Starting phenix.real_space_refine on Thu Sep 26 07:48:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s2e_10088/09_2024/6s2e_10088.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s2e_10088/09_2024/6s2e_10088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s2e_10088/09_2024/6s2e_10088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s2e_10088/09_2024/6s2e_10088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s2e_10088/09_2024/6s2e_10088.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s2e_10088/09_2024/6s2e_10088.cif" } resolution = 4.2 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 68 5.16 5 C 7984 2.51 5 N 2079 2.21 5 O 2324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12459 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 8154 Classifications: {'peptide': 1006} Link IDs: {'PCIS': 2, 'PTRANS': 46, 'TRANS': 957} Chain breaks: 6 Chain: "D" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1031 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 225 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "B" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3041 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4761 SG CYS A 677 74.994 35.130 17.630 1.00143.72 S ATOM 4690 SG CYS A 668 72.088 29.439 18.791 1.00135.31 S ATOM 4963 SG CYS A 763 75.014 33.159 23.280 1.00114.07 S ATOM 4673 SG CYS A 665 77.473 29.916 18.710 1.00136.78 S Time building chain proxies: 7.51, per 1000 atoms: 0.60 Number of scatterers: 12459 At special positions: 0 Unit cell: (126.557, 128.684, 103.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 68 16.00 O 2324 8.00 N 2079 7.00 C 7984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.87 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1401 " pdb="FE1 SF4 A1401 " - pdb=" SG CYS A 677 " pdb="FE4 SF4 A1401 " - pdb=" SG CYS A 665 " pdb="FE3 SF4 A1401 " - pdb=" SG CYS A 763 " pdb="FE2 SF4 A1401 " - pdb=" SG CYS A 668 " Number of angles added : 12 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 0 sheets defined 42.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 195 through 212 Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 354 through 370 Processing helix chain 'A' and resid 382 through 394 removed outlier: 3.542A pdb=" N PHE A 386 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 422 through 430 Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 455 through 466 Proline residue: A 461 - end of helix removed outlier: 4.051A pdb=" N PHE A 464 " --> pdb=" O THR A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 498 removed outlier: 3.618A pdb=" N LEU A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N HIS A 490 " --> pdb=" O MET A 486 " (cutoff:3.500A) Proline residue: A 491 - end of helix Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 511 through 527 Processing helix chain 'A' and resid 577 through 598 removed outlier: 3.576A pdb=" N ILE A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Proline residue: A 589 - end of helix Processing helix chain 'A' and resid 603 through 607 Processing helix chain 'A' and resid 609 through 627 Processing helix chain 'A' and resid 643 through 652 Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 769 through 798 removed outlier: 3.974A pdb=" N ILE A 798 " --> pdb=" O ASN A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 834 removed outlier: 3.710A pdb=" N PHE A 830 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TYR A 831 " --> pdb=" O LEU A 827 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY A 832 " --> pdb=" O ASN A 828 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL A 834 " --> pdb=" O PHE A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 869 Processing helix chain 'A' and resid 905 through 919 removed outlier: 3.868A pdb=" N THR A 919 " --> pdb=" O HIS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1006 removed outlier: 4.731A pdb=" N LYS A1004 " --> pdb=" O SER A1000 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A1005 " --> pdb=" O ASP A1001 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A1006 " --> pdb=" O ILE A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1032 Processing helix chain 'A' and resid 1038 through 1045 removed outlier: 3.608A pdb=" N LEU A1042 " --> pdb=" O GLU A1038 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A1043 " --> pdb=" O ASP A1039 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A1044 " --> pdb=" O GLU A1040 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A1045 " --> pdb=" O ASP A1041 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1038 through 1045' Processing helix chain 'A' and resid 1065 through 1078 removed outlier: 3.575A pdb=" N THR A1069 " --> pdb=" O THR A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1083 Processing helix chain 'A' and resid 1101 through 1105 Processing helix chain 'A' and resid 1137 through 1141 Processing helix chain 'A' and resid 1142 through 1158 Processing helix chain 'A' and resid 1158 through 1165 Processing helix chain 'A' and resid 1177 through 1184 removed outlier: 3.812A pdb=" N LYS A1181 " --> pdb=" O PRO A1177 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A1184 " --> pdb=" O LEU A1180 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'D' and resid 45 through 51 removed outlier: 3.758A pdb=" N ARG D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 740 removed outlier: 3.647A pdb=" N LEU E 739 " --> pdb=" O THR E 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 29 Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.945A pdb=" N LYS B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 181 through 199 Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.597A pdb=" N THR B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 253 through 269 Processing helix chain 'B' and resid 277 through 288 removed outlier: 3.987A pdb=" N PHE B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 324 through 336 Processing helix chain 'B' and resid 340 through 349 Proline residue: B 346 - end of helix Processing helix chain 'B' and resid 357 through 363 401 hydrogen bonds defined for protein. 1146 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 5172 1.40 - 1.59: 7448 1.59 - 1.78: 8 1.78 - 1.96: 99 1.96 - 2.15: 12 Bond restraints: 12739 Sorted by residual: bond pdb=" S2 SF4 A1401 " pdb="FE4 SF4 A1401 " ideal model delta sigma weight residual 2.280 2.098 0.182 3.00e-02 1.11e+03 3.68e+01 bond pdb=" S4 SF4 A1401 " pdb="FE1 SF4 A1401 " ideal model delta sigma weight residual 2.280 2.100 0.180 3.00e-02 1.11e+03 3.59e+01 bond pdb=" S2 SF4 A1401 " pdb="FE3 SF4 A1401 " ideal model delta sigma weight residual 2.280 2.117 0.163 3.00e-02 1.11e+03 2.95e+01 bond pdb=" S3 SF4 A1401 " pdb="FE2 SF4 A1401 " ideal model delta sigma weight residual 2.280 2.125 0.155 3.00e-02 1.11e+03 2.67e+01 bond pdb=" S4 SF4 A1401 " pdb="FE3 SF4 A1401 " ideal model delta sigma weight residual 2.280 2.126 0.154 3.00e-02 1.11e+03 2.62e+01 ... (remaining 12734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 16925 4.68 - 9.36: 266 9.36 - 14.04: 20 14.04 - 18.72: 6 18.72 - 23.40: 3 Bond angle restraints: 17220 Sorted by residual: angle pdb=" CA GLU A 623 " pdb=" CB GLU A 623 " pdb=" CG GLU A 623 " ideal model delta sigma weight residual 114.10 128.77 -14.67 2.00e+00 2.50e-01 5.38e+01 angle pdb=" CA LEU A1045 " pdb=" CB LEU A1045 " pdb=" CG LEU A1045 " ideal model delta sigma weight residual 116.30 139.70 -23.40 3.50e+00 8.16e-02 4.47e+01 angle pdb=" C GLU A 244 " pdb=" N TYR A 245 " pdb=" CA TYR A 245 " ideal model delta sigma weight residual 122.26 111.53 10.73 1.73e+00 3.34e-01 3.85e+01 angle pdb=" CA LEU B 87 " pdb=" CB LEU B 87 " pdb=" CG LEU B 87 " ideal model delta sigma weight residual 116.30 136.03 -19.73 3.50e+00 8.16e-02 3.18e+01 angle pdb=" C THR B 375 " pdb=" N VAL B 376 " pdb=" CA VAL B 376 " ideal model delta sigma weight residual 122.48 116.28 6.20 1.13e+00 7.83e-01 3.01e+01 ... (remaining 17215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6970 17.81 - 35.61: 603 35.61 - 53.42: 115 53.42 - 71.23: 27 71.23 - 89.03: 8 Dihedral angle restraints: 7723 sinusoidal: 3214 harmonic: 4509 Sorted by residual: dihedral pdb=" CA SER B 379 " pdb=" C SER B 379 " pdb=" N ARG B 380 " pdb=" CA ARG B 380 " ideal model delta harmonic sigma weight residual -180.00 -135.01 -44.99 0 5.00e+00 4.00e-02 8.10e+01 dihedral pdb=" CA ARG A 663 " pdb=" C ARG A 663 " pdb=" N ASP A 664 " pdb=" CA ASP A 664 " ideal model delta harmonic sigma weight residual 180.00 153.72 26.28 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ARG A 672 " pdb=" C ARG A 672 " pdb=" N PRO A 673 " pdb=" CA PRO A 673 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 7720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.479: 1892 0.479 - 0.957: 0 0.957 - 1.436: 0 1.436 - 1.914: 0 1.914 - 2.393: 4 Chirality restraints: 1896 Sorted by residual: chirality pdb="FE4 SF4 A1401 " pdb=" S1 SF4 A1401 " pdb=" S2 SF4 A1401 " pdb=" S3 SF4 A1401 " both_signs ideal model delta sigma weight residual False 10.55 8.16 2.39 2.00e-01 2.50e+01 1.43e+02 chirality pdb="FE2 SF4 A1401 " pdb=" S1 SF4 A1401 " pdb=" S3 SF4 A1401 " pdb=" S4 SF4 A1401 " both_signs ideal model delta sigma weight residual False 10.55 8.28 2.28 2.00e-01 2.50e+01 1.30e+02 chirality pdb="FE1 SF4 A1401 " pdb=" S2 SF4 A1401 " pdb=" S3 SF4 A1401 " pdb=" S4 SF4 A1401 " both_signs ideal model delta sigma weight residual False -10.55 -8.39 -2.17 2.00e-01 2.50e+01 1.17e+02 ... (remaining 1893 not shown) Planarity restraints: 2200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 80 " -0.022 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C THR A 80 " 0.074 2.00e-02 2.50e+03 pdb=" O THR A 80 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN A 81 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 863 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C ALA A 863 " -0.074 2.00e-02 2.50e+03 pdb=" O ALA A 863 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU A 864 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 762 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C VAL A 762 " 0.072 2.00e-02 2.50e+03 pdb=" O VAL A 762 " -0.028 2.00e-02 2.50e+03 pdb=" N CYS A 763 " -0.024 2.00e-02 2.50e+03 ... (remaining 2197 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1541 2.75 - 3.29: 12329 3.29 - 3.83: 21221 3.83 - 4.36: 24416 4.36 - 4.90: 40289 Nonbonded interactions: 99796 Sorted by model distance: nonbonded pdb=" OH TYR B 261 " pdb=" O TRP B 284 " model vdw 2.218 3.040 nonbonded pdb=" O LYS B 357 " pdb=" OG SER B 360 " model vdw 2.255 3.040 nonbonded pdb=" O TYR A 135 " pdb=" OH TYR A 249 " model vdw 2.263 3.040 nonbonded pdb=" O LEU D 73 " pdb=" OG SER B 2 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR A1068 " pdb=" O THR A1103 " model vdw 2.296 3.040 ... (remaining 99791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.62 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: 1.020 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: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.310 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 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 : 0.009 0.182 12739 Z= 0.615 Angle : 1.525 23.403 17220 Z= 0.848 Chirality : 0.129 2.393 1896 Planarity : 0.009 0.088 2200 Dihedral : 14.137 89.031 4799 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.68 % Favored : 95.19 % Rotamer: Outliers : 1.88 % Allowed : 8.38 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.19), residues: 1517 helix: -0.89 (0.19), residues: 555 sheet: -0.40 (0.30), residues: 248 loop : -1.11 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 78 HIS 0.011 0.003 HIS A 915 PHE 0.058 0.004 PHE B 288 TYR 0.039 0.005 TYR A 245 ARG 0.027 0.002 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 236 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.8371 (m-80) cc_final: 0.7938 (m-10) REVERT: A 121 PHE cc_start: 0.8616 (m-80) cc_final: 0.8094 (m-80) REVERT: A 135 TYR cc_start: 0.8095 (t80) cc_final: 0.7468 (t80) REVERT: A 148 ARG cc_start: 0.8115 (mtp180) cc_final: 0.7894 (ptm160) REVERT: A 151 ASP cc_start: 0.7662 (m-30) cc_final: 0.7442 (m-30) REVERT: A 186 LYS cc_start: 0.8642 (tttp) cc_final: 0.8232 (tptt) REVERT: A 314 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8353 (tpp) REVERT: A 383 ASP cc_start: 0.7583 (m-30) cc_final: 0.6704 (m-30) REVERT: A 453 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8337 (tp30) REVERT: A 459 MET cc_start: 0.7464 (mtt) cc_final: 0.6782 (mtt) REVERT: A 811 LYS cc_start: 0.8802 (mttp) cc_final: 0.8497 (mttt) REVERT: A 827 LEU cc_start: 0.9539 (tt) cc_final: 0.9319 (tt) REVERT: A 955 LEU cc_start: 0.8945 (mp) cc_final: 0.8693 (mp) REVERT: A 1146 TYR cc_start: 0.8871 (m-80) cc_final: 0.8488 (m-10) REVERT: D 78 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6722 (tm-30) REVERT: D 81 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7671 (t) REVERT: D 109 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8091 (mmmt) REVERT: D 117 ASP cc_start: 0.8615 (t0) cc_final: 0.8332 (t0) REVERT: B 16 LYS cc_start: 0.8870 (mttm) cc_final: 0.8595 (mmpt) REVERT: B 232 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8652 (pt0) REVERT: B 236 ASN cc_start: 0.8921 (m-40) cc_final: 0.8382 (p0) REVERT: B 295 ASP cc_start: 0.7767 (p0) cc_final: 0.7547 (p0) outliers start: 26 outliers final: 9 residues processed: 257 average time/residue: 0.2553 time to fit residues: 92.8635 Evaluate side-chains 175 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 164 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 83 HIS A 444 GLN A 450 ASN A 490 HIS A 638 HIS A 671 ASN A 973 ASN A 999 GLN ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12739 Z= 0.195 Angle : 0.680 8.774 17220 Z= 0.353 Chirality : 0.045 0.201 1896 Planarity : 0.005 0.053 2200 Dihedral : 5.558 69.512 1661 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.14 % Allowed : 2.31 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1517 helix: 0.68 (0.21), residues: 561 sheet: -0.14 (0.32), residues: 243 loop : -0.64 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 841 HIS 0.003 0.001 HIS B 54 PHE 0.019 0.002 PHE B 288 TYR 0.031 0.002 TYR A 412 ARG 0.009 0.001 ARG D 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 203 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 PHE cc_start: 0.8660 (m-80) cc_final: 0.8176 (m-80) REVERT: A 135 TYR cc_start: 0.8043 (t80) cc_final: 0.7386 (t80) REVERT: A 186 LYS cc_start: 0.8411 (tttp) cc_final: 0.8090 (tptt) REVERT: A 453 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8298 (tp30) REVERT: A 459 MET cc_start: 0.7812 (mtt) cc_final: 0.7105 (mtt) REVERT: A 505 ASP cc_start: 0.8553 (m-30) cc_final: 0.8153 (m-30) REVERT: A 517 GLU cc_start: 0.8665 (tt0) cc_final: 0.8330 (tm-30) REVERT: A 521 MET cc_start: 0.9149 (mtt) cc_final: 0.7679 (tpp) REVERT: A 811 LYS cc_start: 0.8620 (mttp) cc_final: 0.8386 (mttt) REVERT: A 998 PHE cc_start: 0.8499 (t80) cc_final: 0.8281 (t80) REVERT: A 1023 CYS cc_start: 0.7937 (t) cc_final: 0.7668 (t) REVERT: A 1036 MET cc_start: 0.4732 (mmp) cc_final: 0.4338 (tpt) REVERT: A 1165 GLN cc_start: 0.8084 (mp10) cc_final: 0.7544 (tm-30) REVERT: D 30 MET cc_start: 0.7631 (mmm) cc_final: 0.7202 (mmm) REVERT: D 109 LYS cc_start: 0.8352 (mmmt) cc_final: 0.8034 (mmmt) REVERT: D 117 ASP cc_start: 0.8358 (t0) cc_final: 0.7956 (t0) REVERT: D 119 MET cc_start: 0.8807 (mmp) cc_final: 0.8354 (mmp) REVERT: B 16 LYS cc_start: 0.8895 (mttm) cc_final: 0.8684 (mmpt) REVERT: B 232 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8802 (mt-10) REVERT: B 295 ASP cc_start: 0.7775 (p0) cc_final: 0.7564 (p0) outliers start: 2 outliers final: 1 residues processed: 203 average time/residue: 0.2403 time to fit residues: 70.8021 Evaluate side-chains 150 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 138 optimal weight: 1.9990 chunk 149 optimal weight: 0.0000 chunk 123 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 110 optimal weight: 0.9990 overall best weight: 0.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A1033 HIS ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN ** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12739 Z= 0.153 Angle : 0.601 8.247 17220 Z= 0.307 Chirality : 0.043 0.174 1896 Planarity : 0.004 0.053 2200 Dihedral : 5.102 63.440 1661 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1517 helix: 0.88 (0.21), residues: 564 sheet: -0.18 (0.32), residues: 255 loop : -0.48 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 284 HIS 0.006 0.001 HIS A 490 PHE 0.014 0.001 PHE A1003 TYR 0.022 0.001 TYR A 412 ARG 0.017 0.000 ARG A1147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8810 (m-30) cc_final: 0.8396 (m-30) REVERT: A 135 TYR cc_start: 0.7973 (t80) cc_final: 0.7269 (t80) REVERT: A 186 LYS cc_start: 0.8355 (tttp) cc_final: 0.8077 (tptt) REVERT: A 415 SER cc_start: 0.8567 (p) cc_final: 0.7776 (p) REVERT: A 452 ILE cc_start: 0.7880 (tp) cc_final: 0.7079 (pt) REVERT: A 459 MET cc_start: 0.7785 (mtt) cc_final: 0.7124 (mtt) REVERT: A 521 MET cc_start: 0.9196 (mtt) cc_final: 0.8575 (mtt) REVERT: A 812 MET cc_start: 0.9288 (ttp) cc_final: 0.9070 (tmm) REVERT: A 835 MET cc_start: 0.9113 (mpp) cc_final: 0.8862 (mpp) REVERT: A 1036 MET cc_start: 0.4831 (mmp) cc_final: 0.4448 (tpt) REVERT: A 1165 GLN cc_start: 0.8009 (mp10) cc_final: 0.7637 (tm-30) REVERT: D 117 ASP cc_start: 0.8213 (t0) cc_final: 0.7977 (t0) REVERT: D 119 MET cc_start: 0.8746 (mmp) cc_final: 0.8023 (mmm) REVERT: B 52 CYS cc_start: 0.7932 (p) cc_final: 0.7695 (t) REVERT: B 232 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8764 (mt-10) REVERT: B 295 ASP cc_start: 0.7750 (p0) cc_final: 0.7542 (p0) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.2348 time to fit residues: 65.3110 Evaluate side-chains 149 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12739 Z= 0.175 Angle : 0.585 8.241 17220 Z= 0.299 Chirality : 0.043 0.165 1896 Planarity : 0.004 0.049 2200 Dihedral : 4.949 63.264 1661 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.21), residues: 1517 helix: 0.93 (0.21), residues: 565 sheet: -0.26 (0.33), residues: 251 loop : -0.47 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 284 HIS 0.005 0.001 HIS A 490 PHE 0.016 0.001 PHE B 361 TYR 0.021 0.001 TYR A 412 ARG 0.005 0.000 ARG D 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8837 (m-30) cc_final: 0.8454 (m-30) REVERT: A 135 TYR cc_start: 0.8054 (t80) cc_final: 0.7310 (t80) REVERT: A 186 LYS cc_start: 0.8460 (tttp) cc_final: 0.8163 (tptt) REVERT: A 415 SER cc_start: 0.8466 (p) cc_final: 0.7615 (p) REVERT: A 459 MET cc_start: 0.7800 (mtt) cc_final: 0.7306 (mtt) REVERT: A 517 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7512 (tm-30) REVERT: A 811 LYS cc_start: 0.8732 (mttp) cc_final: 0.8384 (mttt) REVERT: A 953 MET cc_start: 0.8637 (tpp) cc_final: 0.7939 (tpp) REVERT: A 1036 MET cc_start: 0.4859 (mmp) cc_final: 0.4545 (tpt) REVERT: A 1165 GLN cc_start: 0.7907 (mp10) cc_final: 0.7576 (tm-30) REVERT: D 117 ASP cc_start: 0.8160 (t0) cc_final: 0.7938 (t0) REVERT: D 119 MET cc_start: 0.8809 (mmp) cc_final: 0.7843 (mmm) REVERT: B 52 CYS cc_start: 0.7994 (p) cc_final: 0.7743 (t) REVERT: B 194 MET cc_start: 0.8957 (mtm) cc_final: 0.8714 (mtt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2381 time to fit residues: 64.0499 Evaluate side-chains 146 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.4980 chunk 83 optimal weight: 10.0000 chunk 2 optimal weight: 0.2980 chunk 109 optimal weight: 0.0770 chunk 60 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 HIS ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12739 Z= 0.152 Angle : 0.577 9.075 17220 Z= 0.292 Chirality : 0.042 0.160 1896 Planarity : 0.004 0.043 2200 Dihedral : 4.792 61.526 1661 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1517 helix: 0.98 (0.21), residues: 566 sheet: -0.11 (0.34), residues: 245 loop : -0.51 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 284 HIS 0.007 0.001 HIS A 469 PHE 0.022 0.001 PHE B 288 TYR 0.019 0.001 TYR A 412 ARG 0.004 0.000 ARG D 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8730 (m-30) cc_final: 0.8403 (m-30) REVERT: A 135 TYR cc_start: 0.8003 (t80) cc_final: 0.7262 (t80) REVERT: A 186 LYS cc_start: 0.8385 (tttp) cc_final: 0.8076 (tptt) REVERT: A 452 ILE cc_start: 0.7567 (tp) cc_final: 0.7140 (pt) REVERT: A 459 MET cc_start: 0.7588 (mtt) cc_final: 0.7342 (mtt) REVERT: A 517 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7416 (tm-30) REVERT: A 521 MET cc_start: 0.9222 (mmm) cc_final: 0.8871 (mmm) REVERT: A 811 LYS cc_start: 0.8705 (mttp) cc_final: 0.8472 (mttt) REVERT: A 835 MET cc_start: 0.9078 (mpp) cc_final: 0.8843 (mpp) REVERT: A 846 MET cc_start: 0.8827 (tpp) cc_final: 0.8564 (tpp) REVERT: A 953 MET cc_start: 0.8586 (tpp) cc_final: 0.7947 (tpp) REVERT: A 1036 MET cc_start: 0.4846 (mmp) cc_final: 0.4553 (tpt) REVERT: A 1165 GLN cc_start: 0.7846 (mp10) cc_final: 0.7627 (tm-30) REVERT: D 119 MET cc_start: 0.8799 (mmp) cc_final: 0.7877 (mmm) REVERT: B 232 GLU cc_start: 0.9062 (pt0) cc_final: 0.8693 (pp20) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2379 time to fit residues: 67.6236 Evaluate side-chains 145 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 86 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 HIS ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12739 Z= 0.216 Angle : 0.610 10.501 17220 Z= 0.313 Chirality : 0.043 0.149 1896 Planarity : 0.004 0.045 2200 Dihedral : 4.813 57.160 1661 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1517 helix: 1.00 (0.21), residues: 568 sheet: -0.25 (0.31), residues: 270 loop : -0.46 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 284 HIS 0.004 0.001 HIS A 250 PHE 0.014 0.001 PHE B 288 TYR 0.026 0.002 TYR A 483 ARG 0.011 0.000 ARG A 806 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.336 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: A 47 ASP cc_start: 0.8623 (m-30) cc_final: 0.8329 (m-30) REVERT: A 135 TYR cc_start: 0.8090 (t80) cc_final: 0.7330 (t80) REVERT: A 186 LYS cc_start: 0.8631 (tttp) cc_final: 0.7947 (tptt) REVERT: A 193 PHE cc_start: 0.7778 (m-80) cc_final: 0.7490 (m-10) REVERT: A 459 MET cc_start: 0.7687 (mtt) cc_final: 0.7436 (mtt) REVERT: A 517 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7770 (tm-30) REVERT: A 811 LYS cc_start: 0.8731 (mttp) cc_final: 0.8430 (mttt) REVERT: A 953 MET cc_start: 0.8697 (tpp) cc_final: 0.8013 (tpp) REVERT: A 1036 MET cc_start: 0.4942 (mmp) cc_final: 0.4627 (tpt) REVERT: A 1083 LYS cc_start: 0.6605 (tppt) cc_final: 0.5802 (ttpt) REVERT: D 90 LEU cc_start: 0.9142 (mt) cc_final: 0.8931 (mt) REVERT: B 232 GLU cc_start: 0.9097 (pt0) cc_final: 0.8748 (pp20) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2521 time to fit residues: 68.8555 Evaluate side-chains 141 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 83 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 146 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 89 optimal weight: 0.0370 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12739 Z= 0.151 Angle : 0.582 8.736 17220 Z= 0.294 Chirality : 0.043 0.200 1896 Planarity : 0.004 0.045 2200 Dihedral : 4.672 54.548 1661 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1517 helix: 1.03 (0.22), residues: 573 sheet: -0.21 (0.33), residues: 262 loop : -0.40 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 791 HIS 0.004 0.001 HIS A 250 PHE 0.013 0.001 PHE A 610 TYR 0.019 0.001 TYR A 249 ARG 0.006 0.000 ARG A 780 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.8008 (t80) cc_final: 0.7254 (t80) REVERT: A 186 LYS cc_start: 0.8460 (tttp) cc_final: 0.7832 (tptt) REVERT: A 193 PHE cc_start: 0.7618 (m-80) cc_final: 0.7397 (m-10) REVERT: A 459 MET cc_start: 0.7589 (mtt) cc_final: 0.7350 (mtt) REVERT: A 517 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7828 (tm-30) REVERT: A 811 LYS cc_start: 0.8757 (mttp) cc_final: 0.8415 (mttt) REVERT: A 835 MET cc_start: 0.9092 (mpp) cc_final: 0.8877 (mpp) REVERT: A 846 MET cc_start: 0.8956 (tpp) cc_final: 0.8756 (mmt) REVERT: A 953 MET cc_start: 0.8676 (tpp) cc_final: 0.8018 (tpp) REVERT: A 1036 MET cc_start: 0.4860 (mmp) cc_final: 0.4625 (tpt) REVERT: D 117 ASP cc_start: 0.8194 (t0) cc_final: 0.7943 (t0) REVERT: D 119 MET cc_start: 0.8789 (mmp) cc_final: 0.7927 (mmm) REVERT: B 232 GLU cc_start: 0.9099 (pt0) cc_final: 0.8705 (pp20) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2285 time to fit residues: 60.4285 Evaluate side-chains 141 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.2980 chunk 87 optimal weight: 0.5980 chunk 44 optimal weight: 0.0040 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12739 Z= 0.167 Angle : 0.591 10.230 17220 Z= 0.300 Chirality : 0.043 0.172 1896 Planarity : 0.004 0.045 2200 Dihedral : 4.598 50.947 1661 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1517 helix: 1.05 (0.22), residues: 572 sheet: -0.14 (0.33), residues: 263 loop : -0.40 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 284 HIS 0.004 0.001 HIS A 490 PHE 0.020 0.001 PHE A 594 TYR 0.022 0.001 TYR A 249 ARG 0.006 0.000 ARG A 780 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.347 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: A 47 ASP cc_start: 0.8629 (m-30) cc_final: 0.8335 (m-30) REVERT: A 135 TYR cc_start: 0.8029 (t80) cc_final: 0.7241 (t80) REVERT: A 186 LYS cc_start: 0.8566 (tttp) cc_final: 0.7858 (tptt) REVERT: A 193 PHE cc_start: 0.7520 (m-80) cc_final: 0.7287 (m-10) REVERT: A 459 MET cc_start: 0.7645 (mtt) cc_final: 0.7184 (mtt) REVERT: A 517 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7850 (tm-30) REVERT: A 811 LYS cc_start: 0.8779 (mttp) cc_final: 0.8438 (mttt) REVERT: A 835 MET cc_start: 0.9094 (mpp) cc_final: 0.8891 (mpp) REVERT: A 846 MET cc_start: 0.8935 (tpp) cc_final: 0.8683 (tpp) REVERT: A 953 MET cc_start: 0.8749 (tpp) cc_final: 0.8163 (tpp) REVERT: A 1036 MET cc_start: 0.4854 (mmp) cc_final: 0.4602 (tpt) REVERT: A 1083 LYS cc_start: 0.6456 (tppt) cc_final: 0.5633 (ttmt) REVERT: D 117 ASP cc_start: 0.8179 (t0) cc_final: 0.7968 (t0) REVERT: D 119 MET cc_start: 0.8708 (mmp) cc_final: 0.7967 (mmm) REVERT: B 295 ASP cc_start: 0.8109 (p0) cc_final: 0.7885 (p0) REVERT: B 323 MET cc_start: 0.8357 (mmm) cc_final: 0.8033 (mmm) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2195 time to fit residues: 58.9930 Evaluate side-chains 142 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 129 optimal weight: 0.0670 chunk 89 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 197 ASN ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12739 Z= 0.146 Angle : 0.590 11.003 17220 Z= 0.295 Chirality : 0.042 0.172 1896 Planarity : 0.004 0.045 2200 Dihedral : 4.460 46.080 1661 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1517 helix: 1.07 (0.22), residues: 573 sheet: -0.10 (0.34), residues: 260 loop : -0.35 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 284 HIS 0.004 0.001 HIS A 250 PHE 0.032 0.001 PHE B 288 TYR 0.019 0.001 TYR A 249 ARG 0.005 0.000 ARG A 780 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8459 (m-30) cc_final: 0.8235 (m-30) REVERT: A 121 PHE cc_start: 0.8624 (m-80) cc_final: 0.8280 (m-10) REVERT: A 135 TYR cc_start: 0.8015 (t80) cc_final: 0.7134 (t80) REVERT: A 186 LYS cc_start: 0.8518 (tttp) cc_final: 0.7832 (tptt) REVERT: A 459 MET cc_start: 0.7648 (mtt) cc_final: 0.7413 (mtt) REVERT: A 517 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7841 (tm-30) REVERT: A 637 TYR cc_start: 0.7651 (m-10) cc_final: 0.7250 (m-80) REVERT: A 811 LYS cc_start: 0.8769 (mttp) cc_final: 0.8441 (mttt) REVERT: A 835 MET cc_start: 0.9092 (mpp) cc_final: 0.8869 (mpp) REVERT: A 953 MET cc_start: 0.8681 (tpp) cc_final: 0.8099 (tpp) REVERT: A 1036 MET cc_start: 0.4867 (mmp) cc_final: 0.4652 (tpt) REVERT: A 1083 LYS cc_start: 0.6402 (tppt) cc_final: 0.5550 (ttpt) REVERT: D 119 MET cc_start: 0.8707 (mmp) cc_final: 0.7922 (mmm) REVERT: B 323 MET cc_start: 0.8291 (mmm) cc_final: 0.7955 (mmm) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2368 time to fit residues: 65.1711 Evaluate side-chains 147 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.0070 chunk 68 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 0.0770 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 12739 Z= 0.151 Angle : 0.600 9.667 17220 Z= 0.301 Chirality : 0.043 0.173 1896 Planarity : 0.004 0.045 2200 Dihedral : 4.404 42.420 1661 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1517 helix: 1.11 (0.22), residues: 571 sheet: -0.15 (0.34), residues: 258 loop : -0.33 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 284 HIS 0.009 0.001 HIS A 490 PHE 0.015 0.001 PHE A 998 TYR 0.016 0.001 TYR A 249 ARG 0.005 0.000 ARG A 780 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 PHE cc_start: 0.8592 (m-80) cc_final: 0.8302 (m-10) REVERT: A 135 TYR cc_start: 0.7961 (t80) cc_final: 0.7278 (t80) REVERT: A 186 LYS cc_start: 0.8496 (tttp) cc_final: 0.7792 (tptt) REVERT: A 459 MET cc_start: 0.7639 (mtt) cc_final: 0.7411 (mtt) REVERT: A 517 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7837 (tm-30) REVERT: A 637 TYR cc_start: 0.7632 (m-10) cc_final: 0.7194 (m-80) REVERT: A 811 LYS cc_start: 0.8760 (mttp) cc_final: 0.8418 (mttt) REVERT: A 835 MET cc_start: 0.9116 (mpp) cc_final: 0.8912 (mpp) REVERT: A 846 MET cc_start: 0.8891 (tpp) cc_final: 0.8664 (mmt) REVERT: A 953 MET cc_start: 0.8658 (tpp) cc_final: 0.8084 (tpp) REVERT: A 1036 MET cc_start: 0.4886 (mmp) cc_final: 0.4674 (tpt) REVERT: A 1083 LYS cc_start: 0.6366 (tppt) cc_final: 0.5513 (ttpt) REVERT: D 84 VAL cc_start: 0.7657 (t) cc_final: 0.7450 (t) REVERT: D 119 MET cc_start: 0.8780 (mmp) cc_final: 0.8536 (mmp) REVERT: B 323 MET cc_start: 0.8252 (mmm) cc_final: 0.7918 (mmm) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2303 time to fit residues: 60.1098 Evaluate side-chains 141 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 0.0670 chunk 50 optimal weight: 10.0000 chunk 124 optimal weight: 0.3980 chunk 15 optimal weight: 0.3980 chunk 22 optimal weight: 0.0980 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.085281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.069388 restraints weight = 61774.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.071024 restraints weight = 40290.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.072084 restraints weight = 29763.506| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 12739 Z= 0.143 Angle : 0.612 11.619 17220 Z= 0.301 Chirality : 0.043 0.173 1896 Planarity : 0.004 0.045 2200 Dihedral : 4.330 40.255 1661 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1517 helix: 1.07 (0.22), residues: 572 sheet: -0.06 (0.34), residues: 258 loop : -0.29 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 284 HIS 0.004 0.001 HIS A 250 PHE 0.022 0.001 PHE D 45 TYR 0.016 0.001 TYR A 249 ARG 0.005 0.000 ARG A 780 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2582.56 seconds wall clock time: 47 minutes 4.73 seconds (2824.73 seconds total)