Starting phenix.real_space_refine on Fri Jun 6 02:31:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7swf_25472/06_2025/7swf_25472.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swf_25472/06_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_25472/06_2025/7swf_25472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swf_25472/06_2025/7swf_25472.map" model { file = "/net/cci-nas-00/data/ceres_data/7swf_25472/06_2025/7swf_25472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swf_25472/06_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-5710/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: 4.75, per 1000 atoms: 0.69 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: 1.93 Conformation dependent library (CDL) restraints added in 754.7 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: 2.32 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: 2.45 Time building geometry restraints manager: 2.25 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: 0.550 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.960 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.760 ------------------------------------------------------------------------------- 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= 0.265 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 Details of bonding type rmsd hydrogen bonds : bond 0.16661 ( 247) hydrogen bonds : angle 7.14361 ( 667) covalent geometry : bond 0.00509 ( 7083) covalent geometry : angle 0.72605 ( 9744) *********************** 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 : 0.720 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: 0.2546 time to fit residues: 30.3655 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 : 0.717 ------------------------------------------------------------------------------- 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 = 69)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.080309 restraints weight = 15676.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.082811 restraints weight = 7293.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.084348 restraints weight = 4611.003| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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= 0.144 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 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 247) hydrogen bonds : angle 5.01331 ( 667) covalent geometry : bond 0.00331 ( 7083) covalent geometry : angle 0.61179 ( 9744) *********************** 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 : 0.699 Fit side-chains REVERT: A 184 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8359 (mp) REVERT: A 265 GLN cc_start: 0.6492 (mp10) cc_final: 0.6209 (mp10) REVERT: A 492 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8399 (p0) REVERT: A 493 GLN cc_start: 0.8984 (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: 0.8944 (p90) cc_final: 0.8664 (p90) outliers start: 14 outliers final: 6 residues processed: 84 average time/residue: 0.2048 time to fit residues: 23.3249 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 : 0.779 ------------------------------------------------------------------------------- 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: 6.9990 chunk 63 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 51 optimal weight: 0.3980 chunk 58 optimal weight: 0.0970 chunk 41 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.120205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.081824 restraints weight = 15802.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.084418 restraints weight = 7306.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.085945 restraints weight = 4566.952| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1986 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= 0.108 Angle : 0.602 12.481 9744 Z= 0.289 Chirality : 0.040 0.166 1116 Planarity : 0.004 0.047 1132 Dihedral : 15.466 162.114 1364 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.47 % Allowed : 16.35 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.37 (0.31), residues: 768 helix: 1.76 (0.36), residues: 237 sheet: -2.40 (0.41), residues: 144 loop : -2.08 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 732 HIS 0.002 0.001 HIS A 837 PHE 0.010 0.001 PHE A 902 TYR 0.010 0.001 TYR A 185 ARG 0.002 0.000 ARG A 276 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 247) hydrogen bonds : angle 4.54649 ( 667) covalent geometry : bond 0.00247 ( 7083) covalent geometry : angle 0.60197 ( 9744) *********************** 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 86 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.767 Fit side-chains REVERT: A 265 GLN cc_start: 0.6468 (mp10) cc_final: 0.6191 (mp10) REVERT: A 473 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.7050 (mp10) REVERT: A 481 ASP cc_start: 0.8379 (m-30) cc_final: 0.8153 (t70) REVERT: A 492 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8569 (p0) REVERT: A 493 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8666 (mm-40) REVERT: A 714 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6707 (tm-30) REVERT: A 732 TRP cc_start: 0.7978 (t60) cc_final: 0.7598 (t60) REVERT: A 836 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7796 (mmt-90) outliers start: 10 outliers final: 5 residues processed: 82 average time/residue: 0.2136 time to fit residues: 23.5837 Evaluate side-chains 73 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 838 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.119490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.080851 restraints weight = 16014.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.083317 restraints weight = 7409.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.084752 restraints weight = 4643.598| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2191 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= 0.125 Angle : 0.580 9.293 9744 Z= 0.282 Chirality : 0.040 0.154 1116 Planarity : 0.004 0.042 1132 Dihedral : 15.443 162.236 1362 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.39 % Allowed : 15.76 % 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: -1.26 (0.31), residues: 768 helix: 2.00 (0.36), residues: 231 sheet: -2.28 (0.41), residues: 148 loop : -2.09 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 308 HIS 0.002 0.001 HIS A 837 PHE 0.008 0.001 PHE A 874 TYR 0.017 0.001 TYR A 987 ARG 0.005 0.000 ARG A 794 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 247) hydrogen bonds : angle 4.35749 ( 667) covalent geometry : bond 0.00285 ( 7083) covalent geometry : angle 0.57992 ( 9744) *********************** 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: 23 poor density : 70 time to evaluate : 0.699 Fit side-chains REVERT: A 184 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8447 (mp) REVERT: A 265 GLN cc_start: 0.6528 (mp10) cc_final: 0.6245 (mp10) REVERT: A 335 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7417 (mt-10) REVERT: A 481 ASP cc_start: 0.8333 (m-30) cc_final: 0.8123 (t70) REVERT: A 714 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6693 (tm-30) REVERT: A 836 ARG cc_start: 0.8083 (mmt180) cc_final: 0.7647 (mmt180) REVERT: A 897 TRP cc_start: 0.9049 (t-100) cc_final: 0.8741 (t-100) outliers start: 23 outliers final: 11 residues processed: 88 average time/residue: 0.1888 time to fit residues: 22.5842 Evaluate side-chains 76 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 278 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 661 VAL 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: 4.9990 chunk 5 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.115064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.077047 restraints weight = 16118.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.079502 restraints weight = 7553.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.080851 restraints weight = 4760.348| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2350 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= 0.242 Angle : 0.667 9.482 9744 Z= 0.331 Chirality : 0.043 0.176 1116 Planarity : 0.004 0.040 1132 Dihedral : 15.463 163.499 1362 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.83 % Allowed : 17.97 % Favored : 78.20 % 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: 1.75 (0.36), residues: 233 sheet: -2.29 (0.41), residues: 152 loop : -2.05 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 732 HIS 0.005 0.001 HIS A 609 PHE 0.012 0.001 PHE A 874 TYR 0.014 0.002 TYR A 987 ARG 0.004 0.000 ARG A 570 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 247) hydrogen bonds : angle 4.54202 ( 667) covalent geometry : bond 0.00541 ( 7083) covalent geometry : angle 0.66681 ( 9744) *********************** 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 91 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7500 (mmtt) cc_final: 0.7175 (pttm) REVERT: A 265 GLN cc_start: 0.6541 (mp10) cc_final: 0.6289 (mp10) REVERT: A 473 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6791 (mp10) REVERT: A 492 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8621 (p0) REVERT: A 498 LYS cc_start: 0.9382 (mmtm) cc_final: 0.9179 (mmtm) REVERT: A 714 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6754 (tm-30) outliers start: 26 outliers final: 14 residues processed: 86 average time/residue: 0.2021 time to fit residues: 23.4048 Evaluate side-chains 77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 473 GLN 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: 0.7980 chunk 3 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 47 optimal weight: 0.0870 chunk 7 optimal weight: 0.0980 chunk 30 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 69 optimal weight: 2.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.119444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.081342 restraints weight = 16012.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.083946 restraints weight = 7343.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.085434 restraints weight = 4526.472| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7083 Z= 0.111 Angle : 0.591 9.306 9744 Z= 0.290 Chirality : 0.041 0.152 1116 Planarity : 0.004 0.039 1132 Dihedral : 15.427 162.433 1362 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.36 % Allowed : 19.29 % Favored : 78.35 % 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: 1.99 (0.36), residues: 227 sheet: -2.17 (0.43), residues: 141 loop : -2.03 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 732 HIS 0.002 0.001 HIS A 712 PHE 0.009 0.001 PHE A 986 TYR 0.014 0.001 TYR A 987 ARG 0.004 0.000 ARG A 794 Details of bonding type rmsd hydrogen bonds : bond 0.03049 ( 247) hydrogen bonds : angle 4.28986 ( 667) covalent geometry : bond 0.00251 ( 7083) covalent geometry : angle 0.59124 ( 9744) *********************** 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 88 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7590 (mmtt) cc_final: 0.7270 (pttm) REVERT: A 265 GLN cc_start: 0.6365 (mp10) cc_final: 0.6126 (mp10) REVERT: A 444 MET cc_start: 0.4277 (ppp) cc_final: 0.3981 (tmm) REVERT: A 714 GLU cc_start: 0.7156 (tm-30) cc_final: 0.6741 (tm-30) REVERT: A 732 TRP cc_start: 0.8178 (t60) cc_final: 0.7840 (t60) REVERT: A 836 ARG cc_start: 0.7988 (mmt180) cc_final: 0.7784 (mmt180) REVERT: A 897 TRP cc_start: 0.9026 (t-100) cc_final: 0.8765 (t-100) outliers start: 16 outliers final: 11 residues processed: 85 average time/residue: 0.2105 time to fit residues: 24.0335 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 : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 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 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 71 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.117950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.080057 restraints weight = 15823.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.082588 restraints weight = 7381.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.084088 restraints weight = 4632.320| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7083 Z= 0.151 Angle : 0.619 14.088 9744 Z= 0.301 Chirality : 0.041 0.157 1116 Planarity : 0.004 0.038 1132 Dihedral : 15.422 163.328 1362 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.50 % Allowed : 19.88 % Favored : 77.61 % 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: -1.16 (0.31), residues: 768 helix: 1.94 (0.36), residues: 229 sheet: -2.09 (0.44), residues: 141 loop : -1.98 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 732 HIS 0.003 0.001 HIS A 609 PHE 0.010 0.001 PHE A 874 TYR 0.014 0.001 TYR A 185 ARG 0.003 0.000 ARG A 794 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 247) hydrogen bonds : angle 4.28146 ( 667) covalent geometry : bond 0.00344 ( 7083) covalent geometry : angle 0.61914 ( 9744) *********************** 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: 17 poor density : 67 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7568 (mmtt) cc_final: 0.7277 (pttm) REVERT: A 265 GLN cc_start: 0.6255 (mp10) cc_final: 0.6015 (mp10) REVERT: A 585 MET cc_start: 0.8061 (ptp) cc_final: 0.7757 (ptp) REVERT: A 714 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6763 (tm-30) REVERT: A 821 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7720 (mt-10) REVERT: A 836 ARG cc_start: 0.7994 (mmt180) cc_final: 0.7775 (mmt-90) REVERT: A 897 TRP cc_start: 0.9048 (t-100) cc_final: 0.8737 (t-100) outliers start: 17 outliers final: 12 residues processed: 81 average time/residue: 0.2026 time to fit residues: 22.8358 Evaluate side-chains 78 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.0170 chunk 34 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.117099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.079332 restraints weight = 16061.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.081726 restraints weight = 7454.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.083235 restraints weight = 4656.505| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7083 Z= 0.175 Angle : 0.650 13.102 9744 Z= 0.313 Chirality : 0.042 0.173 1116 Planarity : 0.004 0.038 1132 Dihedral : 15.430 163.705 1362 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.50 % Allowed : 20.62 % Favored : 76.88 % 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: -1.19 (0.31), residues: 768 helix: 1.91 (0.36), residues: 228 sheet: -2.08 (0.43), residues: 142 loop : -1.99 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 732 HIS 0.003 0.001 HIS A 837 PHE 0.011 0.001 PHE A 874 TYR 0.014 0.001 TYR A 185 ARG 0.002 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 247) hydrogen bonds : angle 4.33725 ( 667) covalent geometry : bond 0.00397 ( 7083) covalent geometry : angle 0.65048 ( 9744) *********************** 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 81 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7639 (mmtt) cc_final: 0.7389 (pttm) REVERT: A 265 GLN cc_start: 0.6075 (mp10) cc_final: 0.5847 (mp10) REVERT: A 444 MET cc_start: 0.4014 (ppp) cc_final: 0.3663 (tmm) REVERT: A 714 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6744 (tm-30) REVERT: A 732 TRP cc_start: 0.7990 (t60) cc_final: 0.7656 (t60) REVERT: A 897 TRP cc_start: 0.9053 (t-100) cc_final: 0.8718 (t-100) outliers start: 17 outliers final: 14 residues processed: 78 average time/residue: 0.2015 time to fit residues: 21.6044 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 : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 278 LEU 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 Chi-restraints excluded: chain A residue 907 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 57 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 48 optimal weight: 0.0980 chunk 52 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.118956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.081264 restraints weight = 15906.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.083723 restraints weight = 7350.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.085269 restraints weight = 4557.207| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2899 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= 0.122 Angle : 0.636 13.453 9744 Z= 0.299 Chirality : 0.040 0.163 1116 Planarity : 0.004 0.039 1132 Dihedral : 15.385 162.912 1362 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.06 % Allowed : 21.21 % 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 (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: -1.13 (0.31), residues: 768 helix: 2.03 (0.36), residues: 228 sheet: -1.74 (0.45), residues: 131 loop : -2.14 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 732 HIS 0.002 0.001 HIS A 837 PHE 0.008 0.001 PHE A 874 TYR 0.014 0.001 TYR A 185 ARG 0.003 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.02975 ( 247) hydrogen bonds : angle 4.22397 ( 667) covalent geometry : bond 0.00283 ( 7083) covalent geometry : angle 0.63616 ( 9744) *********************** 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 81 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7658 (mmtt) cc_final: 0.7448 (pttm) REVERT: A 444 MET cc_start: 0.3964 (ppp) cc_final: 0.3623 (tmm) REVERT: A 714 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6679 (tm-30) REVERT: A 897 TRP cc_start: 0.9004 (t-100) cc_final: 0.8755 (t-100) outliers start: 14 outliers final: 12 residues processed: 78 average time/residue: 0.1883 time to fit residues: 21.0630 Evaluate side-chains 76 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 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 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 0 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 25 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.114815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.076932 restraints weight = 16505.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.079277 restraints weight = 7748.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080734 restraints weight = 4937.103| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7083 Z= 0.264 Angle : 0.722 13.053 9744 Z= 0.351 Chirality : 0.044 0.186 1116 Planarity : 0.004 0.038 1132 Dihedral : 15.452 164.653 1362 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.21 % Allowed : 21.06 % 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 (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 (0.31), residues: 768 helix: 1.66 (0.36), residues: 230 sheet: -2.13 (0.42), residues: 149 loop : -2.01 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 732 HIS 0.006 0.001 HIS A 609 PHE 0.015 0.001 PHE A 874 TYR 0.012 0.002 TYR A 185 ARG 0.007 0.000 ARG A 794 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 247) hydrogen bonds : angle 4.49846 ( 667) covalent geometry : bond 0.00587 ( 7083) covalent geometry : angle 0.72164 ( 9744) ********************** 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 74 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.707 Fit side-chains REVERT: A 444 MET cc_start: 0.4486 (ppp) cc_final: 0.3556 (tpp) REVERT: A 701 ILE cc_start: 0.8884 (pt) cc_final: 0.8669 (tp) REVERT: A 714 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6749 (tm-30) REVERT: A 732 TRP cc_start: 0.8074 (t60) cc_final: 0.7730 (t60) outliers start: 15 outliers final: 12 residues processed: 72 average time/residue: 0.1791 time to fit residues: 18.2990 Evaluate side-chains 70 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 41 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.116699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.078892 restraints weight = 16239.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.081280 restraints weight = 7559.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.082641 restraints weight = 4784.177| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7083 Z= 0.169 Angle : 0.685 13.643 9744 Z= 0.324 Chirality : 0.042 0.171 1116 Planarity : 0.004 0.039 1132 Dihedral : 15.469 163.563 1362 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 1.91 % Allowed : 21.80 % 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: -1.36 (0.30), residues: 768 helix: 1.74 (0.36), residues: 229 sheet: -2.16 (0.47), residues: 118 loop : -2.13 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 732 HIS 0.003 0.001 HIS A 837 PHE 0.010 0.001 PHE A 874 TYR 0.013 0.001 TYR A 185 ARG 0.005 0.000 ARG A 794 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 247) hydrogen bonds : angle 4.38822 ( 667) covalent geometry : bond 0.00384 ( 7083) covalent geometry : angle 0.68454 ( 9744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2525.30 seconds wall clock time: 44 minutes 41.00 seconds (2681.00 seconds total)