Starting phenix.real_space_refine on Fri Sep 11 04:23:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w62_21551/09_2026/6w62_21551.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w62_21551/09_2026/6w62_21551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w62_21551/09_2026/6w62_21551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w62_21551/09_2026/6w62_21551.map" model { file = "/net/cci-nas-00/data/ceres_data/6w62_21551/09_2026/6w62_21551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w62_21551/09_2026/6w62_21551.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6w62_21551/09_2026/6w62_21551.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w62_21551/09_2026/6w62_21551.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 30 5.16 5 C 4602 2.51 5 N 1293 2.21 5 O 1438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7387 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 6877 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 29, 'TRANS': 880} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 536 Unresolved non-hydrogen angles: 671 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 16, 'GLU:plan': 16, 'ARG:plan': 8, 'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 6, 'PHE:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 321 Chain: "B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 510 Classifications: {'RNAv2': 24} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 16} Time building chain proxies: 1.43, per 1000 atoms: 0.19 Number of scatterers: 7387 At special positions: 0 Unit cell: (79.8, 122.85, 107.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 24 15.00 O 1438 8.00 N 1293 7.00 C 4602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 290.3 milliseconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 52.7% alpha, 6.7% beta 5 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 23 through 54 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.503A pdb=" N TYR A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 118 removed outlier: 4.085A pdb=" N TYR A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 308 through 331 removed outlier: 4.363A pdb=" N ILE A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.913A pdb=" N GLU A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 423 Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 446 through 462 removed outlier: 3.864A pdb=" N ASP A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 500 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 585 through 602 removed outlier: 3.651A pdb=" N ARG A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 721 removed outlier: 4.168A pdb=" N LYS A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 746 Processing helix chain 'A' and resid 752 through 771 Processing helix chain 'A' and resid 772 through 778 removed outlier: 4.523A pdb=" N LYS A 776 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 787 Processing helix chain 'A' and resid 802 through 822 removed outlier: 3.765A pdb=" N LEU A 822 " --> pdb=" O PHE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 846 through 886 Processing helix chain 'A' and resid 905 through 914 Processing helix chain 'A' and resid 916 through 929 removed outlier: 3.515A pdb=" N VAL A 920 " --> pdb=" O LEU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 971 removed outlier: 3.534A pdb=" N GLU A 970 " --> pdb=" O THR A 967 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 971 " --> pdb=" O PRO A 968 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 967 through 971' Processing helix chain 'A' and resid 972 through 983 removed outlier: 3.699A pdb=" N ARG A 976 " --> pdb=" O THR A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1008 removed outlier: 3.630A pdb=" N ALA A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1015 Processing helix chain 'A' and resid 1018 through 1033 removed outlier: 3.686A pdb=" N PHE A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1082 Processing helix chain 'A' and resid 1085 through 1090 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.517A pdb=" N ALA A 629 " --> pdb=" O ASN A 614 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84 removed outlier: 3.819A pdb=" N LYS A 81 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 478 through 479 removed outlier: 3.786A pdb=" N GLY A 479 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY A 486 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU A 485 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 515 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 678 through 683 removed outlier: 6.179A pdb=" N GLU A 660 " --> pdb=" O PRO A 678 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL A 642 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 688 through 689 removed outlier: 3.633A pdb=" N TYR A 695 " --> pdb=" O SER A 688 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 963 through 966 removed outlier: 3.949A pdb=" N PHE A1040 " --> pdb=" O SER A 964 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1049 through 1050 removed outlier: 3.962A pdb=" N THR A1059 " --> pdb=" O VAL A1070 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 1.36 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2260 1.34 - 1.45: 1159 1.45 - 1.57: 4056 1.57 - 1.69: 47 1.69 - 1.81: 51 Bond restraints: 7573 Sorted by residual: bond pdb=" N ILE A 489 " pdb=" CA ILE A 489 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N SER A 490 " pdb=" CA SER A 490 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.41e-02 5.03e+03 8.79e+00 bond pdb=" N VAL A 684 " pdb=" CA VAL A 684 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.61e+00 bond pdb=" N VAL A 686 " pdb=" CA VAL A 686 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.32e-02 5.74e+03 7.91e+00 bond pdb=" N SER A 803 " pdb=" CA SER A 803 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.20e-02 6.94e+03 7.51e+00 ... (remaining 7568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 10093 2.11 - 4.22: 228 4.22 - 6.33: 20 6.33 - 8.45: 4 8.45 - 10.56: 1 Bond angle restraints: 10346 Sorted by residual: angle pdb=" N PRO A 491 " pdb=" CA PRO A 491 " pdb=" C PRO A 491 " ideal model delta sigma weight residual 113.53 124.09 -10.56 1.39e+00 5.18e-01 5.77e+01 angle pdb=" N PRO A 987 " pdb=" CA PRO A 987 " pdb=" CB PRO A 987 " ideal model delta sigma weight residual 103.25 110.62 -7.37 1.05e+00 9.07e-01 4.93e+01 angle pdb=" N PRO A 955 " pdb=" CA PRO A 955 " pdb=" CB PRO A 955 " ideal model delta sigma weight residual 103.25 110.12 -6.87 1.05e+00 9.07e-01 4.29e+01 angle pdb=" N PRO A 339 " pdb=" CA PRO A 339 " pdb=" CB PRO A 339 " ideal model delta sigma weight residual 103.23 110.01 -6.78 1.07e+00 8.73e-01 4.02e+01 angle pdb=" C ILE A 488 " pdb=" N ILE A 489 " pdb=" CA ILE A 489 " ideal model delta sigma weight residual 120.46 126.77 -6.31 1.37e+00 5.33e-01 2.12e+01 ... (remaining 10341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4117 17.66 - 35.32: 291 35.32 - 52.98: 79 52.98 - 70.64: 41 70.64 - 88.30: 12 Dihedral angle restraints: 4540 sinusoidal: 1866 harmonic: 2674 Sorted by residual: dihedral pdb=" C4' G B 1 " pdb=" C3' G B 1 " pdb=" C2' G B 1 " pdb=" C1' G B 1 " ideal model delta sinusoidal sigma weight residual 36.34 -36.76 73.11 1 3.10e+00 1.04e-01 7.09e+02 dihedral pdb=" C4' U B -6 " pdb=" C3' U B -6 " pdb=" C2' U B -6 " pdb=" C1' U B -6 " ideal model delta sinusoidal sigma weight residual 36.34 -36.42 72.76 1 3.10e+00 1.04e-01 7.03e+02 dihedral pdb=" C4' G B -7 " pdb=" C3' G B -7 " pdb=" C2' G B -7 " pdb=" C1' G B -7 " ideal model delta sinusoidal sigma weight residual 36.34 -36.11 72.46 1 3.10e+00 1.04e-01 6.98e+02 ... (remaining 4537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1029 0.069 - 0.137: 103 0.137 - 0.206: 11 0.206 - 0.275: 32 0.275 - 0.343: 8 Chirality restraints: 1183 Sorted by residual: chirality pdb=" CA SER A 490 " pdb=" N SER A 490 " pdb=" C SER A 490 " pdb=" CB SER A 490 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA PRO A 491 " pdb=" N PRO A 491 " pdb=" C PRO A 491 " pdb=" CB PRO A 491 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C2' G B 1 " pdb=" C3' G B 1 " pdb=" O2' G B 1 " pdb=" C1' G B 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1180 not shown) Planarity restraints: 1236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 798 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C SER A 798 " -0.060 2.00e-02 2.50e+03 pdb=" O SER A 798 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A 799 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 674 " 0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO A 675 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 675 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 675 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 845 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.95e+00 pdb=" C ALA A 845 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA A 845 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 846 " 0.013 2.00e-02 2.50e+03 ... (remaining 1233 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 78 2.49 - 3.09: 5914 3.09 - 3.69: 11592 3.69 - 4.30: 16348 4.30 - 4.90: 25760 Nonbonded interactions: 59692 Sorted by model distance: nonbonded pdb=" O2' U B -5 " pdb=" OP1 G B -4 " model vdw 1.883 3.040 nonbonded pdb=" O2' G B 1 " pdb=" O5' C B 2 " model vdw 2.064 3.040 nonbonded pdb=" N VAL A 686 " pdb=" OD1 ASP A 696 " model vdw 2.198 3.120 nonbonded pdb=" O SER A 798 " pdb=" N SER A 800 " model vdw 2.201 3.120 nonbonded pdb=" OH TYR A 473 " pdb=" O LYS A 619 " model vdw 2.204 3.040 ... (remaining 59687 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: 0.590 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.320 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 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 : 0.003 0.042 7573 Z= 0.212 Angle : 0.707 10.557 10346 Z= 0.423 Chirality : 0.061 0.343 1183 Planarity : 0.004 0.074 1236 Dihedral : 15.032 88.303 2806 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.22 % Favored : 89.44 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.27), residues: 900 helix: 0.41 (0.25), residues: 439 sheet: -2.39 (0.50), residues: 101 loop : -3.38 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 715 TYR 0.012 0.001 TYR A 995 PHE 0.015 0.001 PHE A 51 TRP 0.035 0.002 TRP A 79 HIS 0.004 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.21 ( 7573) covalent geometry : angle 0.70656 / 0.42 (10346) hydrogen bonds : bond 0.16345 / 11.71 ( 371) hydrogen bonds : angle 6.22960 / 4.52 ( 1061) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 821 LEU cc_start: 0.5408 (tp) cc_final: 0.5177 (tp) REVERT: A 880 LEU cc_start: 0.8183 (mm) cc_final: 0.7961 (mm) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.0794 time to fit residues: 15.2931 Evaluate side-chains 111 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 ASN ** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 459 HIS A 477 ASN A 592 GLN A 771 HIS A 993 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.159001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.138722 restraints weight = 15165.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.142042 restraints weight = 9168.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.144317 restraints weight = 6502.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.145922 restraints weight = 5083.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.146552 restraints weight = 4241.474| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7573 Z= 0.176 Angle : 0.876 14.349 10346 Z= 0.400 Chirality : 0.066 0.686 1183 Planarity : 0.004 0.057 1236 Dihedral : 13.225 143.348 1256 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.78 % Favored : 90.00 % Rotamer: Outliers : 1.63 % Allowed : 9.66 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.28), residues: 900 helix: 0.42 (0.24), residues: 456 sheet: -2.29 (0.56), residues: 80 loop : -3.11 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 22 TYR 0.014 0.002 TYR A 996 PHE 0.031 0.003 PHE A1047 TRP 0.030 0.002 TRP A 79 HIS 0.005 0.001 HIS A 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 ( 7573) covalent geometry : angle 0.87645 / 0.40 (10346) hydrogen bonds : bond 0.04816 / 3.28 ( 371) hydrogen bonds : angle 4.72791 / 3.39 ( 1061) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8140 (mm-40) REVERT: A 80 PHE cc_start: 0.7977 (m-80) cc_final: 0.7716 (m-80) REVERT: A 758 MET cc_start: 0.7507 (tmm) cc_final: 0.7213 (tmm) REVERT: A 806 MET cc_start: 0.5918 (mtp) cc_final: 0.5646 (ttt) REVERT: A 844 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8581 (mttm) REVERT: A 880 LEU cc_start: 0.8255 (mm) cc_final: 0.8001 (mm) REVERT: A 968 PRO cc_start: 0.8361 (Cg_exo) cc_final: 0.8138 (Cg_endo) outliers start: 11 outliers final: 8 residues processed: 131 average time/residue: 0.0772 time to fit residues: 14.0801 Evaluate side-chains 116 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 770 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 82 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 44 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 GLN A 862 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.154088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.133557 restraints weight = 15651.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.137026 restraints weight = 9325.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.139292 restraints weight = 6488.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.140842 restraints weight = 5055.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.141889 restraints weight = 4236.542| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7573 Z= 0.237 Angle : 0.879 11.761 10346 Z= 0.417 Chirality : 0.060 0.401 1183 Planarity : 0.005 0.069 1236 Dihedral : 13.337 151.231 1256 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.33 % Favored : 87.56 % Rotamer: Outliers : 3.71 % Allowed : 13.82 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.27), residues: 900 helix: 0.08 (0.24), residues: 457 sheet: -2.53 (0.55), residues: 81 loop : -3.31 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 439 TYR 0.015 0.002 TYR A 656 PHE 0.021 0.002 PHE A1047 TRP 0.030 0.003 TRP A 79 HIS 0.013 0.002 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 ( 7573) covalent geometry : angle 0.87923 / 0.42 (10346) hydrogen bonds : bond 0.05023 / 3.32 ( 371) hydrogen bonds : angle 4.81359 / 3.42 ( 1061) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8355 (mm-40) cc_final: 0.7928 (mm-40) REVERT: A 77 VAL cc_start: 0.8405 (t) cc_final: 0.8124 (p) REVERT: A 758 MET cc_start: 0.7710 (tmm) cc_final: 0.7098 (tmm) REVERT: A 880 LEU cc_start: 0.8334 (mm) cc_final: 0.8009 (mm) outliers start: 25 outliers final: 17 residues processed: 139 average time/residue: 0.0721 time to fit residues: 14.3935 Evaluate side-chains 129 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1059 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.0470 chunk 11 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 84 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.161237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.141294 restraints weight = 15819.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.144941 restraints weight = 9180.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.147433 restraints weight = 6323.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.149123 restraints weight = 4829.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.150049 restraints weight = 3965.097| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7573 Z= 0.137 Angle : 0.780 12.006 10346 Z= 0.361 Chirality : 0.054 0.329 1183 Planarity : 0.004 0.065 1236 Dihedral : 13.093 152.132 1256 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 2.97 % Allowed : 16.20 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.27), residues: 900 helix: 0.34 (0.24), residues: 452 sheet: -2.37 (0.54), residues: 81 loop : -3.10 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 715 TYR 0.013 0.002 TYR A 116 PHE 0.017 0.002 PHE A1047 TRP 0.026 0.002 TRP A 79 HIS 0.010 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 7573) covalent geometry : angle 0.77972 / 0.36 (10346) hydrogen bonds : bond 0.04118 / 2.74 ( 371) hydrogen bonds : angle 4.48653 / 3.25 ( 1061) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 19 MET cc_start: 0.6461 (tpt) cc_final: 0.6138 (tpt) REVERT: A 50 GLN cc_start: 0.8317 (mm-40) cc_final: 0.7842 (mm-40) REVERT: A 758 MET cc_start: 0.8007 (tmm) cc_final: 0.6670 (tmm) REVERT: A 880 LEU cc_start: 0.8245 (mm) cc_final: 0.7926 (mm) outliers start: 20 outliers final: 14 residues processed: 137 average time/residue: 0.0762 time to fit residues: 14.8492 Evaluate side-chains 125 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 1046 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 81 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 477 ASN A 993 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.155728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.135614 restraints weight = 15928.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.139107 restraints weight = 9327.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.141400 restraints weight = 6477.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.142963 restraints weight = 5053.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.143958 restraints weight = 4213.550| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7573 Z= 0.212 Angle : 0.841 12.978 10346 Z= 0.394 Chirality : 0.058 0.373 1183 Planarity : 0.004 0.069 1236 Dihedral : 13.152 149.826 1256 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 4.16 % Allowed : 17.68 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.27), residues: 900 helix: 0.17 (0.24), residues: 450 sheet: -2.44 (0.55), residues: 81 loop : -3.05 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 715 TYR 0.020 0.002 TYR A 995 PHE 0.017 0.002 PHE A 476 TRP 0.023 0.002 TRP A 79 HIS 0.017 0.002 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 ( 7573) covalent geometry : angle 0.84071 / 0.39 (10346) hydrogen bonds : bond 0.04687 / 3.07 ( 371) hydrogen bonds : angle 4.66019 / 3.34 ( 1061) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7426 (mp) cc_final: 0.6566 (mm) REVERT: A 50 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7843 (mm-40) REVERT: A 77 VAL cc_start: 0.8374 (t) cc_final: 0.8028 (p) REVERT: A 758 MET cc_start: 0.7999 (tmm) cc_final: 0.7083 (tmm) REVERT: A 996 TYR cc_start: 0.6530 (m-80) cc_final: 0.5656 (t80) outliers start: 28 outliers final: 20 residues processed: 133 average time/residue: 0.0704 time to fit residues: 13.2989 Evaluate side-chains 130 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1059 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 56 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 993 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.156882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.136962 restraints weight = 15867.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.140547 restraints weight = 9202.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.142986 restraints weight = 6326.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.144614 restraints weight = 4840.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.145593 restraints weight = 3998.504| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7573 Z= 0.175 Angle : 0.817 13.019 10346 Z= 0.381 Chirality : 0.056 0.366 1183 Planarity : 0.004 0.073 1236 Dihedral : 13.097 148.003 1256 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 4.01 % Allowed : 19.17 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.27), residues: 900 helix: 0.19 (0.24), residues: 453 sheet: -2.50 (0.54), residues: 85 loop : -3.07 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 715 TYR 0.023 0.002 TYR A 995 PHE 0.016 0.002 PHE A1047 TRP 0.023 0.002 TRP A 79 HIS 0.012 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 ( 7573) covalent geometry : angle 0.81671 / 0.38 (10346) hydrogen bonds : bond 0.04359 / 2.88 ( 371) hydrogen bonds : angle 4.55271 / 3.27 ( 1061) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7492 (mp) cc_final: 0.6678 (mm) REVERT: A 50 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7764 (mm-40) REVERT: A 78 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7582 (t0) REVERT: A 80 PHE cc_start: 0.7786 (m-80) cc_final: 0.7566 (m-80) REVERT: A 758 MET cc_start: 0.7583 (tmm) cc_final: 0.6897 (tmm) REVERT: A 880 LEU cc_start: 0.8174 (mm) cc_final: 0.7826 (mm) REVERT: A 913 MET cc_start: 0.4011 (mmm) cc_final: 0.3584 (tpp) outliers start: 27 outliers final: 19 residues processed: 138 average time/residue: 0.0715 time to fit residues: 14.1918 Evaluate side-chains 133 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1059 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 88 optimal weight: 0.0030 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 477 ASN A 993 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.157419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.137974 restraints weight = 15620.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.141418 restraints weight = 9047.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.143770 restraints weight = 6229.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.145181 restraints weight = 4767.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.146426 restraints weight = 3992.433| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7573 Z= 0.161 Angle : 0.806 13.174 10346 Z= 0.374 Chirality : 0.056 0.358 1183 Planarity : 0.004 0.071 1236 Dihedral : 13.100 150.206 1256 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 5.35 % Allowed : 18.42 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.28), residues: 900 helix: 0.36 (0.24), residues: 453 sheet: -2.45 (0.54), residues: 85 loop : -3.04 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 715 TYR 0.013 0.002 TYR A 707 PHE 0.015 0.002 PHE A1047 TRP 0.033 0.002 TRP A 79 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 7573) covalent geometry : angle 0.80596 / 0.37 (10346) hydrogen bonds : bond 0.04278 / 2.84 ( 371) hydrogen bonds : angle 4.49322 / 3.25 ( 1061) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7495 (mp) cc_final: 0.6692 (mm) REVERT: A 50 GLN cc_start: 0.8346 (mm-40) cc_final: 0.7768 (mm-40) REVERT: A 78 ASN cc_start: 0.7567 (OUTLIER) cc_final: 0.7350 (t0) REVERT: A 448 ILE cc_start: 0.2892 (tt) cc_final: 0.2655 (tt) REVERT: A 680 GLU cc_start: 0.6539 (pt0) cc_final: 0.6287 (tt0) REVERT: A 744 GLU cc_start: 0.5361 (OUTLIER) cc_final: 0.4143 (pt0) REVERT: A 758 MET cc_start: 0.7596 (tmm) cc_final: 0.7033 (tmm) REVERT: A 880 LEU cc_start: 0.8206 (mm) cc_final: 0.7850 (mm) REVERT: A 913 MET cc_start: 0.3921 (mmm) cc_final: 0.3542 (tpp) REVERT: A 996 TYR cc_start: 0.6378 (m-80) cc_final: 0.5547 (t80) outliers start: 36 outliers final: 25 residues processed: 145 average time/residue: 0.0733 time to fit residues: 15.2625 Evaluate side-chains 138 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1059 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 37 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.156179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.135885 restraints weight = 16124.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.139429 restraints weight = 9477.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.141808 restraints weight = 6569.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.143434 restraints weight = 5067.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.144391 restraints weight = 4212.385| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7573 Z= 0.173 Angle : 0.833 13.378 10346 Z= 0.385 Chirality : 0.057 0.370 1183 Planarity : 0.004 0.077 1236 Dihedral : 13.143 151.265 1256 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 4.75 % Allowed : 19.91 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.28), residues: 900 helix: 0.31 (0.24), residues: 453 sheet: -2.46 (0.54), residues: 85 loop : -3.09 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 715 TYR 0.017 0.002 TYR A 700 PHE 0.019 0.002 PHE A 476 TRP 0.029 0.002 TRP A 79 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 7573) covalent geometry : angle 0.83343 / 0.38 (10346) hydrogen bonds : bond 0.04376 / 2.89 ( 371) hydrogen bonds : angle 4.53148 / 3.28 ( 1061) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7748 (mm-40) REVERT: A 78 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.7345 (t0) REVERT: A 680 GLU cc_start: 0.6544 (pt0) cc_final: 0.6280 (tt0) REVERT: A 744 GLU cc_start: 0.5387 (OUTLIER) cc_final: 0.4181 (pt0) REVERT: A 758 MET cc_start: 0.7570 (tmm) cc_final: 0.7010 (tmm) REVERT: A 802 LEU cc_start: 0.5558 (OUTLIER) cc_final: 0.4221 (tp) REVERT: A 880 LEU cc_start: 0.8214 (mm) cc_final: 0.7844 (mm) outliers start: 32 outliers final: 26 residues processed: 137 average time/residue: 0.0652 time to fit residues: 12.8954 Evaluate side-chains 140 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1059 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 87 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 0.0270 chunk 83 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 993 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.154779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.135265 restraints weight = 15620.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.138627 restraints weight = 9152.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.140888 restraints weight = 6359.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.142440 restraints weight = 4922.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.143392 restraints weight = 4098.595| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7573 Z= 0.201 Angle : 0.866 13.489 10346 Z= 0.403 Chirality : 0.058 0.398 1183 Planarity : 0.005 0.078 1236 Dihedral : 13.233 152.212 1256 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 5.79 % Allowed : 19.47 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.28), residues: 900 helix: 0.16 (0.24), residues: 457 sheet: -2.51 (0.54), residues: 87 loop : -3.08 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 715 TYR 0.020 0.002 TYR A 995 PHE 0.014 0.002 PHE A1047 TRP 0.045 0.003 TRP A 79 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 ( 7573) covalent geometry : angle 0.86648 / 0.40 (10346) hydrogen bonds : bond 0.04636 / 3.05 ( 371) hydrogen bonds : angle 4.65024 / 3.36 ( 1061) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7729 (mm-40) REVERT: A 77 VAL cc_start: 0.8570 (t) cc_final: 0.8231 (p) REVERT: A 542 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.6279 (t80) REVERT: A 680 GLU cc_start: 0.6567 (pt0) cc_final: 0.6324 (tt0) REVERT: A 758 MET cc_start: 0.7456 (tmm) cc_final: 0.6799 (tmm) REVERT: A 880 LEU cc_start: 0.8225 (mm) cc_final: 0.7855 (mm) outliers start: 39 outliers final: 30 residues processed: 143 average time/residue: 0.0643 time to fit residues: 13.5240 Evaluate side-chains 142 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 542 TYR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1059 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 975 ASN A 993 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.158447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.138880 restraints weight = 15774.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.142387 restraints weight = 9237.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.144738 restraints weight = 6404.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.146331 restraints weight = 4943.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.147312 restraints weight = 4093.635| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7573 Z= 0.152 Angle : 0.845 13.290 10346 Z= 0.389 Chirality : 0.057 0.369 1183 Planarity : 0.004 0.080 1236 Dihedral : 13.173 151.856 1256 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 4.01 % Allowed : 20.65 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.28), residues: 900 helix: 0.29 (0.24), residues: 458 sheet: -2.41 (0.53), residues: 87 loop : -3.07 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 715 TYR 0.015 0.002 TYR A 707 PHE 0.020 0.002 PHE A 80 TRP 0.092 0.003 TRP A 79 HIS 0.004 0.001 HIS A 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 7573) covalent geometry : angle 0.84541 / 0.39 (10346) hydrogen bonds : bond 0.04272 / 2.84 ( 371) hydrogen bonds : angle 4.53169 / 3.29 ( 1061) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.292 Fit side-chains REVERT: A 19 MET cc_start: 0.6485 (tpt) cc_final: 0.6122 (tpt) REVERT: A 50 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7766 (mm-40) REVERT: A 77 VAL cc_start: 0.8548 (t) cc_final: 0.8210 (p) REVERT: A 448 ILE cc_start: 0.3178 (tt) cc_final: 0.2960 (tt) REVERT: A 542 TYR cc_start: 0.6676 (OUTLIER) cc_final: 0.6100 (t80) REVERT: A 758 MET cc_start: 0.7516 (tmm) cc_final: 0.6985 (tmm) REVERT: A 880 LEU cc_start: 0.8139 (mm) cc_final: 0.7779 (mm) outliers start: 27 outliers final: 24 residues processed: 137 average time/residue: 0.0655 time to fit residues: 13.1144 Evaluate side-chains 136 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 542 TYR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1059 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 993 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.159575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.140240 restraints weight = 15778.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.143754 restraints weight = 9226.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.146122 restraints weight = 6356.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.147685 restraints weight = 4879.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.148627 restraints weight = 4040.566| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7573 Z= 0.154 Angle : 0.853 13.274 10346 Z= 0.394 Chirality : 0.057 0.398 1183 Planarity : 0.004 0.080 1236 Dihedral : 13.131 152.536 1256 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 3.86 % Allowed : 21.10 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.28), residues: 900 helix: 0.32 (0.24), residues: 456 sheet: -2.19 (0.54), residues: 87 loop : -3.05 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 715 TYR 0.029 0.002 TYR A 995 PHE 0.019 0.002 PHE A 536 TRP 0.101 0.004 TRP A 79 HIS 0.004 0.001 HIS A 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 7573) covalent geometry : angle 0.85322 / 0.39 (10346) hydrogen bonds : bond 0.04319 / 2.87 ( 371) hydrogen bonds : angle 4.49777 / 3.28 ( 1061) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1423.78 seconds wall clock time: 25 minutes 25.78 seconds (1525.78 seconds total)