Starting phenix.real_space_refine on Thu Jul 2 05:56:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7swf_25472/07_2026/7swf_25472.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swf_25472/07_2026/7swf_25472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7swf_25472/07_2026/7swf_25472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swf_25472/07_2026/7swf_25472.map" model { file = "/net/cci-nas-00/data/ceres_data/7swf_25472/07_2026/7swf_25472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swf_25472/07_2026/7swf_25472.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7swf_25472/07_2026/7swf_25472.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7swf_25472/07_2026/7swf_25472.cif" } resolution = 3.79 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= 0.003 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: 6 Type Number sf(0) Gaussians P 34 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 4227 2.51 5 N 1214 2.21 5 O 1361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6873 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 6167 Classifications: {'peptide': 778} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 43, 'TRANS': 734} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 370 Classifications: {'RNA': 17} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "D" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 335 Classifications: {'DNA': 1, 'RNA': 16} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 11} Link IDs: {'rna2p': 1, 'rna3p': 15} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.48, per 1000 atoms: 0.22 Number of scatterers: 6873 At special positions: 0 Unit cell: (80.99, 101.92, 114.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 34 15.00 Mg 1 11.99 O 1361 8.00 N 1214 7.00 C 4227 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: 0.47 Conformation dependent library (CDL) restraints added in 339.3 milliseconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 11 sheets defined 31.9% alpha, 10.3% beta 15 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 263 through 283 removed outlier: 3.521A pdb=" N ALA A 267 " --> pdb=" O CYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 460 through 472 removed outlier: 3.806A pdb=" N ALA A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS A 472 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 488 removed outlier: 3.917A pdb=" N VAL A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 565 through 584 Processing helix chain 'A' and resid 602 through 617 Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 636 through 648 removed outlier: 4.212A pdb=" N GLU A 646 " --> pdb=" O LYS A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 663 Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.826A pdb=" N LYS A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing helix chain 'A' and resid 801 through 819 Processing helix chain 'A' and resid 903 through 915 Processing helix chain 'A' and resid 928 through 941 removed outlier: 4.038A pdb=" N ALA A 934 " --> pdb=" O PRO A 930 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N HIS A 935 " --> pdb=" O ALA A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 945 removed outlier: 3.791A pdb=" N LEU A 945 " --> pdb=" O ARG A 942 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 942 through 945' Processing helix chain 'A' and resid 978 through 982 Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 144 Processing sheet with id=AA2, first strand: chain 'A' and resid 314 through 316 removed outlier: 3.590A pdb=" N SER A 314 " --> pdb=" O ASN A 325 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 196 through 197 Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 300 removed outlier: 3.727A pdb=" N GLN A 299 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 374 Processing sheet with id=AA6, first strand: chain 'A' and resid 387 through 390 removed outlier: 4.042A pdb=" N SER A 440 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 531 through 532 removed outlier: 3.563A pdb=" N LEU A 521 " --> pdb=" O CYS A 532 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 686 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 596 through 597 removed outlier: 7.008A pdb=" N ALA A 556 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A 629 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL A 558 " --> pdb=" O ILE A 629 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 703 through 705 removed outlier: 5.994A pdb=" N ILE A 704 " --> pdb=" O ILE A 791 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 828 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASP A 898 " --> pdb=" O VAL A 828 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N PHE A 830 " --> pdb=" O LEU A 896 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 707 through 711 removed outlier: 3.623A pdb=" N ILE A 723 " --> pdb=" O THR A 711 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 722 " --> pdb=" O GLN A 745 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 759 through 761 removed outlier: 3.707A pdb=" N TRP A 759 " --> pdb=" O VAL A 767 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 767 " --> pdb=" O TRP A 759 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.68 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: 1751 1.33 - 1.45: 1422 1.45 - 1.57: 3794 1.57 - 1.69: 66 1.69 - 1.81: 50 Bond restraints: 7083 Sorted by residual: bond pdb=" N VAL A 173 " pdb=" CA VAL A 173 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 6.80e+00 bond pdb=" N VAL A 286 " pdb=" CA VAL A 286 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.80e+00 bond pdb=" N ARG A 288 " pdb=" CA ARG A 288 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.50e+00 bond pdb=" N ILE A 178 " pdb=" CA ILE A 178 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.19e-02 7.06e+03 6.35e+00 bond pdb=" N VAL A 182 " pdb=" CA VAL A 182 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.17e-02 7.31e+03 6.26e+00 ... (remaining 7078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 9438 1.89 - 3.77: 267 3.77 - 5.66: 26 5.66 - 7.54: 12 7.54 - 9.43: 1 Bond angle restraints: 9744 Sorted by residual: angle pdb=" C3' C D 7 " pdb=" O3' C D 7 " pdb=" P A D 8 " ideal model delta sigma weight residual 120.20 110.77 9.43 1.50e+00 4.44e-01 3.95e+01 angle pdb=" C3' U D 9 " pdb=" O3' U D 9 " pdb=" P U D 10 " ideal model delta sigma weight residual 120.20 113.70 6.50 1.50e+00 4.44e-01 1.88e+01 angle pdb=" CA ARG A 836 " pdb=" C ARG A 836 " pdb=" O ARG A 836 " ideal model delta sigma weight residual 122.64 118.36 4.28 1.25e+00 6.40e-01 1.17e+01 angle pdb=" C THR A 711 " pdb=" CA THR A 711 " pdb=" CB THR A 711 " ideal model delta sigma weight residual 111.23 115.95 -4.72 1.42e+00 4.96e-01 1.11e+01 angle pdb=" CA HIS A 837 " pdb=" C HIS A 837 " pdb=" O HIS A 837 " ideal model delta sigma weight residual 121.16 117.41 3.75 1.13e+00 7.83e-01 1.10e+01 ... (remaining 9739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 4138 35.68 - 71.36: 93 71.36 - 107.03: 6 107.03 - 142.71: 0 142.71 - 178.39: 2 Dihedral angle restraints: 4239 sinusoidal: 1968 harmonic: 2271 Sorted by residual: dihedral pdb=" C4' C D 20 " pdb=" C3' C D 20 " pdb=" O3' C D 20 " pdb=" P A D 21 " ideal model delta sinusoidal sigma weight residual -140.00 38.39 -178.39 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA SER A 855 " pdb=" C SER A 855 " pdb=" N GLY A 856 " pdb=" CA GLY A 856 " ideal model delta harmonic sigma weight residual 180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA MET A 320 " pdb=" C MET A 320 " pdb=" N GLY A 321 " pdb=" CA GLY A 321 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 4236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1019 0.086 - 0.171: 92 0.171 - 0.257: 3 0.257 - 0.343: 0 0.343 - 0.429: 2 Chirality restraints: 1116 Sorted by residual: chirality pdb=" P A D 8 " pdb=" OP1 A D 8 " pdb=" OP2 A D 8 " pdb=" O5' A D 8 " both_signs ideal model delta sigma weight residual True 2.41 -2.84 -0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" P U D 9 " pdb=" OP1 U D 9 " pdb=" OP2 U D 9 " pdb=" O5' U D 9 " both_signs ideal model delta sigma weight residual True 2.41 -2.79 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA ILE A 177 " pdb=" N ILE A 177 " pdb=" C ILE A 177 " pdb=" CB ILE A 177 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1113 not shown) Planarity restraints: 1132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 169 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" C SER A 169 " -0.039 2.00e-02 2.50e+03 pdb=" O SER A 169 " 0.015 2.00e-02 2.50e+03 pdb=" N SER A 170 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 6 " 0.020 2.00e-02 2.50e+03 1.07e-02 2.57e+00 pdb=" N1 U B 6 " -0.024 2.00e-02 2.50e+03 pdb=" C2 U B 6 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U B 6 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U B 6 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U B 6 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U B 6 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U B 6 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 6 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 929 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 930 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 930 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 930 " 0.022 5.00e-02 4.00e+02 ... (remaining 1129 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 94 2.61 - 3.18: 6083 3.18 - 3.76: 10865 3.76 - 4.33: 14065 4.33 - 4.90: 23025 Nonbonded interactions: 54132 Sorted by model distance: nonbonded pdb=" OP1 U D 12 " pdb="MG MG A1001 " model vdw 2.039 2.170 nonbonded pdb=" OD2 ASP A 709 " pdb="MG MG A1001 " model vdw 2.044 2.170 nonbonded pdb=" OD1 ASP A 709 " pdb="MG MG A1001 " model vdw 2.096 2.170 nonbonded pdb=" O VAL A 470 " pdb=" NE2 GLN A 473 " model vdw 2.176 3.120 nonbonded pdb=" OG1 THR A 852 " pdb=" O ARG A 854 " model vdw 2.187 3.040 ... (remaining 54127 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.930 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.140 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.005 0.057 7083 Z= 0.265 Angle : 0.726 9.427 9744 Z= 0.415 Chirality : 0.049 0.429 1116 Planarity : 0.004 0.038 1132 Dihedral : 15.160 178.388 2771 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 1.33 % Allowed : 0.88 % Favored : 97.79 % 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: -1.82 (0.31), residues: 768 helix: 1.31 (0.36), residues: 230 sheet: -2.83 (0.42), residues: 131 loop : -2.21 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 484 TYR 0.017 0.002 TYR A 312 PHE 0.018 0.002 PHE A 802 TRP 0.017 0.002 TRP A 308 HIS 0.004 0.001 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.27 ( 7083) covalent geometry : angle 0.72605 / 0.41 ( 9744) hydrogen bonds : bond 0.16661 / 10.89 ( 247) hydrogen bonds : angle 7.14361 / 5.37 ( 667) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 265 GLN cc_start: 0.6494 (mp10) cc_final: 0.6281 (mp10) REVERT: A 335 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7765 (mt-10) REVERT: A 504 ILE cc_start: 0.9138 (mt) cc_final: 0.8937 (pt) REVERT: A 987 TYR cc_start: 0.8390 (p90) cc_final: 0.8111 (p90) outliers start: 9 outliers final: 4 residues processed: 94 average time/residue: 0.1067 time to fit residues: 12.8547 Evaluate side-chains 69 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 837 HIS Chi-restraints excluded: chain A residue 838 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 489 ASN A 671 ASN A 677 ASN A 760 GLN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.120629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.081935 restraints weight = 15839.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.084538 restraints weight = 7317.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.085970 restraints weight = 4595.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.086981 restraints weight = 3561.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087453 restraints weight = 3045.171| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7083 Z= 0.116 Angle : 0.606 7.908 9744 Z= 0.298 Chirality : 0.041 0.188 1116 Planarity : 0.004 0.037 1132 Dihedral : 9.929 161.615 1251 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 1.33 % Allowed : 11.49 % Favored : 87.19 % 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: -1.44 (0.31), residues: 768 helix: 1.76 (0.36), residues: 231 sheet: -2.57 (0.41), residues: 147 loop : -2.04 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.021 0.001 TYR A 185 PHE 0.015 0.001 PHE A 902 TRP 0.020 0.002 TRP A 732 HIS 0.003 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 7083) covalent geometry : angle 0.60554 / 0.30 ( 9744) hydrogen bonds : bond 0.03335 / 2.18 ( 247) hydrogen bonds : angle 4.92267 / 3.64 ( 667) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.173 Fit side-chains REVERT: A 184 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8349 (mp) REVERT: A 265 GLN cc_start: 0.6542 (mp10) cc_final: 0.6257 (mp10) REVERT: A 492 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8351 (p0) REVERT: A 493 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8644 (mm-40) REVERT: A 498 LYS cc_start: 0.9388 (mmtm) cc_final: 0.9079 (mmtt) REVERT: A 732 TRP cc_start: 0.8086 (t60) cc_final: 0.7627 (t60) REVERT: A 987 TYR cc_start: 0.8931 (p90) cc_final: 0.8730 (p90) outliers start: 9 outliers final: 2 residues processed: 85 average time/residue: 0.0849 time to fit residues: 9.6931 Evaluate side-chains 66 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 838 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 22 optimal weight: 0.0470 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 chunk 18 optimal weight: 6.9990 chunk 56 optimal weight: 0.0770 chunk 20 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 ASN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.122039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.083425 restraints weight = 15611.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.086047 restraints weight = 7237.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.087551 restraints weight = 4535.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088582 restraints weight = 3485.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.089119 restraints weight = 2983.746| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7083 Z= 0.096 Angle : 0.583 12.468 9744 Z= 0.279 Chirality : 0.040 0.162 1116 Planarity : 0.004 0.038 1132 Dihedral : 9.575 161.507 1246 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.77 % Allowed : 15.32 % Favored : 82.92 % 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: -1.36 (0.31), residues: 768 helix: 1.78 (0.36), residues: 235 sheet: -2.32 (0.41), residues: 143 loop : -2.11 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 794 TYR 0.009 0.001 TYR A 185 PHE 0.011 0.001 PHE A 902 TRP 0.007 0.001 TRP A 308 HIS 0.002 0.000 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 7083) covalent geometry : angle 0.58349 / 0.28 ( 9744) hydrogen bonds : bond 0.03006 / 1.94 ( 247) hydrogen bonds : angle 4.45256 / 3.25 ( 667) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.238 Fit side-chains REVERT: A 265 GLN cc_start: 0.6333 (mp10) cc_final: 0.6049 (mp10) REVERT: A 492 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8550 (p0) REVERT: A 493 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8676 (mm-40) REVERT: A 714 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6647 (tm-30) REVERT: A 836 ARG cc_start: 0.8069 (mmt180) cc_final: 0.7809 (mmt180) REVERT: A 845 ASN cc_start: 0.7003 (t0) cc_final: 0.6754 (t0) outliers start: 12 outliers final: 7 residues processed: 86 average time/residue: 0.0760 time to fit residues: 9.0470 Evaluate side-chains 75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 838 HIS Chi-restraints excluded: chain A residue 884 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 40 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 52 optimal weight: 0.3980 chunk 26 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 23 optimal weight: 0.0370 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 ASN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.121330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.082921 restraints weight = 16006.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.085489 restraints weight = 7358.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.087079 restraints weight = 4571.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.088097 restraints weight = 3458.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088596 restraints weight = 2946.645| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7083 Z= 0.101 Angle : 0.563 9.391 9744 Z= 0.271 Chirality : 0.040 0.155 1116 Planarity : 0.004 0.038 1132 Dihedral : 9.551 161.416 1246 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.65 % Allowed : 15.61 % Favored : 81.74 % 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: -1.19 (0.31), residues: 768 helix: 1.96 (0.36), residues: 235 sheet: -2.26 (0.41), residues: 143 loop : -2.02 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.012 0.001 TYR A 185 PHE 0.007 0.001 PHE A 902 TRP 0.011 0.001 TRP A 308 HIS 0.002 0.001 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 7083) covalent geometry : angle 0.56296 / 0.27 ( 9744) hydrogen bonds : bond 0.02882 / 1.89 ( 247) hydrogen bonds : angle 4.27320 / 3.10 ( 667) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8445 (mp) REVERT: A 265 GLN cc_start: 0.6484 (mp10) cc_final: 0.6195 (mp10) REVERT: A 335 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7375 (mt-10) REVERT: A 502 MET cc_start: 0.8446 (ppp) cc_final: 0.8223 (ppp) REVERT: A 714 GLU cc_start: 0.7047 (tm-30) cc_final: 0.6650 (tm-30) REVERT: A 836 ARG cc_start: 0.8089 (mmt180) cc_final: 0.7788 (mmt-90) REVERT: A 897 TRP cc_start: 0.9015 (t-100) cc_final: 0.8788 (t-100) outliers start: 18 outliers final: 9 residues processed: 87 average time/residue: 0.0736 time to fit residues: 8.8217 Evaluate side-chains 81 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 838 HIS Chi-restraints excluded: chain A residue 884 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 33 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 36 optimal weight: 0.4980 chunk 76 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 671 ASN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.114239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.075947 restraints weight = 16579.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.078283 restraints weight = 7721.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.079644 restraints weight = 4871.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.080536 restraints weight = 3787.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.080826 restraints weight = 3264.367| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 7083 Z= 0.302 Angle : 0.727 12.311 9744 Z= 0.361 Chirality : 0.045 0.193 1116 Planarity : 0.004 0.036 1132 Dihedral : 9.994 165.375 1246 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 4.27 % Allowed : 16.05 % Favored : 79.68 % 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: -1.42 (0.31), residues: 768 helix: 1.66 (0.36), residues: 231 sheet: -2.26 (0.41), residues: 152 loop : -2.07 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 183 TYR 0.011 0.002 TYR A 185 PHE 0.016 0.002 PHE A 874 TRP 0.011 0.002 TRP A 308 HIS 0.007 0.002 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.30 ( 7083) covalent geometry : angle 0.72668 / 0.36 ( 9744) hydrogen bonds : bond 0.04012 / 2.72 ( 247) hydrogen bonds : angle 4.65415 / 3.35 ( 667) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 GLN cc_start: 0.6254 (mp10) cc_final: 0.6010 (mp10) REVERT: A 444 MET cc_start: 0.4044 (ppp) cc_final: 0.3791 (tmm) REVERT: A 492 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8526 (p0) REVERT: A 671 ASN cc_start: 0.9469 (OUTLIER) cc_final: 0.9219 (t0) REVERT: A 714 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6725 (tm-30) REVERT: A 987 TYR cc_start: 0.8898 (p90) cc_final: 0.8517 (p90) outliers start: 29 outliers final: 15 residues processed: 89 average time/residue: 0.0737 time to fit residues: 8.8462 Evaluate side-chains 74 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 838 HIS Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 927 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 40.0000 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 823 ASN A 885 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.117873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.079680 restraints weight = 16084.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082141 restraints weight = 7459.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.083571 restraints weight = 4706.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.084499 restraints weight = 3647.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.084954 restraints weight = 3130.324| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7083 Z= 0.137 Angle : 0.617 10.274 9744 Z= 0.299 Chirality : 0.041 0.161 1116 Planarity : 0.004 0.038 1132 Dihedral : 9.679 162.958 1246 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.21 % Allowed : 19.00 % Favored : 78.79 % 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: -1.30 (0.31), residues: 768 helix: 1.87 (0.36), residues: 228 sheet: -2.16 (0.43), residues: 141 loop : -2.09 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 794 TYR 0.013 0.001 TYR A 185 PHE 0.008 0.001 PHE A 874 TRP 0.014 0.001 TRP A 732 HIS 0.002 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 7083) covalent geometry : angle 0.61713 / 0.30 ( 9744) hydrogen bonds : bond 0.03077 / 2.04 ( 247) hydrogen bonds : angle 4.32796 / 3.13 ( 667) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 GLN cc_start: 0.6186 (mp10) cc_final: 0.5959 (mp10) REVERT: A 714 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6679 (tm-30) REVERT: A 836 ARG cc_start: 0.7911 (mmt180) cc_final: 0.7699 (mmt180) outliers start: 15 outliers final: 11 residues processed: 80 average time/residue: 0.0771 time to fit residues: 8.5813 Evaluate side-chains 75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 838 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.0170 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.119080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.081273 restraints weight = 15942.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.083723 restraints weight = 7335.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.085271 restraints weight = 4558.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.086199 restraints weight = 3462.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.086666 restraints weight = 2963.754| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7083 Z= 0.113 Angle : 0.615 10.422 9744 Z= 0.296 Chirality : 0.041 0.243 1116 Planarity : 0.004 0.043 1132 Dihedral : 9.532 162.921 1246 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.21 % Allowed : 19.73 % Favored : 78.06 % 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: -1.25 (0.30), residues: 768 helix: 1.94 (0.36), residues: 228 sheet: -2.07 (0.43), residues: 141 loop : -2.11 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 789 TYR 0.016 0.001 TYR A 987 PHE 0.007 0.001 PHE A 874 TRP 0.011 0.001 TRP A 732 HIS 0.002 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 7083) covalent geometry : angle 0.61497 / 0.30 ( 9744) hydrogen bonds : bond 0.02943 / 1.95 ( 247) hydrogen bonds : angle 4.16556 / 3.02 ( 667) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7504 (mmtt) cc_final: 0.7212 (pttm) REVERT: A 265 GLN cc_start: 0.6110 (mp10) cc_final: 0.5885 (mp10) REVERT: A 714 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6646 (tm-30) REVERT: A 897 TRP cc_start: 0.8987 (t-100) cc_final: 0.8738 (t-100) REVERT: A 920 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8478 (ptm-80) outliers start: 15 outliers final: 11 residues processed: 80 average time/residue: 0.0781 time to fit residues: 8.5644 Evaluate side-chains 77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 838 HIS Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 920 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.116254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.078459 restraints weight = 16368.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.080947 restraints weight = 7577.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.082402 restraints weight = 4739.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.083189 restraints weight = 3604.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.083727 restraints weight = 3122.404| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7083 Z= 0.205 Angle : 0.674 11.617 9744 Z= 0.327 Chirality : 0.042 0.217 1116 Planarity : 0.004 0.041 1132 Dihedral : 9.704 164.151 1246 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.21 % Allowed : 20.32 % Favored : 77.47 % 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: -1.24 (0.31), residues: 768 helix: 1.85 (0.36), residues: 230 sheet: -2.10 (0.43), residues: 147 loop : -2.03 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.014 0.001 TYR A 185 PHE 0.011 0.001 PHE A 874 TRP 0.020 0.002 TRP A 732 HIS 0.004 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 7083) covalent geometry : angle 0.67385 / 0.33 ( 9744) hydrogen bonds : bond 0.03437 / 2.29 ( 247) hydrogen bonds : angle 4.30006 / 3.10 ( 667) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7510 (mmtt) cc_final: 0.7210 (pttm) REVERT: A 265 GLN cc_start: 0.6032 (mp10) cc_final: 0.5791 (mp10) REVERT: A 498 LYS cc_start: 0.9293 (mmtm) cc_final: 0.8984 (mmtt) REVERT: A 714 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6713 (tm-30) REVERT: A 732 TRP cc_start: 0.8203 (t60) cc_final: 0.7829 (t60) REVERT: A 897 TRP cc_start: 0.9091 (t-100) cc_final: 0.8732 (t-100) REVERT: A 987 TYR cc_start: 0.8922 (p90) cc_final: 0.8677 (p90) outliers start: 15 outliers final: 12 residues processed: 73 average time/residue: 0.0837 time to fit residues: 8.4737 Evaluate side-chains 71 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 838 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.114550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.076739 restraints weight = 16576.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.079183 restraints weight = 7707.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080664 restraints weight = 4837.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.081513 restraints weight = 3676.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.082063 restraints weight = 3169.636| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7083 Z= 0.256 Angle : 0.714 10.610 9744 Z= 0.349 Chirality : 0.044 0.201 1116 Planarity : 0.004 0.044 1132 Dihedral : 9.901 164.398 1246 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.65 % Allowed : 20.18 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.39 (0.31), residues: 768 helix: 1.69 (0.36), residues: 230 sheet: -2.23 (0.43), residues: 147 loop : -2.07 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 276 TYR 0.012 0.002 TYR A 185 PHE 0.012 0.001 PHE A 874 TRP 0.025 0.002 TRP A 732 HIS 0.005 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.26 ( 7083) covalent geometry : angle 0.71437 / 0.35 ( 9744) hydrogen bonds : bond 0.03700 / 2.47 ( 247) hydrogen bonds : angle 4.49372 / 3.24 ( 667) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 492 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8743 (p0) REVERT: A 671 ASN cc_start: 0.9428 (OUTLIER) cc_final: 0.9212 (t0) REVERT: A 714 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6716 (tm-30) outliers start: 18 outliers final: 14 residues processed: 73 average time/residue: 0.0642 time to fit residues: 6.6898 Evaluate side-chains 71 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 838 HIS Chi-restraints excluded: chain A residue 907 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 885 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.117730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.079788 restraints weight = 16142.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.082172 restraints weight = 7479.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.083592 restraints weight = 4700.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.084551 restraints weight = 3625.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.085034 restraints weight = 3120.509| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7083 Z= 0.139 Angle : 0.674 12.866 9744 Z= 0.319 Chirality : 0.042 0.206 1116 Planarity : 0.004 0.043 1132 Dihedral : 9.715 162.841 1246 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.91 % Allowed : 21.35 % Favored : 76.73 % 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: -1.33 (0.31), residues: 768 helix: 1.80 (0.36), residues: 230 sheet: -2.25 (0.43), residues: 142 loop : -2.06 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.013 0.001 TYR A 185 PHE 0.008 0.001 PHE A 874 TRP 0.028 0.002 TRP A 732 HIS 0.002 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 7083) covalent geometry : angle 0.67415 / 0.32 ( 9744) hydrogen bonds : bond 0.03170 / 2.05 ( 247) hydrogen bonds : angle 4.37366 / 3.14 ( 667) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.220 Fit side-chains REVERT: A 201 LYS cc_start: 0.7492 (mmtt) cc_final: 0.7164 (pttm) REVERT: A 579 MET cc_start: 0.8735 (tpp) cc_final: 0.8491 (tpp) REVERT: A 714 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6700 (tm-30) REVERT: A 732 TRP cc_start: 0.8076 (t60) cc_final: 0.7718 (t60) REVERT: A 897 TRP cc_start: 0.9048 (t-100) cc_final: 0.8771 (t-100) outliers start: 13 outliers final: 11 residues processed: 72 average time/residue: 0.0620 time to fit residues: 6.2700 Evaluate side-chains 67 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 838 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 5 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 34 optimal weight: 0.2980 chunk 48 optimal weight: 0.6980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 GLN A 671 ASN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.120764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.083085 restraints weight = 15633.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.085631 restraints weight = 7253.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087209 restraints weight = 4498.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.088231 restraints weight = 3390.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088685 restraints weight = 2877.357| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7083 Z= 0.108 Angle : 0.660 12.124 9744 Z= 0.310 Chirality : 0.040 0.155 1116 Planarity : 0.004 0.042 1132 Dihedral : 9.489 163.105 1246 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.06 % Allowed : 21.80 % Favored : 76.14 % 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: -1.18 (0.31), residues: 768 helix: 2.08 (0.36), residues: 228 sheet: -2.14 (0.43), residues: 142 loop : -2.06 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 794 TYR 0.014 0.001 TYR A 987 PHE 0.008 0.001 PHE A 986 TRP 0.023 0.002 TRP A 732 HIS 0.002 0.000 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 7083) covalent geometry : angle 0.65960 / 0.31 ( 9744) hydrogen bonds : bond 0.02783 / 1.81 ( 247) hydrogen bonds : angle 4.16195 / 3.00 ( 667) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1284.93 seconds wall clock time: 22 minutes 53.61 seconds (1373.61 seconds total)