Starting phenix.real_space_refine on Tue Jan 13 17:36:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gzp_34400/01_2026/8gzp_34400.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gzp_34400/01_2026/8gzp_34400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gzp_34400/01_2026/8gzp_34400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gzp_34400/01_2026/8gzp_34400.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gzp_34400/01_2026/8gzp_34400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gzp_34400/01_2026/8gzp_34400.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 69 5.49 5 Mg 1 5.21 5 S 43 5.16 5 C 4939 2.51 5 N 1493 2.21 5 O 1690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8237 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 854, 6778 Classifications: {'peptide': 854} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 40, 'TRANS': 813} Chain breaks: 4 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 18, 'ARG:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 114 Chain: "S" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1428 Classifications: {'RNA': 67} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 27} Link IDs: {'rna2p': 7, 'rna3p': 59} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5448 SG CYS A 728 59.201 34.952 35.842 1.00 46.20 S ATOM 6434 SG CYS A 847 62.392 36.937 36.572 1.00 56.00 S ATOM 3330 SG CYS A 446 19.311 55.009 40.583 1.00 71.46 S ATOM 3346 SG CYS A 449 19.952 51.491 39.994 1.00 65.65 S Time building chain proxies: 1.96, per 1000 atoms: 0.24 Number of scatterers: 8237 At special positions: 0 Unit cell: (124.275, 95.2775, 101.905, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 43 16.00 P 69 15.00 Mg 1 11.99 O 1690 8.00 N 1493 7.00 C 4939 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 248.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 714 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 712 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 728 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 847 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" NE2 HIS A 441 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 446 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 449 " Number of angles added : 2 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 5 sheets defined 54.7% alpha, 8.2% beta 22 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 8 through 19 Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 38 through 48 Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.853A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG A 68 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.563A pdb=" N TYR A 134 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 226 through 244 removed outlier: 3.939A pdb=" N THR A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 272 through 287 removed outlier: 5.966A pdb=" N GLU A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 329 through 333 removed outlier: 4.200A pdb=" N VAL A 333 " --> pdb=" O PRO A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.654A pdb=" N THR A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 358 Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.789A pdb=" N LYS A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 404 Processing helix chain 'A' and resid 417 through 427 removed outlier: 4.009A pdb=" N ALA A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 444 Processing helix chain 'A' and resid 472 through 489 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 510 through 523 removed outlier: 4.173A pdb=" N GLY A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N TYR A 516 " --> pdb=" O HIS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.588A pdb=" N ILE A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 550 removed outlier: 3.523A pdb=" N LEU A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'A' and resid 557 through 572 removed outlier: 3.970A pdb=" N LEU A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 572 " --> pdb=" O PHE A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 625 Processing helix chain 'A' and resid 629 through 635 Processing helix chain 'A' and resid 639 through 656 removed outlier: 4.661A pdb=" N ILE A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLU A 653 " --> pdb=" O THR A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 removed outlier: 3.534A pdb=" N PHE A 674 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 675 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 684 removed outlier: 4.311A pdb=" N LEU A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 Processing helix chain 'A' and resid 730 through 739 removed outlier: 3.911A pdb=" N LEU A 734 " --> pdb=" O PRO A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 766 removed outlier: 3.691A pdb=" N CYS A 753 " --> pdb=" O LYS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 782 Processing helix chain 'A' and resid 808 through 818 Processing helix chain 'A' and resid 840 through 847 Processing helix chain 'A' and resid 853 through 875 removed outlier: 5.449A pdb=" N LEU A 864 " --> pdb=" O ALA A 860 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 866 " --> pdb=" O ASN A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 886 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 127 removed outlier: 8.770A pdb=" N LYS A 125 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL A 100 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N MET A 127 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY A 102 " --> pdb=" O MET A 127 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLY A 75 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 99 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 310 removed outlier: 5.765A pdb=" N TYR A 304 " --> pdb=" O SER A 593 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER A 593 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY A 306 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR A 587 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 658 through 661 Processing sheet with id=AA5, first strand: chain 'A' and resid 712 through 717 327 hydrogen bonds defined for protein. 921 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2064 1.33 - 1.45: 1997 1.45 - 1.57: 4305 1.57 - 1.69: 135 1.69 - 1.80: 72 Bond restraints: 8573 Sorted by residual: bond pdb=" CB ILE A 660 " pdb=" CG2 ILE A 660 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.07e+00 bond pdb=" CB TRP A 762 " pdb=" CG TRP A 762 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.57e+00 bond pdb=" CG1 ILE A 660 " pdb=" CD1 ILE A 660 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.82e+00 bond pdb=" CG LEU A 618 " pdb=" CD2 LEU A 618 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.44e+00 bond pdb=" CB GLN A 731 " pdb=" CG GLN A 731 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.41e+00 ... (remaining 8568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 11070 1.30 - 2.59: 725 2.59 - 3.89: 109 3.89 - 5.18: 32 5.18 - 6.48: 7 Bond angle restraints: 11943 Sorted by residual: angle pdb=" C3' G S 60 " pdb=" O3' G S 60 " pdb=" P U S 61 " ideal model delta sigma weight residual 120.20 124.27 -4.07 1.50e+00 4.44e-01 7.35e+00 angle pdb=" NE ARG A 657 " pdb=" CZ ARG A 657 " pdb=" NH1 ARG A 657 " ideal model delta sigma weight residual 121.50 119.00 2.50 1.00e+00 1.00e+00 6.27e+00 angle pdb=" N ARG A 792 " pdb=" CA ARG A 792 " pdb=" C ARG A 792 " ideal model delta sigma weight residual 110.35 113.83 -3.48 1.40e+00 5.10e-01 6.17e+00 angle pdb=" C3' A S 19 " pdb=" O3' A S 19 " pdb=" P C S 20 " ideal model delta sigma weight residual 120.20 123.90 -3.70 1.50e+00 4.44e-01 6.10e+00 angle pdb=" C HIS A 712 " pdb=" N PHE A 713 " pdb=" CA PHE A 713 " ideal model delta sigma weight residual 122.73 118.75 3.98 1.62e+00 3.81e-01 6.03e+00 ... (remaining 11938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.35: 4856 29.35 - 58.70: 231 58.70 - 88.05: 71 88.05 - 117.40: 8 117.40 - 146.75: 1 Dihedral angle restraints: 5167 sinusoidal: 2709 harmonic: 2458 Sorted by residual: dihedral pdb=" C5' GDP S 201 " pdb=" O5' GDP S 201 " pdb=" PA GDP S 201 " pdb=" O3A GDP S 201 " ideal model delta sinusoidal sigma weight residual 179.98 -65.56 -114.46 1 2.00e+01 2.50e-03 3.39e+01 dihedral pdb=" O2B GDP S 201 " pdb=" O3A GDP S 201 " pdb=" PB GDP S 201 " pdb=" PA GDP S 201 " ideal model delta sinusoidal sigma weight residual 180.00 68.98 111.02 1 2.00e+01 2.50e-03 3.26e+01 dihedral pdb=" CA HIS A 711 " pdb=" C HIS A 711 " pdb=" N HIS A 712 " pdb=" CA HIS A 712 " ideal model delta harmonic sigma weight residual 180.00 160.26 19.74 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 5164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 989 0.049 - 0.097: 293 0.097 - 0.146: 60 0.146 - 0.194: 4 0.194 - 0.243: 2 Chirality restraints: 1348 Sorted by residual: chirality pdb=" C1' G S 60 " pdb=" O4' G S 60 " pdb=" C2' G S 60 " pdb=" N9 G S 60 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" P A S 1 " pdb=" OP1 A S 1 " pdb=" OP2 A S 1 " pdb=" O5' A S 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.63 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C1' G S 18 " pdb=" O4' G S 18 " pdb=" C2' G S 18 " pdb=" N9 G S 18 " both_signs ideal model delta sigma weight residual False 2.46 2.28 0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 1345 not shown) Planarity restraints: 1268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 136 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO A 137 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 137 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 137 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 364 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO A 365 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 740 " -0.008 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C ILE A 740 " 0.026 2.00e-02 2.50e+03 pdb=" O ILE A 740 " -0.010 2.00e-02 2.50e+03 pdb=" N SER A 741 " -0.009 2.00e-02 2.50e+03 ... (remaining 1265 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 53 2.57 - 3.15: 6806 3.15 - 3.73: 13435 3.73 - 4.32: 18294 4.32 - 4.90: 29176 Nonbonded interactions: 67764 Sorted by model distance: nonbonded pdb=" OE2 GLU A 437 " pdb="ZN ZN A1002 " model vdw 1.984 2.230 nonbonded pdb=" O2A GDP S 201 " pdb="MG MG S 202 " model vdw 1.986 2.170 nonbonded pdb=" OP1 A S 1 " pdb="MG MG S 202 " model vdw 2.042 2.170 nonbonded pdb=" O1B GDP S 201 " pdb="MG MG S 202 " model vdw 2.103 2.170 nonbonded pdb=" O2' A S 31 " pdb=" OP2 G S 32 " model vdw 2.244 3.040 ... (remaining 67759 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 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: 1.330 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.000 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 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 : 0.010 0.067 8581 Z= 0.433 Angle : 0.744 6.477 11945 Z= 0.402 Chirality : 0.047 0.243 1348 Planarity : 0.004 0.039 1268 Dihedral : 17.825 146.748 3583 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.14 % Allowed : 3.68 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.29), residues: 844 helix: 0.98 (0.26), residues: 390 sheet: -0.87 (0.57), residues: 88 loop : -1.44 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 792 TYR 0.019 0.002 TYR A 838 PHE 0.021 0.002 PHE A 674 TRP 0.014 0.002 TRP A 833 HIS 0.004 0.001 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.01001 ( 8573) covalent geometry : angle 0.74396 (11943) hydrogen bonds : bond 0.13484 ( 382) hydrogen bonds : angle 5.66929 ( 1027) metal coordination : bond 0.03407 ( 7) metal coordination : angle 2.26749 ( 2) Misc. bond : bond 0.00061 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.326 Fit side-chains REVERT: A 84 ARG cc_start: 0.8586 (mtp85) cc_final: 0.8241 (mmm-85) REVERT: A 192 HIS cc_start: 0.8316 (OUTLIER) cc_final: 0.8047 (t-170) REVERT: A 240 ASN cc_start: 0.8593 (m110) cc_final: 0.8310 (m110) REVERT: A 634 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7810 (mm-30) REVERT: A 765 MET cc_start: 0.8956 (mmt) cc_final: 0.8613 (mmt) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.1019 time to fit residues: 13.8888 Evaluate side-chains 80 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 731 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.123598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.081827 restraints weight = 15432.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.084692 restraints weight = 8014.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.086471 restraints weight = 5438.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.087532 restraints weight = 4304.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.088262 restraints weight = 3761.275| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8581 Z= 0.118 Angle : 0.529 8.939 11945 Z= 0.268 Chirality : 0.039 0.230 1348 Planarity : 0.004 0.041 1268 Dihedral : 18.646 162.209 1964 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.99 % Allowed : 7.08 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.29), residues: 844 helix: 1.56 (0.26), residues: 400 sheet: -0.69 (0.56), residues: 88 loop : -1.10 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 262 TYR 0.012 0.001 TYR A 838 PHE 0.013 0.001 PHE A 242 TRP 0.010 0.001 TRP A 171 HIS 0.003 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8573) covalent geometry : angle 0.52937 (11943) hydrogen bonds : bond 0.04065 ( 382) hydrogen bonds : angle 4.38919 ( 1027) metal coordination : bond 0.01212 ( 7) metal coordination : angle 0.19324 ( 2) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.206 Fit side-chains REVERT: A 37 ASP cc_start: 0.8708 (m-30) cc_final: 0.8346 (t0) REVERT: A 240 ASN cc_start: 0.8553 (m110) cc_final: 0.8183 (m110) REVERT: A 256 ASP cc_start: 0.8514 (t0) cc_final: 0.8280 (t0) REVERT: A 634 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7918 (mm-30) REVERT: A 746 TRP cc_start: 0.7697 (m-90) cc_final: 0.6394 (m-90) REVERT: A 765 MET cc_start: 0.9022 (mmt) cc_final: 0.8575 (mmt) outliers start: 7 outliers final: 5 residues processed: 109 average time/residue: 0.0839 time to fit residues: 13.2102 Evaluate side-chains 95 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 771 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 83 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.0060 chunk 27 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 731 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.121377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.080638 restraints weight = 15364.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.083437 restraints weight = 7996.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.085151 restraints weight = 5415.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.086249 restraints weight = 4297.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.086824 restraints weight = 3735.132| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8581 Z= 0.147 Angle : 0.511 8.671 11945 Z= 0.259 Chirality : 0.039 0.191 1348 Planarity : 0.004 0.041 1268 Dihedral : 18.191 163.516 1964 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.84 % Allowed : 8.64 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.29), residues: 844 helix: 1.70 (0.26), residues: 395 sheet: -0.62 (0.55), residues: 90 loop : -1.06 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 792 TYR 0.012 0.001 TYR A 482 PHE 0.015 0.001 PHE A 674 TRP 0.009 0.001 TRP A 833 HIS 0.003 0.001 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8573) covalent geometry : angle 0.51074 (11943) hydrogen bonds : bond 0.03922 ( 382) hydrogen bonds : angle 4.28360 ( 1027) metal coordination : bond 0.01301 ( 7) metal coordination : angle 0.80987 ( 2) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8715 (m-30) cc_final: 0.8352 (t0) REVERT: A 167 MET cc_start: 0.8952 (tmm) cc_final: 0.8742 (ppp) REVERT: A 186 MET cc_start: 0.8554 (mmm) cc_final: 0.8278 (mmm) REVERT: A 240 ASN cc_start: 0.8518 (m110) cc_final: 0.8241 (m110) REVERT: A 340 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7591 (mmm) REVERT: A 746 TRP cc_start: 0.7799 (m-90) cc_final: 0.6633 (m-90) outliers start: 13 outliers final: 7 residues processed: 99 average time/residue: 0.0855 time to fit residues: 12.1005 Evaluate side-chains 97 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 797 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 59 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.0060 chunk 70 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.0138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.123107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.082208 restraints weight = 15600.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.085035 restraints weight = 8133.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.086809 restraints weight = 5513.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.087825 restraints weight = 4353.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.088506 restraints weight = 3807.814| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8581 Z= 0.110 Angle : 0.481 9.285 11945 Z= 0.244 Chirality : 0.038 0.173 1348 Planarity : 0.004 0.043 1268 Dihedral : 17.950 162.003 1964 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.12 % Allowed : 9.77 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.29), residues: 844 helix: 1.84 (0.26), residues: 401 sheet: -0.55 (0.55), residues: 90 loop : -1.00 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 792 TYR 0.010 0.001 TYR A 838 PHE 0.013 0.001 PHE A 674 TRP 0.008 0.001 TRP A 331 HIS 0.003 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8573) covalent geometry : angle 0.48139 (11943) hydrogen bonds : bond 0.03471 ( 382) hydrogen bonds : angle 4.10995 ( 1027) metal coordination : bond 0.00799 ( 7) metal coordination : angle 0.42951 ( 2) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8632 (m-30) cc_final: 0.8359 (t0) REVERT: A 240 ASN cc_start: 0.8510 (m110) cc_final: 0.8170 (m110) REVERT: A 340 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7531 (mmm) REVERT: A 634 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7845 (mm-30) REVERT: A 792 ARG cc_start: 0.8011 (ptp-110) cc_final: 0.7739 (ptp-110) outliers start: 15 outliers final: 10 residues processed: 108 average time/residue: 0.0849 time to fit residues: 13.1672 Evaluate side-chains 99 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 797 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 33 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.123831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.083203 restraints weight = 15454.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.085985 restraints weight = 8188.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.087732 restraints weight = 5578.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.088748 restraints weight = 4432.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.089435 restraints weight = 3879.742| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8581 Z= 0.129 Angle : 0.498 9.602 11945 Z= 0.250 Chirality : 0.038 0.198 1348 Planarity : 0.004 0.042 1268 Dihedral : 17.859 161.367 1964 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.27 % Allowed : 11.05 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.29), residues: 844 helix: 1.83 (0.26), residues: 402 sheet: -0.45 (0.55), residues: 90 loop : -0.95 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 792 TYR 0.010 0.001 TYR A 482 PHE 0.014 0.001 PHE A 674 TRP 0.029 0.001 TRP A 795 HIS 0.003 0.001 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8573) covalent geometry : angle 0.49795 (11943) hydrogen bonds : bond 0.03542 ( 382) hydrogen bonds : angle 4.08484 ( 1027) metal coordination : bond 0.01134 ( 7) metal coordination : angle 1.03998 ( 2) Misc. bond : bond 0.00073 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8625 (m-30) cc_final: 0.8375 (t0) REVERT: A 182 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8488 (tt) REVERT: A 240 ASN cc_start: 0.8445 (m110) cc_final: 0.8164 (m110) REVERT: A 340 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7465 (mmm) REVERT: A 637 HIS cc_start: 0.6889 (p90) cc_final: 0.6654 (p90) REVERT: A 746 TRP cc_start: 0.7701 (m-90) cc_final: 0.6466 (m-90) outliers start: 16 outliers final: 12 residues processed: 99 average time/residue: 0.0857 time to fit residues: 12.1355 Evaluate side-chains 102 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 797 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 12 optimal weight: 0.0670 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.123525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.082554 restraints weight = 15367.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.085439 restraints weight = 7959.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.087207 restraints weight = 5368.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.088248 restraints weight = 4249.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.088957 restraints weight = 3711.408| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8581 Z= 0.105 Angle : 0.490 11.257 11945 Z= 0.243 Chirality : 0.037 0.198 1348 Planarity : 0.004 0.042 1268 Dihedral : 17.716 160.938 1964 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.98 % Allowed : 11.05 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.29), residues: 844 helix: 1.93 (0.26), residues: 404 sheet: -0.33 (0.55), residues: 90 loop : -0.89 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.009 0.001 TYR A 838 PHE 0.013 0.001 PHE A 674 TRP 0.015 0.001 TRP A 795 HIS 0.002 0.001 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8573) covalent geometry : angle 0.49002 (11943) hydrogen bonds : bond 0.03385 ( 382) hydrogen bonds : angle 4.01271 ( 1027) metal coordination : bond 0.01077 ( 7) metal coordination : angle 1.07860 ( 2) Misc. bond : bond 0.00073 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8670 (m-30) cc_final: 0.8364 (t0) REVERT: A 158 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7904 (tm-30) REVERT: A 182 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8454 (tt) REVERT: A 186 MET cc_start: 0.8398 (mmm) cc_final: 0.8141 (mmm) REVERT: A 240 ASN cc_start: 0.8507 (m110) cc_final: 0.8163 (m110) REVERT: A 637 HIS cc_start: 0.7043 (p90) cc_final: 0.6775 (p90) outliers start: 14 outliers final: 11 residues processed: 101 average time/residue: 0.0810 time to fit residues: 11.8134 Evaluate side-chains 101 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 771 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 70 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 51 optimal weight: 0.0570 chunk 7 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.122306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.081715 restraints weight = 15615.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.084492 restraints weight = 8232.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.086216 restraints weight = 5608.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.087184 restraints weight = 4449.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.087895 restraints weight = 3896.290| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8581 Z= 0.165 Angle : 0.530 11.432 11945 Z= 0.261 Chirality : 0.039 0.204 1348 Planarity : 0.004 0.043 1268 Dihedral : 17.644 160.046 1964 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.12 % Allowed : 11.19 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.29), residues: 844 helix: 1.85 (0.26), residues: 402 sheet: -0.37 (0.56), residues: 90 loop : -0.89 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.013 0.001 TYR A 482 PHE 0.015 0.001 PHE A 674 TRP 0.010 0.001 TRP A 795 HIS 0.004 0.001 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8573) covalent geometry : angle 0.52937 (11943) hydrogen bonds : bond 0.03701 ( 382) hydrogen bonds : angle 4.12885 ( 1027) metal coordination : bond 0.01765 ( 7) metal coordination : angle 1.51754 ( 2) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8693 (m-30) cc_final: 0.8352 (t0) REVERT: A 158 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 182 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8459 (tt) REVERT: A 186 MET cc_start: 0.8494 (mmm) cc_final: 0.8227 (mmm) REVERT: A 240 ASN cc_start: 0.8502 (m110) cc_final: 0.8177 (m110) REVERT: A 637 HIS cc_start: 0.7071 (p90) cc_final: 0.6820 (p90) outliers start: 15 outliers final: 13 residues processed: 98 average time/residue: 0.0819 time to fit residues: 11.5053 Evaluate side-chains 102 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 771 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.122361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.082052 restraints weight = 15526.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.084831 restraints weight = 7981.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.086592 restraints weight = 5357.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087721 restraints weight = 4228.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.088227 restraints weight = 3654.041| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8581 Z= 0.098 Angle : 0.497 11.681 11945 Z= 0.242 Chirality : 0.037 0.195 1348 Planarity : 0.004 0.043 1268 Dihedral : 17.501 160.405 1964 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.98 % Allowed : 11.33 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.29), residues: 844 helix: 1.99 (0.26), residues: 403 sheet: -0.23 (0.56), residues: 90 loop : -0.81 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.009 0.001 TYR A 838 PHE 0.012 0.001 PHE A 674 TRP 0.020 0.001 TRP A 171 HIS 0.002 0.000 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 8573) covalent geometry : angle 0.49636 (11943) hydrogen bonds : bond 0.03326 ( 382) hydrogen bonds : angle 3.99886 ( 1027) metal coordination : bond 0.00905 ( 7) metal coordination : angle 1.46364 ( 2) Misc. bond : bond 0.00073 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8683 (m-30) cc_final: 0.8363 (t0) REVERT: A 158 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7887 (tm-30) REVERT: A 182 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8425 (tt) REVERT: A 186 MET cc_start: 0.8502 (mmm) cc_final: 0.8205 (mmm) REVERT: A 240 ASN cc_start: 0.8504 (m110) cc_final: 0.8181 (m-40) REVERT: A 637 HIS cc_start: 0.7125 (p90) cc_final: 0.6866 (p90) outliers start: 14 outliers final: 11 residues processed: 104 average time/residue: 0.0776 time to fit residues: 11.8455 Evaluate side-chains 104 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 771 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.122942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.082476 restraints weight = 15477.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.085250 restraints weight = 8018.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.086980 restraints weight = 5414.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.087953 restraints weight = 4291.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.088706 restraints weight = 3753.723| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8581 Z= 0.096 Angle : 0.496 11.998 11945 Z= 0.239 Chirality : 0.037 0.241 1348 Planarity : 0.004 0.042 1268 Dihedral : 17.357 160.312 1962 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.27 % Allowed : 11.47 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.29), residues: 844 helix: 2.02 (0.26), residues: 406 sheet: -0.15 (0.56), residues: 90 loop : -0.81 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 842 TYR 0.009 0.001 TYR A 838 PHE 0.012 0.001 PHE A 674 TRP 0.013 0.001 TRP A 171 HIS 0.003 0.000 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 8573) covalent geometry : angle 0.49564 (11943) hydrogen bonds : bond 0.03245 ( 382) hydrogen bonds : angle 3.95798 ( 1027) metal coordination : bond 0.00962 ( 7) metal coordination : angle 1.13425 ( 2) Misc. bond : bond 0.00069 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8703 (m-30) cc_final: 0.8372 (t0) REVERT: A 158 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7876 (tm-30) REVERT: A 182 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8389 (tt) REVERT: A 186 MET cc_start: 0.8483 (mmm) cc_final: 0.8166 (mmm) REVERT: A 240 ASN cc_start: 0.8527 (m110) cc_final: 0.8217 (m-40) REVERT: A 340 MET cc_start: 0.8007 (ttm) cc_final: 0.7765 (ttm) REVERT: A 637 HIS cc_start: 0.7132 (p90) cc_final: 0.6888 (p90) outliers start: 16 outliers final: 12 residues processed: 105 average time/residue: 0.0837 time to fit residues: 12.6337 Evaluate side-chains 105 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 771 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 0.0370 chunk 39 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 75 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.123460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.081879 restraints weight = 15544.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.084687 restraints weight = 8179.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.086415 restraints weight = 5579.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.087554 restraints weight = 4454.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.088186 restraints weight = 3869.844| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8581 Z= 0.122 Angle : 0.520 13.144 11945 Z= 0.249 Chirality : 0.038 0.220 1348 Planarity : 0.004 0.043 1268 Dihedral : 17.299 160.022 1962 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.84 % Allowed : 11.61 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.29), residues: 844 helix: 2.05 (0.26), residues: 404 sheet: -0.13 (0.56), residues: 90 loop : -0.73 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 842 TYR 0.009 0.001 TYR A 482 PHE 0.013 0.001 PHE A 674 TRP 0.011 0.001 TRP A 171 HIS 0.003 0.001 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8573) covalent geometry : angle 0.51989 (11943) hydrogen bonds : bond 0.03366 ( 382) hydrogen bonds : angle 4.01502 ( 1027) metal coordination : bond 0.01220 ( 7) metal coordination : angle 1.16709 ( 2) Misc. bond : bond 0.00072 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8714 (m-30) cc_final: 0.8374 (t0) REVERT: A 158 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7913 (tm-30) REVERT: A 182 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8400 (tt) REVERT: A 186 MET cc_start: 0.8506 (mmm) cc_final: 0.8177 (mmm) REVERT: A 240 ASN cc_start: 0.8573 (m110) cc_final: 0.8253 (m-40) REVERT: A 340 MET cc_start: 0.8009 (ttm) cc_final: 0.7779 (ttm) REVERT: A 637 HIS cc_start: 0.7148 (p90) cc_final: 0.6898 (p90) outliers start: 13 outliers final: 12 residues processed: 101 average time/residue: 0.0796 time to fit residues: 11.7274 Evaluate side-chains 104 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 771 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.124170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.082623 restraints weight = 15603.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.085471 restraints weight = 8172.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.087317 restraints weight = 5549.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088401 restraints weight = 4389.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.088934 restraints weight = 3832.257| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 8581 Z= 0.103 Angle : 0.513 13.336 11945 Z= 0.244 Chirality : 0.037 0.228 1348 Planarity : 0.004 0.043 1268 Dihedral : 17.249 160.064 1962 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.12 % Allowed : 11.33 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.29), residues: 844 helix: 2.03 (0.26), residues: 405 sheet: -0.09 (0.56), residues: 90 loop : -0.69 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 842 TYR 0.009 0.001 TYR A 838 PHE 0.013 0.001 PHE A 674 TRP 0.011 0.001 TRP A 171 HIS 0.003 0.000 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8573) covalent geometry : angle 0.51308 (11943) hydrogen bonds : bond 0.03270 ( 382) hydrogen bonds : angle 3.99823 ( 1027) metal coordination : bond 0.00823 ( 7) metal coordination : angle 1.04338 ( 2) Misc. bond : bond 0.00069 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1444.90 seconds wall clock time: 25 minutes 42.68 seconds (1542.68 seconds total)