Starting phenix.real_space_refine on Wed Feb 12 02:26:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7swf_25472/02_2025/7swf_25472.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swf_25472/02_2025/7swf_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_25472/02_2025/7swf_25472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swf_25472/02_2025/7swf_25472.map" model { file = "/net/cci-nas-00/data/ceres_data/7swf_25472/02_2025/7swf_25472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swf_25472/02_2025/7swf_25472.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.44, per 1000 atoms: 0.65 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: 2.10 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.64 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: 2.49 Time building geometry restraints manager: 2.20 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: 4189 35.68 - 71.36: 150 71.36 - 107.03: 14 107.03 - 142.71: 0 142.71 - 178.39: 2 Dihedral angle restraints: 4355 sinusoidal: 2084 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 4352 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: 0.390 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.870 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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= 0.334 Angle : 0.726 9.427 9744 Z= 0.415 Chirality : 0.049 0.429 1116 Planarity : 0.004 0.038 1132 Dihedral : 17.156 178.388 2887 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.69 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (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 TRP 0.017 0.002 TRP A 308 HIS 0.004 0.001 HIS A 837 PHE 0.018 0.002 PHE A 802 TYR 0.017 0.002 TYR A 312 ARG 0.003 0.000 ARG A 484 *********************** 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 : 0.771 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: 0.8389 (p90) cc_final: 0.8110 (p90) outliers start: 9 outliers final: 4 residues processed: 94 average time/residue: 0.2705 time to fit residues: 32.0455 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 : 0.757 ------------------------------------------------------------------------------- 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 66 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 23 optimal weight: 50.0000 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.118602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.080304 restraints weight = 15676.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.082797 restraints weight = 7336.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.084320 restraints weight = 4613.654| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1496 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= 0.218 Angle : 0.612 7.756 9744 Z= 0.303 Chirality : 0.041 0.186 1116 Planarity : 0.004 0.037 1132 Dihedral : 15.595 162.765 1367 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.06 % Allowed : 11.78 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.31), residues: 768 helix: 1.70 (0.36), residues: 232 sheet: -2.59 (0.40), residues: 152 loop : -2.07 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 732 HIS 0.003 0.001 HIS A 837 PHE 0.012 0.001 PHE A 874 TYR 0.022 0.001 TYR A 185 ARG 0.002 0.000 ARG A 942 *********************** 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 88 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.741 Fit side-chains REVERT: A 184 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8360 (mp) REVERT: A 265 GLN cc_start: 0.6492 (mp10) cc_final: 0.6209 (mp10) REVERT: A 492 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8401 (p0) REVERT: A 493 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8648 (mm-40) REVERT: A 498 LYS cc_start: 0.9389 (mmtm) cc_final: 0.9094 (mmtt) REVERT: A 625 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8966 (tp) REVERT: A 987 TYR cc_start: 0.8943 (p90) cc_final: 0.8663 (p90) outliers start: 14 outliers final: 6 residues processed: 84 average time/residue: 0.2042 time to fit residues: 22.9778 Evaluate side-chains 71 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 564 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 837 HIS 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 7 optimal weight: 9.9990 chunk 63 optimal weight: 0.0770 chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 51 optimal weight: 0.0060 chunk 58 optimal weight: 0.0870 chunk 41 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 489 ASN A 671 ASN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.121559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.083262 restraints weight = 15721.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.085900 restraints weight = 7249.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.087476 restraints weight = 4520.496| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7083 Z= 0.145 Angle : 0.597 12.204 9744 Z= 0.286 Chirality : 0.040 0.163 1116 Planarity : 0.004 0.055 1132 Dihedral : 15.446 161.471 1364 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.33 % Allowed : 16.35 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.31), residues: 768 helix: 1.81 (0.36), residues: 236 sheet: -2.37 (0.41), residues: 144 loop : -2.10 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 732 HIS 0.002 0.000 HIS A 892 PHE 0.011 0.001 PHE A 902 TYR 0.010 0.001 TYR A 185 ARG 0.003 0.000 ARG A 276 *********************** 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 88 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 265 GLN cc_start: 0.6333 (mp10) cc_final: 0.6078 (mp10) REVERT: A 473 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.7027 (mp10) REVERT: A 714 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6697 (tm-30) REVERT: A 732 TRP cc_start: 0.7922 (t60) cc_final: 0.7631 (t60) REVERT: A 836 ARG cc_start: 0.8108 (mmt180) cc_final: 0.7827 (mmt180) REVERT: A 845 ASN cc_start: 0.7025 (t0) cc_final: 0.6746 (t0) outliers start: 9 outliers final: 4 residues processed: 83 average time/residue: 0.2094 time to fit residues: 23.1964 Evaluate side-chains 72 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 564 VAL 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 63 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 22 optimal weight: 0.0050 chunk 4 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.0870 chunk 41 optimal weight: 6.9990 overall best weight: 1.0574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 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 = 0.3740 r_free = 0.3740 target = 0.120929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.082532 restraints weight = 15825.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.085202 restraints weight = 7290.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.086776 restraints weight = 4519.616| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2284 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= 0.168 Angle : 0.575 9.543 9744 Z= 0.279 Chirality : 0.040 0.154 1116 Planarity : 0.004 0.046 1132 Dihedral : 15.411 161.625 1362 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.65 % Allowed : 16.49 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.31), residues: 768 helix: 1.89 (0.36), residues: 235 sheet: -2.28 (0.41), residues: 144 loop : -2.03 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 732 HIS 0.002 0.001 HIS A 837 PHE 0.007 0.001 PHE A 874 TYR 0.013 0.001 TYR A 185 ARG 0.002 0.000 ARG A 599 *********************** 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 96 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8438 (mp) REVERT: A 201 LYS cc_start: 0.7438 (mmtt) cc_final: 0.7079 (pttm) REVERT: A 265 GLN cc_start: 0.6493 (mp10) cc_final: 0.6201 (mp10) REVERT: A 335 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7394 (mt-10) REVERT: A 473 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: A 714 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6657 (tm-30) REVERT: A 732 TRP cc_start: 0.8013 (t60) cc_final: 0.7616 (t60) REVERT: A 836 ARG cc_start: 0.8109 (mmt180) cc_final: 0.7821 (mmt-90) REVERT: A 897 TRP cc_start: 0.9002 (t-100) cc_final: 0.8721 (t-100) outliers start: 18 outliers final: 8 residues processed: 90 average time/residue: 0.2114 time to fit residues: 25.2768 Evaluate side-chains 80 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 473 GLN 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 60 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN ** A 574 ASN ** 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 = 0.3662 r_free = 0.3662 target = 0.116208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.077891 restraints weight = 16118.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.080327 restraints weight = 7558.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.081832 restraints weight = 4794.764| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.005 0.048 7083 Z= 0.336 Angle : 0.657 8.536 9744 Z= 0.327 Chirality : 0.042 0.167 1116 Planarity : 0.004 0.045 1132 Dihedral : 15.464 164.384 1362 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 3.68 % Allowed : 17.38 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.31), residues: 768 helix: 1.81 (0.36), residues: 231 sheet: -2.27 (0.41), residues: 153 loop : -2.04 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 308 HIS 0.005 0.001 HIS A 609 PHE 0.013 0.001 PHE A 874 TYR 0.016 0.002 TYR A 987 ARG 0.003 0.000 ARG A 183 *********************** 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: 25 poor density : 68 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7428 (mmtt) cc_final: 0.7118 (pttm) REVERT: A 265 GLN cc_start: 0.6536 (mp10) cc_final: 0.6289 (mp10) REVERT: A 464 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6896 (tp) REVERT: A 492 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8549 (p0) REVERT: A 714 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6729 (tm-30) outliers start: 25 outliers final: 12 residues processed: 88 average time/residue: 0.1922 time to fit residues: 22.6666 Evaluate side-chains 76 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE 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 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 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 72 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 61 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3713 r_free = 0.3713 target = 0.119313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081103 restraints weight = 16109.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.083688 restraints weight = 7466.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.085201 restraints weight = 4676.345| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7083 Z= 0.181 Angle : 0.596 9.595 9744 Z= 0.293 Chirality : 0.040 0.149 1116 Planarity : 0.004 0.044 1132 Dihedral : 15.416 162.687 1362 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.50 % Allowed : 20.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.31), residues: 768 helix: 1.97 (0.36), residues: 229 sheet: -2.14 (0.42), residues: 142 loop : -2.04 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 732 HIS 0.002 0.001 HIS A 712 PHE 0.008 0.001 PHE A 986 TYR 0.017 0.001 TYR A 987 ARG 0.004 0.000 ARG A 794 *********************** 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 87 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7548 (mmtt) cc_final: 0.7230 (pttm) REVERT: A 265 GLN cc_start: 0.6542 (mp10) cc_final: 0.6295 (mp10) REVERT: A 444 MET cc_start: 0.4266 (ppp) cc_final: 0.3971 (tmm) REVERT: A 464 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6848 (tp) REVERT: A 625 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8941 (tp) REVERT: A 714 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6708 (tm-30) REVERT: A 732 TRP cc_start: 0.7871 (t60) cc_final: 0.7426 (t60) REVERT: A 836 ARG cc_start: 0.7992 (mmt180) cc_final: 0.7778 (mmt180) REVERT: A 897 TRP cc_start: 0.9006 (t-100) cc_final: 0.8738 (t-100) outliers start: 17 outliers final: 9 residues processed: 82 average time/residue: 0.1827 time to fit residues: 20.6700 Evaluate side-chains 76 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 71 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 49 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.116310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.078313 restraints weight = 16060.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.080641 restraints weight = 7514.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.082129 restraints weight = 4761.700| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.005 0.045 7083 Z= 0.300 Angle : 0.651 13.148 9744 Z= 0.318 Chirality : 0.042 0.160 1116 Planarity : 0.004 0.043 1132 Dihedral : 15.439 163.786 1362 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 3.09 % Allowed : 19.15 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.31), residues: 768 helix: 1.78 (0.36), residues: 231 sheet: -2.01 (0.43), residues: 144 loop : -2.05 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 732 HIS 0.004 0.001 HIS A 609 PHE 0.011 0.001 PHE A 874 TYR 0.014 0.001 TYR A 185 ARG 0.005 0.000 ARG A 794 *********************** 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 87 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7599 (mmtt) cc_final: 0.7323 (pttm) REVERT: A 265 GLN cc_start: 0.6284 (mp10) cc_final: 0.6052 (mp10) REVERT: A 492 ASP cc_start: 0.8984 (OUTLIER) cc_final: 0.8749 (p0) REVERT: A 714 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6724 (tm-30) REVERT: A 732 TRP cc_start: 0.8043 (t60) cc_final: 0.7669 (t60) outliers start: 21 outliers final: 14 residues processed: 82 average time/residue: 0.2033 time to fit residues: 22.5346 Evaluate side-chains 77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 289 SER 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 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 907 ILE Chi-restraints excluded: chain A residue 927 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3622 r_free = 0.3622 target = 0.113757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.075764 restraints weight = 16442.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.078118 restraints weight = 7754.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.079589 restraints weight = 4922.329| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 7083 Z= 0.446 Angle : 0.746 12.354 9744 Z= 0.371 Chirality : 0.046 0.237 1116 Planarity : 0.005 0.041 1132 Dihedral : 15.567 164.731 1362 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 3.24 % Allowed : 20.47 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.31), residues: 768 helix: 1.42 (0.35), residues: 232 sheet: -2.25 (0.42), residues: 148 loop : -2.06 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 732 HIS 0.006 0.002 HIS A 609 PHE 0.014 0.001 PHE A 874 TYR 0.013 0.002 TYR A 185 ARG 0.006 0.001 ARG A 794 *********************** 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 83 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 444 MET cc_start: 0.4449 (ppp) cc_final: 0.3523 (tpp) REVERT: A 492 ASP cc_start: 0.9034 (OUTLIER) cc_final: 0.8747 (p0) REVERT: A 671 ASN cc_start: 0.9437 (OUTLIER) cc_final: 0.9232 (t0) REVERT: A 714 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6786 (tm-30) REVERT: A 732 TRP cc_start: 0.8334 (t60) cc_final: 0.8008 (t60) REVERT: A 987 TYR cc_start: 0.8788 (p90) cc_final: 0.8571 (p90) outliers start: 22 outliers final: 14 residues processed: 78 average time/residue: 0.1765 time to fit residues: 19.4379 Evaluate side-chains 76 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 289 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3708 r_free = 0.3708 target = 0.118747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.080856 restraints weight = 15996.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.083363 restraints weight = 7390.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084903 restraints weight = 4634.789| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7083 Z= 0.179 Angle : 0.660 13.317 9744 Z= 0.315 Chirality : 0.042 0.223 1116 Planarity : 0.004 0.038 1132 Dihedral : 15.424 163.258 1362 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.77 % Allowed : 21.65 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.30), residues: 768 helix: 1.88 (0.36), residues: 227 sheet: -2.25 (0.46), residues: 118 loop : -2.16 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 732 HIS 0.003 0.001 HIS A 712 PHE 0.007 0.001 PHE A 986 TYR 0.014 0.001 TYR A 185 ARG 0.003 0.000 ARG A 794 *********************** 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 80 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7496 (mmtt) cc_final: 0.7131 (pttm) REVERT: A 276 ARG cc_start: 0.9178 (tpp-160) cc_final: 0.8784 (tpp80) REVERT: A 464 ILE cc_start: 0.7432 (mm) cc_final: 0.7189 (tp) REVERT: A 714 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6735 (tm-30) REVERT: A 732 TRP cc_start: 0.8008 (t60) cc_final: 0.7519 (t60) REVERT: A 821 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7673 (mt-10) REVERT: A 897 TRP cc_start: 0.9031 (t-100) cc_final: 0.8785 (t-100) REVERT: A 985 MET cc_start: 0.8879 (mtp) cc_final: 0.8219 (mtp) outliers start: 12 outliers final: 11 residues processed: 78 average time/residue: 0.1729 time to fit residues: 19.2372 Evaluate side-chains 76 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 0 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3612 r_free = 0.3612 target = 0.112828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.074923 restraints weight = 16731.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.077246 restraints weight = 7885.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.078670 restraints weight = 5017.434| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 7083 Z= 0.513 Angle : 0.786 12.320 9744 Z= 0.388 Chirality : 0.047 0.209 1116 Planarity : 0.005 0.040 1132 Dihedral : 15.545 165.065 1362 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 2.21 % Allowed : 21.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.31), residues: 768 helix: 1.47 (0.36), residues: 231 sheet: -2.24 (0.42), residues: 158 loop : -2.04 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 732 HIS 0.007 0.002 HIS A 609 PHE 0.018 0.002 PHE A 874 TYR 0.012 0.002 TYR A 185 ARG 0.005 0.001 ARG A 276 ********************** 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 70 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 671 ASN cc_start: 0.9478 (OUTLIER) cc_final: 0.9262 (t0) REVERT: A 714 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6787 (tm-30) REVERT: A 732 TRP cc_start: 0.8331 (t60) cc_final: 0.8041 (t60) REVERT: A 821 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7699 (mt-10) REVERT: A 870 HIS cc_start: 0.8282 (t-90) cc_final: 0.7839 (t-90) REVERT: A 985 MET cc_start: 0.8843 (mtp) cc_final: 0.8600 (mtp) REVERT: A 987 TYR cc_start: 0.8856 (p90) cc_final: 0.8498 (p90) outliers start: 15 outliers final: 11 residues processed: 69 average time/residue: 0.1602 time to fit residues: 16.0045 Evaluate side-chains 68 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 41 optimal weight: 0.1980 chunk 76 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN A 823 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.117421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.079356 restraints weight = 16097.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.081765 restraints weight = 7485.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.083224 restraints weight = 4716.974| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3085 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= 0.204 Angle : 0.675 14.003 9744 Z= 0.320 Chirality : 0.042 0.197 1116 Planarity : 0.004 0.038 1132 Dihedral : 15.516 162.413 1362 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.77 % Allowed : 22.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.30), residues: 768 helix: 1.74 (0.36), residues: 228 sheet: -2.24 (0.46), residues: 118 loop : -2.27 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 732 HIS 0.002 0.001 HIS A 712 PHE 0.011 0.001 PHE A 874 TYR 0.012 0.001 TYR A 185 ARG 0.004 0.000 ARG A 794 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2372.60 seconds wall clock time: 43 minutes 16.05 seconds (2596.05 seconds total)