Starting phenix.real_space_refine on Fri Dec 27 23:56:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7swf_25472/12_2024/7swf_25472.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swf_25472/12_2024/7swf_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_25472/12_2024/7swf_25472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swf_25472/12_2024/7swf_25472.map" model { file = "/net/cci-nas-00/data/ceres_data/7swf_25472/12_2024/7swf_25472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swf_25472/12_2024/7swf_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-5532/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: 4.60, per 1000 atoms: 0.67 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: 1.83 Conformation dependent library (CDL) restraints added in 684.8 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: 2.38 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: 2.70 Time building geometry restraints manager: 2.11 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: 0.470 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 22.570 Find NCS groups from input model: 0.070 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.610 ------------------------------------------------------------------------------- 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 : 0.821 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: 0.2603 time to fit residues: 30.9599 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 : 0.745 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.687 Fit side-chains REVERT: A 184 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8274 (mp) REVERT: A 265 GLN cc_start: 0.6427 (mp10) cc_final: 0.6208 (mp10) REVERT: A 289 SER cc_start: 0.8337 (t) cc_final: 0.8070 (t) REVERT: A 498 LYS cc_start: 0.9269 (mmtm) cc_final: 0.9044 (mmtt) outliers start: 14 outliers final: 6 residues processed: 84 average time/residue: 0.2189 time to fit residues: 24.9525 Evaluate side-chains 69 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 616 ASN 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 39 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 7083 Z= 0.460 Angle : 0.741 12.648 9744 Z= 0.370 Chirality : 0.045 0.234 1116 Planarity : 0.005 0.047 1132 Dihedral : 15.643 164.343 1364 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.65 % Allowed : 15.46 % Favored : 81.89 % 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: -1.68 (0.31), residues: 768 helix: 1.40 (0.35), residues: 233 sheet: -2.54 (0.40), residues: 153 loop : -2.15 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 732 HIS 0.007 0.002 HIS A 609 PHE 0.016 0.002 PHE A 874 TYR 0.013 0.002 TYR A 987 ARG 0.005 0.000 ARG A 183 *********************** 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 78 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 502 MET cc_start: 0.7609 (ppp) cc_final: 0.7258 (ptm) REVERT: A 714 GLU cc_start: 0.6774 (tm-30) cc_final: 0.6517 (tm-30) REVERT: A 987 TYR cc_start: 0.8382 (p90) cc_final: 0.8156 (p90) outliers start: 18 outliers final: 14 residues processed: 74 average time/residue: 0.2173 time to fit residues: 21.5260 Evaluate side-chains 66 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS 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 661 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 837 HIS Chi-restraints excluded: chain A residue 838 HIS Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 985 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2309 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= 0.178 Angle : 0.599 9.602 9744 Z= 0.291 Chirality : 0.041 0.159 1116 Planarity : 0.004 0.040 1132 Dihedral : 15.508 163.059 1364 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.50 % Allowed : 17.67 % Favored : 79.82 % 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: -1.31 (0.31), residues: 768 helix: 1.86 (0.36), residues: 232 sheet: -2.33 (0.42), residues: 144 loop : -2.06 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 308 HIS 0.002 0.001 HIS A 870 PHE 0.011 0.001 PHE A 902 TYR 0.011 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 88 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 ARG cc_start: 0.8456 (mmp80) cc_final: 0.8166 (tpp-160) REVERT: A 502 MET cc_start: 0.7553 (ppp) cc_final: 0.7224 (ptm) REVERT: A 675 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8231 (mtmm) REVERT: A 714 GLU cc_start: 0.6596 (tm-30) cc_final: 0.6381 (tm-30) outliers start: 17 outliers final: 10 residues processed: 85 average time/residue: 0.2467 time to fit residues: 28.1704 Evaluate side-chains 73 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 488 HIS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 675 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 671 ASN A 885 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2479 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= 0.221 Angle : 0.599 8.430 9744 Z= 0.293 Chirality : 0.041 0.152 1116 Planarity : 0.004 0.038 1132 Dihedral : 15.447 163.024 1362 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.95 % Allowed : 20.03 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.31), residues: 768 helix: 1.95 (0.36), residues: 230 sheet: -2.17 (0.42), residues: 149 loop : -2.05 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 308 HIS 0.003 0.001 HIS A 609 PHE 0.009 0.001 PHE A 874 TYR 0.018 0.001 TYR A 987 ARG 0.004 0.000 ARG A 794 *********************** 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 83 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 502 MET cc_start: 0.7576 (ppp) cc_final: 0.7245 (ptm) REVERT: A 675 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8319 (mtmm) REVERT: A 714 GLU cc_start: 0.6644 (tm-30) cc_final: 0.6399 (tm-30) outliers start: 20 outliers final: 10 residues processed: 81 average time/residue: 0.1904 time to fit residues: 21.2787 Evaluate side-chains 70 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 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 675 LYS Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 838 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 25 optimal weight: 30.0000 chunk 40 optimal weight: 0.0970 chunk 73 optimal weight: 4.9990 chunk 8 optimal weight: 30.0000 chunk 43 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2626 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= 0.244 Angle : 0.611 7.712 9744 Z= 0.305 Chirality : 0.041 0.151 1116 Planarity : 0.004 0.044 1132 Dihedral : 15.429 163.479 1362 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.09 % Allowed : 19.59 % Favored : 77.32 % 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: -1.32 (0.31), residues: 768 helix: 1.95 (0.36), residues: 230 sheet: -2.25 (0.41), residues: 156 loop : -2.12 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 732 HIS 0.005 0.001 HIS A 870 PHE 0.007 0.001 PHE A 986 TYR 0.015 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 81 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 444 MET cc_start: 0.3849 (ppp) cc_final: 0.3632 (tmm) REVERT: A 579 MET cc_start: 0.8758 (tpp) cc_final: 0.8510 (tpp) REVERT: A 675 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8332 (mtmm) outliers start: 21 outliers final: 13 residues processed: 78 average time/residue: 0.1899 time to fit residues: 20.4247 Evaluate side-chains 71 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 488 HIS Chi-restraints excluded: chain A residue 511 VAL 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 675 LYS 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 872 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 671 ASN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7083 Z= 0.307 Angle : 0.653 8.458 9744 Z= 0.328 Chirality : 0.042 0.166 1116 Planarity : 0.004 0.042 1132 Dihedral : 15.454 164.014 1362 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.39 % Allowed : 19.44 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.84 (0.36), residues: 231 sheet: -2.17 (0.43), residues: 151 loop : -2.02 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 732 HIS 0.004 0.001 HIS A 609 PHE 0.011 0.001 PHE A 874 TYR 0.012 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 85 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 276 ARG cc_start: 0.8507 (mmp80) cc_final: 0.8150 (tpp-160) REVERT: A 498 LYS cc_start: 0.9160 (mmtm) cc_final: 0.8867 (mmtt) REVERT: A 579 MET cc_start: 0.8690 (tpp) cc_final: 0.8470 (tpp) outliers start: 23 outliers final: 16 residues processed: 81 average time/residue: 0.2145 time to fit residues: 23.6741 Evaluate side-chains 75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 511 VAL 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 837 HIS Chi-restraints excluded: chain A residue 838 HIS Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 988 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2936 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= 0.176 Angle : 0.614 8.377 9744 Z= 0.301 Chirality : 0.040 0.152 1116 Planarity : 0.004 0.039 1132 Dihedral : 15.365 161.579 1362 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.06 % Allowed : 20.62 % Favored : 77.32 % 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: 2.04 (0.36), residues: 228 sheet: -2.16 (0.43), residues: 146 loop : -2.14 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 732 HIS 0.002 0.001 HIS A 870 PHE 0.008 0.001 PHE A 986 TYR 0.012 0.001 TYR A 185 ARG 0.005 0.000 ARG A 276 *********************** 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 77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.847 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 74 average time/residue: 0.1916 time to fit residues: 19.6726 Evaluate side-chains 66 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 511 VAL 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 671 ASN Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 838 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3067 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= 0.175 Angle : 0.654 14.233 9744 Z= 0.310 Chirality : 0.040 0.156 1116 Planarity : 0.004 0.038 1132 Dihedral : 15.343 162.505 1362 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.06 % Allowed : 21.35 % 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: -1.16 (0.31), residues: 768 helix: 2.08 (0.36), residues: 227 sheet: -1.74 (0.46), residues: 131 loop : -2.22 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 732 HIS 0.003 0.001 HIS A 870 PHE 0.008 0.001 PHE A 902 TYR 0.012 0.001 TYR A 185 ARG 0.004 0.000 ARG A 276 *********************** 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 72 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.742 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 70 average time/residue: 0.1580 time to fit residues: 16.3014 Evaluate side-chains 68 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 511 VAL 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 671 ASN 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 78 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 62 optimal weight: 0.3980 chunk 6 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7083 Z= 0.208 Angle : 0.657 13.890 9744 Z= 0.314 Chirality : 0.041 0.168 1116 Planarity : 0.004 0.039 1132 Dihedral : 15.347 162.909 1362 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % 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: -1.21 (0.30), residues: 768 helix: 2.01 (0.36), residues: 229 sheet: -1.82 (0.45), residues: 135 loop : -2.22 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 732 HIS 0.004 0.001 HIS A 870 PHE 0.007 0.001 PHE A 874 TYR 0.012 0.001 TYR A 185 ARG 0.004 0.000 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 71 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.754 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 70 average time/residue: 0.1571 time to fit residues: 16.4023 Evaluate side-chains 68 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 511 VAL 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 719 SER Chi-restraints excluded: chain A residue 837 HIS 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 17 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 HIS ** 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 = 0.3651 r_free = 0.3651 target = 0.114817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.077156 restraints weight = 16020.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.079517 restraints weight = 7499.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.080982 restraints weight = 4758.047| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3072 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= 0.378 Angle : 0.744 12.895 9744 Z= 0.361 Chirality : 0.044 0.217 1116 Planarity : 0.005 0.041 1132 Dihedral : 15.435 164.668 1362 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 2.36 % Allowed : 21.65 % Favored : 75.99 % 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: -1.40 (0.31), residues: 768 helix: 1.65 (0.36), residues: 231 sheet: -2.17 (0.41), residues: 162 loop : -2.06 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 732 HIS 0.006 0.001 HIS A 870 PHE 0.012 0.001 PHE A 874 TYR 0.011 0.002 TYR A 793 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: 1460.78 seconds wall clock time: 28 minutes 18.27 seconds (1698.27 seconds total)