... (remaining 24805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 5694 17.01 - 34.02: 412 34.02 - 51.03: 71 51.03 - 68.04: 10 68.04 - 85.05: 12 Dihedral angle restraints: 6199 sinusoidal: 3401 harmonic: 2798 Sorted by residual: dihedral pdb=" CB CYS A 496 " pdb=" SG CYS A 496 " pdb=" SG CYS A 499 " pdb=" CB CYS A 499 " ideal model delta sinusoidal sigma weight residual 93.00 119.14 -26.14 1 1.00e+01 1.00e-02 9.82e+00 dihedral pdb=" CB MET A 993 " pdb=" CG MET A 993 " pdb=" SD MET A 993 " pdb=" CE MET A 993 " ideal model delta sinusoidal sigma weight residual 60.00 118.69 -58.69 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB LYS A1234 " pdb=" CG LYS A1234 " pdb=" CD LYS A1234 " pdb=" CE LYS A1234 " ideal model delta sinusoidal sigma weight residual 60.00 112.40 -52.40 3 1.50e+01 4.44e-03 9.11e+00 ... (remaining 6196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 716 0.027 - 0.055: 201 0.055 - 0.082: 104 0.082 - 0.109: 65 0.109 - 0.136: 31 Chirality restraints: 1117 Sorted by residual: chirality pdb=" CA VAL A1094 " pdb=" N VAL A1094 " pdb=" C VAL A1094 " pdb=" CB VAL A1094 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA VAL A1152 " pdb=" N VAL A1152 " pdb=" C VAL A1152 " pdb=" CB VAL A1152 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA VAL A 686 " pdb=" N VAL A 686 " pdb=" C VAL A 686 " pdb=" CB VAL A 686 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 1114 not shown) Planarity restraints: 1963 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 951 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 952 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 952 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 952 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1342 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A1343 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A1343 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1343 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1321 " -0.006 2.00e-02 2.50e+03 1.22e-02 1.48e+00 pdb=" C LYS A1321 " 0.021 2.00e-02 2.50e+03 pdb=" O LYS A1321 " -0.008 2.00e-02 2.50e+03 pdb=" N ARG A1322 " -0.007 2.00e-02 2.50e+03 ... (remaining 1960 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1039 2.23 - 2.82: 30825 2.82 - 3.41: 35419 3.41 - 4.01: 47345 4.01 - 4.60: 72950 Nonbonded interactions: 187578 Sorted by model distance: nonbonded pdb=" OD1 ASP A 839 " pdb=" H ALA A 871 " model vdw 1.637 1.850 nonbonded pdb=" O LEU A1012 " pdb=" HG SER A1320 " model vdw 1.650 1.850 nonbonded pdb=" H VAL A 803 " pdb=" O ILE A 827 " model vdw 1.696 1.850 nonbonded pdb=" HZ2 LYS A1254 " pdb=" OD1 ASP A1277 " model vdw 1.699 1.850 nonbonded pdb=" O ASP A1312 " pdb=" H SER A1316 " model vdw 1.715 1.850 ... (remaining 187573 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 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: 0.200 Extract box with map and model: 1.340 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 44.890 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 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 : 0.003 0.101 6704 Z= 0.210 Angle : 1.218 71.188 9081 Z= 0.452 Chirality : 0.042 0.136 1117 Planarity : 0.003 0.039 1130 Dihedral : 13.578 85.051 2459 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 2.88 (0.29), residues: 861 helix: 2.71 (0.24), residues: 464 sheet: 1.07 (0.46), residues: 128 loop : 1.01 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 936 HIS 0.002 0.000 HIS A 721 PHE 0.011 0.001 PHE A 696 TYR 0.006 0.001 TYR A 710 ARG 0.007 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 814 GLU cc_start: 0.6837 (mp0) cc_final: 0.6605 (mp0) REVERT: A 815 GLU cc_start: 0.6773 (tt0) cc_final: 0.6510 (tt0) REVERT: A 1217 SER cc_start: 0.8208 (m) cc_final: 0.7973 (m) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.3255 time to fit residues: 62.5652 Evaluate side-chains 108 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.0616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6704 Z= 0.126 Angle : 0.818 30.259 9081 Z= 0.320 Chirality : 0.042 0.139 1117 Planarity : 0.003 0.029 1130 Dihedral : 3.233 12.389 913 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.28 % Allowed : 4.14 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.29), residues: 861 helix: 2.71 (0.24), residues: 464 sheet: 1.06 (0.45), residues: 127 loop : 0.93 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 936 HIS 0.002 0.000 HIS A 721 PHE 0.018 0.001 PHE A 944 TYR 0.004 0.001 TYR A 712 ARG 0.003 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 874 ILE cc_start: 0.8285 (mm) cc_final: 0.8061 (mm) REVERT: A 1217 SER cc_start: 0.8226 (m) cc_final: 0.8014 (m) outliers start: 2 outliers final: 1 residues processed: 112 average time/residue: 0.3274 time to fit residues: 52.1233 Evaluate side-chains 106 residues out of total 727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 0.0770 chunk 70 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1090 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: