Starting phenix.real_space_refine on Thu Jul 31 19:18:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ed9_47941/07_2025/9ed9_47941.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ed9_47941/07_2025/9ed9_47941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ed9_47941/07_2025/9ed9_47941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ed9_47941/07_2025/9ed9_47941.map" model { file = "/net/cci-nas-00/data/ceres_data/9ed9_47941/07_2025/9ed9_47941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ed9_47941/07_2025/9ed9_47941.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 143 5.49 5 S 22 5.16 5 C 8244 2.51 5 N 2400 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13785 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 2038 Classifications: {'RNA': 95} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 83} Chain: "C" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 302 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "c" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 10767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10767 Classifications: {'peptide': 1337} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 35, 'TRANS': 1301} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'HIS:plan': 1, 'ARG:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 87 Time building chain proxies: 10.50, per 1000 atoms: 0.76 Number of scatterers: 13785 At special positions: 0 Unit cell: (89.9856, 137.478, 122.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 143 15.00 O 2976 8.00 N 2400 7.00 C 8244 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: 3.57 Conformation dependent library (CDL) restraints added in 1.3 seconds 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2546 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 9 sheets defined 54.7% alpha, 7.6% beta 50 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 5.41 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.890A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.772A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.551A pdb=" N PHE A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 286 through 304 removed outlier: 3.930A pdb=" N ASP A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 382 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.837A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.229A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 4.045A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 445 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 512 through 527 removed outlier: 3.689A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 557 removed outlier: 4.300A pdb=" N LYS A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.516A pdb=" N LEU A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 639 through 643 removed outlier: 3.562A pdb=" N LEU A 642 " --> pdb=" O TYR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 703 through 714 Processing helix chain 'A' and resid 719 through 727 removed outlier: 3.720A pdb=" N LEU A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 Processing helix chain 'A' and resid 776 through 792 Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 803 through 807 Processing helix chain 'A' and resid 808 through 817 removed outlier: 3.598A pdb=" N GLN A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 removed outlier: 3.789A pdb=" N ASN A 863 " --> pdb=" O SER A 860 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 865 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 888 removed outlier: 5.657A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 902 Processing helix chain 'A' and resid 909 through 919 Processing helix chain 'A' and resid 925 through 940 Processing helix chain 'A' and resid 959 through 969 removed outlier: 4.228A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.312A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 Processing helix chain 'A' and resid 1032 through 1041 Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 4.530A pdb=" N SER A1172 " --> pdb=" O ILE A1168 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1263 through 1281 removed outlier: 4.311A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 Processing helix chain 'A' and resid 1340 through 1344 Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 955 through 957 removed outlier: 6.187A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 9.705A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 509 removed outlier: 5.330A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA5, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA6, first strand: chain 'A' and resid 1049 through 1050 Processing sheet with id=AA7, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.978A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 Processing sheet with id=AA9, first strand: chain 'A' and resid 1324 through 1326 520 hydrogen bonds defined for protein. 1503 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 7.44 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2478 1.33 - 1.45: 4237 1.45 - 1.57: 7298 1.57 - 1.70: 283 1.70 - 1.82: 42 Bond restraints: 14338 Sorted by residual: bond pdb=" CB PHE A 185 " pdb=" CG PHE A 185 " ideal model delta sigma weight residual 1.502 1.556 -0.054 2.30e-02 1.89e+03 5.52e+00 bond pdb=" CG ARG A 307 " pdb=" CD ARG A 307 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.30e+00 bond pdb=" CB PHE A1038 " pdb=" CG PHE A1038 " ideal model delta sigma weight residual 1.502 1.543 -0.041 2.30e-02 1.89e+03 3.13e+00 bond pdb=" CB TYR A 812 " pdb=" CG TYR A 812 " ideal model delta sigma weight residual 1.512 1.551 -0.039 2.20e-02 2.07e+03 3.12e+00 bond pdb=" CB ASN A1066 " pdb=" CG ASN A1066 " ideal model delta sigma weight residual 1.516 1.560 -0.044 2.50e-02 1.60e+03 3.04e+00 ... (remaining 14333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 19758 3.11 - 6.21: 200 6.21 - 9.32: 27 9.32 - 12.43: 16 12.43 - 15.53: 2 Bond angle restraints: 20003 Sorted by residual: angle pdb=" CG ARG A 664 " pdb=" CD ARG A 664 " pdb=" NE ARG A 664 " ideal model delta sigma weight residual 112.00 123.52 -11.52 2.20e+00 2.07e-01 2.74e+01 angle pdb=" CA LYS A 558 " pdb=" CB LYS A 558 " pdb=" CG LYS A 558 " ideal model delta sigma weight residual 114.10 123.72 -9.62 2.00e+00 2.50e-01 2.31e+01 angle pdb=" CA LYS A 382 " pdb=" CB LYS A 382 " pdb=" CG LYS A 382 " ideal model delta sigma weight residual 114.10 123.39 -9.29 2.00e+00 2.50e-01 2.16e+01 angle pdb=" CG ARG A 307 " pdb=" CD ARG A 307 " pdb=" NE ARG A 307 " ideal model delta sigma weight residual 112.00 121.86 -9.86 2.20e+00 2.07e-01 2.01e+01 angle pdb=" CA LEU A 636 " pdb=" CB LEU A 636 " pdb=" CG LEU A 636 " ideal model delta sigma weight residual 116.30 131.83 -15.53 3.50e+00 8.16e-02 1.97e+01 ... (remaining 19998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7254 17.97 - 35.93: 854 35.93 - 53.90: 336 53.90 - 71.86: 168 71.86 - 89.83: 32 Dihedral angle restraints: 8644 sinusoidal: 4710 harmonic: 3934 Sorted by residual: dihedral pdb=" CA ASP A 969 " pdb=" C ASP A 969 " pdb=" N PHE A 970 " pdb=" CA PHE A 970 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA THR A 555 " pdb=" C THR A 555 " pdb=" N ASN A 556 " pdb=" CA ASN A 556 " ideal model delta harmonic sigma weight residual -180.00 -156.36 -23.64 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ASN A 692 " pdb=" C ASN A 692 " pdb=" N PHE A 693 " pdb=" CA PHE A 693 " ideal model delta harmonic sigma weight residual -180.00 -158.48 -21.52 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 8641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2268 0.117 - 0.234: 40 0.234 - 0.351: 0 0.351 - 0.469: 1 0.469 - 0.586: 1 Chirality restraints: 2310 Sorted by residual: chirality pdb=" CG LEU A 636 " pdb=" CB LEU A 636 " pdb=" CD1 LEU A 636 " pdb=" CD2 LEU A 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.58e+00 chirality pdb=" P DT C 4 " pdb=" OP1 DT C 4 " pdb=" OP2 DT C 4 " pdb=" O5' DT C 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.75 -0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CG LEU A 540 " pdb=" CB LEU A 540 " pdb=" CD1 LEU A 540 " pdb=" CD2 LEU A 540 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2307 not shown) Planarity restraints: 2041 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 549 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C VAL A 549 " -0.066 2.00e-02 2.50e+03 pdb=" O VAL A 549 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP A 550 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 565 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.64e+00 pdb=" C LYS A 565 " 0.054 2.00e-02 2.50e+03 pdb=" O LYS A 565 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 566 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 382 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.86e+00 pdb=" C LYS A 382 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS A 382 " 0.019 2.00e-02 2.50e+03 pdb=" N MET A 383 " 0.015 2.00e-02 2.50e+03 ... (remaining 2038 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3007 2.79 - 3.31: 12191 3.31 - 3.84: 24853 3.84 - 4.37: 29097 4.37 - 4.90: 45443 Nonbonded interactions: 114591 Sorted by model distance: nonbonded pdb=" O2' U B 22 " pdb=" O ILE A1110 " model vdw 2.258 3.040 nonbonded pdb=" O2' A B 47 " pdb=" O LEU A 101 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR A 249 " pdb=" OE1 GLN A 265 " model vdw 2.271 3.040 nonbonded pdb=" NE2 GLN A 817 " pdb=" O ARG A 820 " model vdw 2.309 3.120 nonbonded pdb=" O LYS A 209 " pdb=" OG SER A 213 " model vdw 2.310 3.040 ... (remaining 114586 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=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: 7.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 41.520 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14338 Z= 0.196 Angle : 0.861 15.532 20003 Z= 0.444 Chirality : 0.047 0.586 2310 Planarity : 0.006 0.063 2041 Dihedral : 19.236 89.831 6098 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.52 % Allowed : 21.23 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.21), residues: 1329 helix: -0.24 (0.18), residues: 648 sheet: -0.01 (0.47), residues: 133 loop : -1.04 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 883 HIS 0.009 0.001 HIS A 595 PHE 0.047 0.003 PHE A 970 TYR 0.038 0.002 TYR A 594 ARG 0.014 0.001 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.13248 ( 641) hydrogen bonds : angle 6.12496 ( 1741) covalent geometry : bond 0.00427 (14338) covalent geometry : angle 0.86106 (20003) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.9437 (tm) cc_final: 0.9229 (tm) REVERT: A 500 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7836 (mmtm) REVERT: A 648 MET cc_start: 0.7319 (ppp) cc_final: 0.7094 (tmm) REVERT: A 828 LEU cc_start: 0.6784 (pp) cc_final: 0.6344 (mm) REVERT: A 846 PHE cc_start: 0.8416 (m-10) cc_final: 0.8031 (m-10) REVERT: A 933 GLN cc_start: 0.9001 (tt0) cc_final: 0.8676 (tp40) REVERT: A 964 SER cc_start: 0.9118 (t) cc_final: 0.8735 (m) REVERT: A 1043 MET cc_start: 0.7997 (mmm) cc_final: 0.7731 (mmp) REVERT: A 1192 LYS cc_start: 0.8373 (tttt) cc_final: 0.8007 (tmtt) outliers start: 6 outliers final: 3 residues processed: 112 average time/residue: 1.2622 time to fit residues: 155.8515 Evaluate side-chains 101 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 762 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 281 GLN A 501 ASN ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 ASN A1208 ASN A1364 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.121902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.077873 restraints weight = 24493.423| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.33 r_work: 0.2894 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14338 Z= 0.218 Angle : 0.599 9.962 20003 Z= 0.319 Chirality : 0.040 0.182 2310 Planarity : 0.004 0.049 2041 Dihedral : 19.142 86.829 3407 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.16 % Allowed : 19.41 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.22), residues: 1329 helix: 0.82 (0.20), residues: 654 sheet: -0.13 (0.48), residues: 131 loop : -0.81 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 883 HIS 0.007 0.001 HIS A 116 PHE 0.033 0.002 PHE A 970 TYR 0.014 0.002 TYR A 155 ARG 0.010 0.001 ARG A 664 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 641) hydrogen bonds : angle 4.81292 ( 1741) covalent geometry : bond 0.00487 (14338) covalent geometry : angle 0.59907 (20003) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8886 (mttp) cc_final: 0.8684 (mtpp) REVERT: A 500 LYS cc_start: 0.8241 (mmtt) cc_final: 0.7786 (mmtm) REVERT: A 628 ASP cc_start: 0.7900 (t0) cc_final: 0.7564 (t0) REVERT: A 648 MET cc_start: 0.7348 (ppp) cc_final: 0.7020 (tmm) REVERT: A 828 LEU cc_start: 0.6441 (pp) cc_final: 0.6133 (mm) REVERT: A 846 PHE cc_start: 0.8414 (m-10) cc_final: 0.8083 (m-10) REVERT: A 933 GLN cc_start: 0.8909 (tt0) cc_final: 0.8423 (tm-30) REVERT: A 1043 MET cc_start: 0.7947 (mmm) cc_final: 0.7745 (mmp) REVERT: A 1192 LYS cc_start: 0.8497 (tttt) cc_final: 0.7917 (tmtt) REVERT: A 1340 LYS cc_start: 0.8763 (tptt) cc_final: 0.8444 (mptt) outliers start: 25 outliers final: 9 residues processed: 120 average time/residue: 1.2559 time to fit residues: 166.8698 Evaluate side-chains 106 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1072 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 17 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN A 990 ASN A1364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.121455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.077877 restraints weight = 24665.072| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.15 r_work: 0.2885 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14338 Z= 0.183 Angle : 0.542 10.260 20003 Z= 0.290 Chirality : 0.038 0.144 2310 Planarity : 0.004 0.048 2041 Dihedral : 18.996 87.507 3402 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.19 % Allowed : 17.69 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1329 helix: 1.21 (0.20), residues: 659 sheet: -0.35 (0.46), residues: 131 loop : -0.64 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 883 HIS 0.006 0.001 HIS A 116 PHE 0.014 0.001 PHE A 446 TYR 0.016 0.001 TYR A 882 ARG 0.010 0.001 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 641) hydrogen bonds : angle 4.53606 ( 1741) covalent geometry : bond 0.00407 (14338) covalent geometry : angle 0.54152 (20003) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 LYS cc_start: 0.8393 (mmtt) cc_final: 0.7908 (mmtm) REVERT: A 645 ASP cc_start: 0.7804 (p0) cc_final: 0.7602 (p0) REVERT: A 648 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7112 (tmm) REVERT: A 694 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7885 (tpt) REVERT: A 815 TYR cc_start: 0.9084 (m-10) cc_final: 0.8855 (m-10) REVERT: A 828 LEU cc_start: 0.6579 (pp) cc_final: 0.6197 (mm) REVERT: A 846 PHE cc_start: 0.8564 (m-10) cc_final: 0.8191 (m-10) REVERT: A 933 GLN cc_start: 0.8981 (tt0) cc_final: 0.8460 (tm-30) REVERT: A 1043 MET cc_start: 0.7989 (mmm) cc_final: 0.7747 (mmp) REVERT: A 1192 LYS cc_start: 0.8547 (tttt) cc_final: 0.8015 (tmtt) REVERT: A 1340 LYS cc_start: 0.8771 (tptt) cc_final: 0.8493 (mptt) outliers start: 37 outliers final: 14 residues processed: 132 average time/residue: 1.2607 time to fit residues: 183.1842 Evaluate side-chains 112 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1250 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 139 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 ASN A1364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.121699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.078439 restraints weight = 24608.093| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.15 r_work: 0.2896 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14338 Z= 0.161 Angle : 0.525 10.473 20003 Z= 0.279 Chirality : 0.037 0.141 2310 Planarity : 0.003 0.046 2041 Dihedral : 18.921 88.620 3400 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.59 % Allowed : 18.29 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1329 helix: 1.44 (0.21), residues: 660 sheet: -0.36 (0.47), residues: 122 loop : -0.69 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 464 HIS 0.005 0.001 HIS A 116 PHE 0.013 0.001 PHE A 446 TYR 0.014 0.001 TYR A 155 ARG 0.008 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 641) hydrogen bonds : angle 4.43465 ( 1741) covalent geometry : bond 0.00358 (14338) covalent geometry : angle 0.52493 (20003) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.8040 (mtmt) cc_final: 0.7789 (mtmt) REVERT: A 648 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7188 (tmm) REVERT: A 694 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.8007 (tmm) REVERT: A 709 GLN cc_start: 0.8352 (pp30) cc_final: 0.7893 (tp40) REVERT: A 746 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8572 (tt0) REVERT: A 822 MET cc_start: 0.5996 (mmt) cc_final: 0.4175 (mpt) REVERT: A 846 PHE cc_start: 0.8598 (m-10) cc_final: 0.8144 (m-10) REVERT: A 916 PHE cc_start: 0.8832 (m-10) cc_final: 0.8533 (m-10) REVERT: A 920 GLN cc_start: 0.8933 (mp10) cc_final: 0.8496 (mp10) REVERT: A 933 GLN cc_start: 0.8963 (tt0) cc_final: 0.8425 (tm-30) REVERT: A 969 ASP cc_start: 0.8402 (m-30) cc_final: 0.8166 (m-30) REVERT: A 1043 MET cc_start: 0.7939 (mmm) cc_final: 0.7683 (mmp) REVERT: A 1340 LYS cc_start: 0.8762 (tptt) cc_final: 0.8503 (mptt) outliers start: 30 outliers final: 10 residues processed: 122 average time/residue: 1.2082 time to fit residues: 163.1989 Evaluate side-chains 110 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1250 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 66 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 142 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 ASN A1364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.121792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.078439 restraints weight = 24604.550| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.14 r_work: 0.2891 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14338 Z= 0.159 Angle : 0.522 11.136 20003 Z= 0.277 Chirality : 0.037 0.141 2310 Planarity : 0.003 0.045 2041 Dihedral : 18.870 89.256 3400 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.76 % Allowed : 18.21 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.23), residues: 1329 helix: 1.55 (0.20), residues: 667 sheet: -0.44 (0.46), residues: 126 loop : -0.63 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 464 HIS 0.005 0.001 HIS A 116 PHE 0.012 0.001 PHE A 446 TYR 0.014 0.001 TYR A 155 ARG 0.005 0.000 ARG A 655 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 641) hydrogen bonds : angle 4.36879 ( 1741) covalent geometry : bond 0.00355 (14338) covalent geometry : angle 0.52223 (20003) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 ASP cc_start: 0.8039 (t0) cc_final: 0.7645 (t70) REVERT: A 631 MET cc_start: 0.8593 (mmp) cc_final: 0.8334 (mmp) REVERT: A 694 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8047 (tmm) REVERT: A 709 GLN cc_start: 0.8551 (pp30) cc_final: 0.7936 (tp40) REVERT: A 746 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: A 846 PHE cc_start: 0.8641 (m-10) cc_final: 0.8294 (m-10) REVERT: A 916 PHE cc_start: 0.8813 (m-10) cc_final: 0.8490 (m-10) REVERT: A 920 GLN cc_start: 0.8959 (mp10) cc_final: 0.8553 (mp10) REVERT: A 933 GLN cc_start: 0.8948 (tt0) cc_final: 0.8400 (tm-30) REVERT: A 1043 MET cc_start: 0.7948 (mmm) cc_final: 0.7731 (mmp) REVERT: A 1340 LYS cc_start: 0.8786 (tptt) cc_final: 0.8520 (mptt) outliers start: 32 outliers final: 11 residues processed: 121 average time/residue: 1.2123 time to fit residues: 161.7677 Evaluate side-chains 108 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1250 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 0.0060 chunk 136 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.122848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.079616 restraints weight = 24778.211| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.15 r_work: 0.2917 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14338 Z= 0.129 Angle : 0.505 12.156 20003 Z= 0.267 Chirality : 0.036 0.137 2310 Planarity : 0.003 0.043 2041 Dihedral : 18.792 89.520 3400 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.50 % Allowed : 18.46 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.23), residues: 1329 helix: 1.67 (0.20), residues: 667 sheet: -0.35 (0.47), residues: 122 loop : -0.56 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 464 HIS 0.004 0.001 HIS A 116 PHE 0.011 0.001 PHE A 446 TYR 0.015 0.001 TYR A 812 ARG 0.007 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.03301 ( 641) hydrogen bonds : angle 4.28036 ( 1741) covalent geometry : bond 0.00281 (14338) covalent geometry : angle 0.50530 (20003) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7756 (mtmt) REVERT: A 558 LYS cc_start: 0.8645 (mmtp) cc_final: 0.8311 (mmmt) REVERT: A 628 ASP cc_start: 0.8110 (t0) cc_final: 0.7737 (t70) REVERT: A 631 MET cc_start: 0.8572 (mmp) cc_final: 0.8317 (mmp) REVERT: A 694 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8099 (tmm) REVERT: A 709 GLN cc_start: 0.8584 (pp30) cc_final: 0.7942 (tp40) REVERT: A 746 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: A 822 MET cc_start: 0.6178 (mmt) cc_final: 0.4521 (mpt) REVERT: A 846 PHE cc_start: 0.8722 (m-10) cc_final: 0.8287 (m-10) REVERT: A 916 PHE cc_start: 0.8876 (m-10) cc_final: 0.8461 (m-10) REVERT: A 920 GLN cc_start: 0.9006 (mp10) cc_final: 0.8557 (mp10) REVERT: A 933 GLN cc_start: 0.8944 (tt0) cc_final: 0.8392 (tm-30) REVERT: A 1043 MET cc_start: 0.7926 (mmm) cc_final: 0.7712 (mmp) REVERT: A 1049 GLU cc_start: 0.8085 (pm20) cc_final: 0.7086 (pp20) REVERT: A 1340 LYS cc_start: 0.8768 (tptt) cc_final: 0.8531 (mptt) outliers start: 29 outliers final: 11 residues processed: 119 average time/residue: 1.1881 time to fit residues: 157.6322 Evaluate side-chains 105 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1072 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 104 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 59 optimal weight: 0.0570 chunk 134 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 ASN A1364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.122158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.078885 restraints weight = 24701.101| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.14 r_work: 0.2899 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14338 Z= 0.144 Angle : 0.517 12.342 20003 Z= 0.270 Chirality : 0.036 0.137 2310 Planarity : 0.003 0.044 2041 Dihedral : 18.782 90.256 3400 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.98 % Allowed : 19.41 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1329 helix: 1.76 (0.20), residues: 666 sheet: -0.42 (0.46), residues: 128 loop : -0.52 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 464 HIS 0.004 0.001 HIS A 116 PHE 0.018 0.001 PHE A 518 TYR 0.019 0.001 TYR A 812 ARG 0.009 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 641) hydrogen bonds : angle 4.27224 ( 1741) covalent geometry : bond 0.00320 (14338) covalent geometry : angle 0.51663 (20003) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.7968 (mtmt) cc_final: 0.7709 (mtmt) REVERT: A 628 ASP cc_start: 0.8049 (t0) cc_final: 0.7633 (t70) REVERT: A 631 MET cc_start: 0.8580 (mmp) cc_final: 0.8317 (mmp) REVERT: A 694 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8181 (tmm) REVERT: A 709 GLN cc_start: 0.8606 (pp30) cc_final: 0.7990 (tp40) REVERT: A 746 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: A 822 MET cc_start: 0.6068 (mmt) cc_final: 0.4471 (mpt) REVERT: A 846 PHE cc_start: 0.8728 (m-10) cc_final: 0.8321 (m-10) REVERT: A 916 PHE cc_start: 0.8903 (m-10) cc_final: 0.8436 (m-10) REVERT: A 917 ILE cc_start: 0.9116 (mm) cc_final: 0.8832 (mt) REVERT: A 920 GLN cc_start: 0.8966 (mp10) cc_final: 0.8539 (mp10) REVERT: A 933 GLN cc_start: 0.8962 (tt0) cc_final: 0.8411 (tm-30) REVERT: A 1043 MET cc_start: 0.7914 (mmm) cc_final: 0.7685 (mmp) REVERT: A 1340 LYS cc_start: 0.8809 (tptt) cc_final: 0.8514 (mptt) outliers start: 23 outliers final: 13 residues processed: 113 average time/residue: 1.1466 time to fit residues: 144.1008 Evaluate side-chains 107 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1224 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 3 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 118 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 ASN A1364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.121931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.078383 restraints weight = 24726.250| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.16 r_work: 0.2890 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14338 Z= 0.155 Angle : 0.534 11.485 20003 Z= 0.280 Chirality : 0.036 0.137 2310 Planarity : 0.003 0.044 2041 Dihedral : 18.796 90.450 3400 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.81 % Allowed : 20.02 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1329 helix: 1.77 (0.20), residues: 667 sheet: -0.43 (0.46), residues: 128 loop : -0.51 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 464 HIS 0.004 0.001 HIS A 116 PHE 0.018 0.001 PHE A 518 TYR 0.022 0.001 TYR A 812 ARG 0.009 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 641) hydrogen bonds : angle 4.27996 ( 1741) covalent geometry : bond 0.00346 (14338) covalent geometry : angle 0.53411 (20003) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7633 (mtmt) REVERT: A 558 LYS cc_start: 0.8327 (mmmt) cc_final: 0.8066 (mmmm) REVERT: A 628 ASP cc_start: 0.8035 (t0) cc_final: 0.7586 (t70) REVERT: A 631 MET cc_start: 0.8569 (mmp) cc_final: 0.8291 (mmp) REVERT: A 661 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8595 (ptp-110) REVERT: A 694 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8195 (tmm) REVERT: A 709 GLN cc_start: 0.8637 (pp30) cc_final: 0.8014 (tp40) REVERT: A 746 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: A 822 MET cc_start: 0.6019 (mmt) cc_final: 0.4457 (mpt) REVERT: A 846 PHE cc_start: 0.8746 (m-10) cc_final: 0.8313 (m-10) REVERT: A 916 PHE cc_start: 0.8909 (m-10) cc_final: 0.8412 (m-10) REVERT: A 917 ILE cc_start: 0.9117 (mm) cc_final: 0.8831 (mt) REVERT: A 920 GLN cc_start: 0.8949 (mp10) cc_final: 0.8491 (mp10) REVERT: A 933 GLN cc_start: 0.8953 (tt0) cc_final: 0.8396 (tm-30) REVERT: A 1043 MET cc_start: 0.7910 (mmm) cc_final: 0.7677 (mmp) REVERT: A 1242 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.7099 (m-80) REVERT: A 1340 LYS cc_start: 0.8798 (tptt) cc_final: 0.8493 (mptt) outliers start: 21 outliers final: 13 residues processed: 108 average time/residue: 1.1764 time to fit residues: 140.6351 Evaluate side-chains 107 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1242 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 2 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 117 optimal weight: 0.3980 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 0.3980 chunk 135 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 ASN A1364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.122411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.079066 restraints weight = 24499.722| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.14 r_work: 0.2900 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14338 Z= 0.138 Angle : 0.526 13.016 20003 Z= 0.275 Chirality : 0.036 0.137 2310 Planarity : 0.003 0.045 2041 Dihedral : 18.800 90.487 3400 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.07 % Allowed : 19.76 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1329 helix: 1.81 (0.20), residues: 668 sheet: -0.41 (0.47), residues: 124 loop : -0.48 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 464 HIS 0.004 0.001 HIS A 116 PHE 0.018 0.001 PHE A 518 TYR 0.019 0.001 TYR A 812 ARG 0.010 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 641) hydrogen bonds : angle 4.23657 ( 1741) covalent geometry : bond 0.00308 (14338) covalent geometry : angle 0.52597 (20003) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.7971 (mtmt) cc_final: 0.7680 (mtmt) REVERT: A 631 MET cc_start: 0.8527 (mmp) cc_final: 0.8313 (mmp) REVERT: A 661 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8661 (ptp-110) REVERT: A 694 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7701 (tmm) REVERT: A 698 HIS cc_start: 0.8449 (m-70) cc_final: 0.7991 (m90) REVERT: A 709 GLN cc_start: 0.8668 (pp30) cc_final: 0.8057 (tp40) REVERT: A 746 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: A 822 MET cc_start: 0.6109 (mmt) cc_final: 0.4568 (mpt) REVERT: A 846 PHE cc_start: 0.8766 (m-10) cc_final: 0.8228 (m-10) REVERT: A 916 PHE cc_start: 0.8890 (m-10) cc_final: 0.8466 (m-10) REVERT: A 920 GLN cc_start: 0.8933 (mp10) cc_final: 0.8519 (mp10) REVERT: A 933 GLN cc_start: 0.8947 (tt0) cc_final: 0.8384 (tm-30) REVERT: A 990 ASN cc_start: 0.9266 (OUTLIER) cc_final: 0.8837 (m110) REVERT: A 1043 MET cc_start: 0.7914 (mmm) cc_final: 0.7681 (mmp) REVERT: A 1340 LYS cc_start: 0.8793 (tptt) cc_final: 0.8508 (mptt) outliers start: 24 outliers final: 13 residues processed: 110 average time/residue: 1.3184 time to fit residues: 160.3610 Evaluate side-chains 109 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1224 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 ASN A1364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.121583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.078114 restraints weight = 24730.123| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.14 r_work: 0.2886 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14338 Z= 0.163 Angle : 0.545 13.552 20003 Z= 0.286 Chirality : 0.037 0.167 2310 Planarity : 0.003 0.046 2041 Dihedral : 18.821 90.900 3400 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.81 % Allowed : 19.93 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.23), residues: 1329 helix: 1.81 (0.20), residues: 665 sheet: -0.47 (0.46), residues: 128 loop : -0.48 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 464 HIS 0.005 0.001 HIS A 116 PHE 0.020 0.001 PHE A 518 TYR 0.019 0.001 TYR A 812 ARG 0.010 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 641) hydrogen bonds : angle 4.27455 ( 1741) covalent geometry : bond 0.00369 (14338) covalent geometry : angle 0.54453 (20003) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.7950 (mtmt) cc_final: 0.7635 (mtmt) REVERT: A 694 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7851 (tmm) REVERT: A 698 HIS cc_start: 0.8452 (m-70) cc_final: 0.8043 (m90) REVERT: A 709 GLN cc_start: 0.8686 (pp30) cc_final: 0.8096 (tp40) REVERT: A 746 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8508 (tt0) REVERT: A 822 MET cc_start: 0.6080 (mmt) cc_final: 0.4588 (mpt) REVERT: A 846 PHE cc_start: 0.8812 (m-10) cc_final: 0.8277 (m-10) REVERT: A 920 GLN cc_start: 0.8929 (mp10) cc_final: 0.8387 (mp10) REVERT: A 933 GLN cc_start: 0.8965 (tt0) cc_final: 0.8413 (tm-30) REVERT: A 990 ASN cc_start: 0.9274 (OUTLIER) cc_final: 0.8879 (m-40) REVERT: A 1340 LYS cc_start: 0.8829 (tptt) cc_final: 0.8513 (mptt) outliers start: 21 outliers final: 13 residues processed: 107 average time/residue: 1.8348 time to fit residues: 221.7494 Evaluate side-chains 107 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1224 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 43 optimal weight: 0.3980 chunk 101 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 140 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 76 optimal weight: 0.0370 chunk 18 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 ASN A1364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.122956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.079755 restraints weight = 24994.859| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.15 r_work: 0.2920 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14338 Z= 0.122 Angle : 0.528 9.769 20003 Z= 0.277 Chirality : 0.036 0.149 2310 Planarity : 0.003 0.059 2041 Dihedral : 18.810 90.659 3400 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.38 % Allowed : 20.36 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.23), residues: 1329 helix: 1.86 (0.20), residues: 668 sheet: -0.42 (0.47), residues: 124 loop : -0.46 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 464 HIS 0.004 0.001 HIS A 595 PHE 0.019 0.001 PHE A 518 TYR 0.017 0.001 TYR A 812 ARG 0.013 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 641) hydrogen bonds : angle 4.23470 ( 1741) covalent geometry : bond 0.00271 (14338) covalent geometry : angle 0.52780 (20003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10804.46 seconds wall clock time: 189 minutes 1.58 seconds (11341.58 seconds total)