Starting phenix.real_space_refine on Wed Feb 12 08:09:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w62_21551/02_2025/6w62_21551.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w62_21551/02_2025/6w62_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_21551/02_2025/6w62_21551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w62_21551/02_2025/6w62_21551.map" model { file = "/net/cci-nas-00/data/ceres_data/6w62_21551/02_2025/6w62_21551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w62_21551/02_2025/6w62_21551.cif" } resolution = 3.9 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: 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 7, 'ASP:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 16, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 321 Chain: "B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 510 Classifications: {'RNA': 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: 4.75, per 1000 atoms: 0.64 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: 2.30 Conformation dependent library (CDL) restraints added in 865.1 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: 2.52 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: 2.43 Time building geometry restraints manager: 2.57 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: 10169 2.11 - 4.22: 159 4.22 - 6.33: 13 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 - 35.75: 4499 35.75 - 71.50: 124 71.50 - 107.25: 15 107.25 - 142.99: 0 142.99 - 178.74: 2 Dihedral angle restraints: 4640 sinusoidal: 1966 harmonic: 2674 Sorted by residual: dihedral pdb=" O4' U B -6 " pdb=" C1' U B -6 " pdb=" N1 U B -6 " pdb=" C2 U B -6 " ideal model delta sinusoidal sigma weight residual 232.00 53.26 178.74 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C B -11 " pdb=" C1' C B -11 " pdb=" N1 C B -11 " pdb=" C2 C B -11 " ideal model delta sinusoidal sigma weight residual 232.00 55.42 176.58 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA LYS A 487 " pdb=" C LYS A 487 " pdb=" N ILE A 488 " pdb=" CA ILE A 488 " ideal model delta harmonic sigma weight residual 180.00 153.84 26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 4637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1076 0.069 - 0.137: 96 0.137 - 0.206: 6 0.206 - 0.275: 3 0.275 - 0.343: 2 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=" CA LEU A 799 " pdb=" N LEU A 799 " pdb=" C LEU A 799 " pdb=" CB LEU A 799 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.320 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 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= 0.220 Angle : 0.642 10.557 10346 Z= 0.410 Chirality : 0.043 0.343 1183 Planarity : 0.004 0.074 1236 Dihedral : 16.092 178.742 2906 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 (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: -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 TRP 0.035 0.002 TRP A 79 HIS 0.004 0.001 HIS A 459 PHE 0.015 0.001 PHE A 51 TYR 0.012 0.001 TYR A 995 ARG 0.012 0.001 ARG A 715 *********************** 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 : 0.788 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: 0.8182 (mm) cc_final: 0.7961 (mm) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1921 time to fit residues: 35.9309 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 : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 592 GLN A 600 GLN A 771 HIS A 946 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 = 0.4299 r_free = 0.4299 target = 0.156095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.135586 restraints weight = 15709.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.139072 restraints weight = 9350.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.141346 restraints weight = 6567.217| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7573 Z= 0.294 Angle : 0.742 9.381 10346 Z= 0.386 Chirality : 0.046 0.190 1183 Planarity : 0.005 0.061 1236 Dihedral : 16.917 179.080 1356 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.22 % Favored : 88.56 % Rotamer: Outliers : 1.93 % Allowed : 11.29 % Favored : 86.78 % 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: -2.07 (0.27), residues: 900 helix: 0.14 (0.24), residues: 456 sheet: -2.48 (0.55), residues: 81 loop : -3.16 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 79 HIS 0.005 0.002 HIS A 459 PHE 0.029 0.003 PHE A1047 TYR 0.014 0.002 TYR A 542 ARG 0.004 0.001 ARG A 652 *********************** 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 140 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8101 (mm-40) REVERT: A 655 THR cc_start: 0.8411 (t) cc_final: 0.8164 (t) REVERT: A 674 LEU cc_start: 0.7983 (pp) cc_final: 0.7630 (pp) REVERT: A 758 MET cc_start: 0.7621 (tmm) cc_final: 0.7178 (tmm) REVERT: A 880 LEU cc_start: 0.8342 (mm) cc_final: 0.8011 (mm) REVERT: A 968 PRO cc_start: 0.8272 (Cg_exo) cc_final: 0.8052 (Cg_endo) outliers start: 13 outliers final: 11 residues processed: 134 average time/residue: 0.1948 time to fit residues: 35.6793 Evaluate side-chains 112 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 368 ILE Chi-restraints excluded: chain A residue 375 THR 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 666 ASP 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 9 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN A 407 GLN A 459 HIS ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.156994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.136790 restraints weight = 15978.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.140271 restraints weight = 9480.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.142644 restraints weight = 6616.885| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7573 Z= 0.235 Angle : 0.678 9.153 10346 Z= 0.352 Chirality : 0.043 0.177 1183 Planarity : 0.004 0.059 1236 Dihedral : 16.851 179.335 1356 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.33 % Favored : 89.56 % Rotamer: Outliers : 3.57 % Allowed : 14.26 % Favored : 82.17 % 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: -1.99 (0.27), residues: 900 helix: 0.28 (0.24), residues: 449 sheet: -2.43 (0.55), residues: 81 loop : -3.17 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 79 HIS 0.010 0.002 HIS A 367 PHE 0.021 0.002 PHE A1047 TYR 0.013 0.002 TYR A 996 ARG 0.003 0.000 ARG A 918 *********************** 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 144 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7932 (mm-40) REVERT: A 77 VAL cc_start: 0.8388 (t) cc_final: 0.8164 (p) REVERT: A 758 MET cc_start: 0.7943 (tmm) cc_final: 0.7538 (tmm) REVERT: A 802 LEU cc_start: 0.5181 (OUTLIER) cc_final: 0.3846 (tp) REVERT: A 880 LEU cc_start: 0.8211 (mm) cc_final: 0.7908 (mm) REVERT: A 978 GLU cc_start: 0.8026 (tt0) cc_final: 0.7753 (tt0) outliers start: 24 outliers final: 14 residues processed: 135 average time/residue: 0.1638 time to fit residues: 31.2941 Evaluate side-chains 121 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 THR 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 668 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 802 LEU 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 62 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 HIS A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.156154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.136689 restraints weight = 15434.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.140140 restraints weight = 8933.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.142458 restraints weight = 6161.491| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.2714 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= 0.242 Angle : 0.675 8.818 10346 Z= 0.351 Chirality : 0.044 0.180 1183 Planarity : 0.004 0.065 1236 Dihedral : 16.800 179.450 1356 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 4.01 % Allowed : 15.01 % Favored : 80.98 % 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: -1.98 (0.27), residues: 900 helix: 0.22 (0.24), residues: 450 sheet: -2.44 (0.54), residues: 80 loop : -3.08 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 79 HIS 0.015 0.002 HIS A 367 PHE 0.019 0.002 PHE A1047 TYR 0.019 0.002 TYR A 995 ARG 0.003 0.000 ARG A 960 *********************** 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 151 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7366 (mp) cc_final: 0.6486 (mm) REVERT: A 50 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7830 (mm-40) REVERT: A 758 MET cc_start: 0.8056 (tmm) cc_final: 0.7467 (tmm) REVERT: A 802 LEU cc_start: 0.5412 (OUTLIER) cc_final: 0.4065 (tp) REVERT: A 927 MET cc_start: 0.6993 (OUTLIER) cc_final: 0.6744 (mtm) outliers start: 27 outliers final: 18 residues processed: 139 average time/residue: 0.1734 time to fit residues: 34.5237 Evaluate side-chains 134 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE 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 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 666 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1059 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.158412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.138677 restraints weight = 15701.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.142143 restraints weight = 9292.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.144498 restraints weight = 6456.876| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.2917 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= 0.210 Angle : 0.664 9.465 10346 Z= 0.340 Chirality : 0.044 0.223 1183 Planarity : 0.004 0.069 1236 Dihedral : 16.720 178.766 1356 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 4.75 % Allowed : 16.49 % Favored : 78.75 % 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: -1.86 (0.28), residues: 900 helix: 0.31 (0.24), residues: 452 sheet: -2.42 (0.53), residues: 86 loop : -3.01 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 79 HIS 0.003 0.001 HIS A 126 PHE 0.017 0.002 PHE A 80 TYR 0.019 0.002 TYR A 995 ARG 0.005 0.000 ARG A 715 *********************** 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: 32 poor density : 112 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7328 (mp) cc_final: 0.6490 (mm) REVERT: A 50 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7847 (mm-40) REVERT: A 78 ASN cc_start: 0.7538 (OUTLIER) cc_final: 0.7336 (t0) REVERT: A 758 MET cc_start: 0.8074 (tmm) cc_final: 0.7452 (tmm) REVERT: A 802 LEU cc_start: 0.5189 (OUTLIER) cc_final: 0.3900 (tp) REVERT: A 880 LEU cc_start: 0.8171 (mm) cc_final: 0.7828 (mm) REVERT: A 996 TYR cc_start: 0.6444 (m-80) cc_final: 0.5579 (t80) outliers start: 32 outliers final: 23 residues processed: 135 average time/residue: 0.1646 time to fit residues: 31.8034 Evaluate side-chains 131 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR 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 368 ILE 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 452 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 703 VAL Chi-restraints excluded: chain A residue 770 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 55 optimal weight: 0.0370 chunk 88 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.1980 overall best weight: 1.8464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4294 r_free = 0.4294 target = 0.156123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.136139 restraints weight = 15837.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.139599 restraints weight = 9424.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.141898 restraints weight = 6575.545| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7573 Z= 0.254 Angle : 0.688 10.088 10346 Z= 0.353 Chirality : 0.045 0.202 1183 Planarity : 0.004 0.069 1236 Dihedral : 16.714 179.448 1356 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 5.50 % Allowed : 17.09 % Favored : 77.41 % 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: -1.89 (0.28), residues: 900 helix: 0.29 (0.24), residues: 451 sheet: -2.45 (0.54), residues: 85 loop : -3.01 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 79 HIS 0.004 0.001 HIS A 367 PHE 0.015 0.002 PHE A1047 TYR 0.014 0.002 TYR A 116 ARG 0.004 0.001 ARG A 715 *********************** 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 153 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7460 (mp) cc_final: 0.6642 (mm) REVERT: A 50 GLN cc_start: 0.8423 (mm-40) cc_final: 0.7802 (mm-40) REVERT: A 680 GLU cc_start: 0.6559 (pt0) cc_final: 0.6304 (tt0) REVERT: A 758 MET cc_start: 0.8061 (tmm) cc_final: 0.7379 (tmm) REVERT: A 802 LEU cc_start: 0.5495 (OUTLIER) cc_final: 0.4103 (tp) REVERT: A 880 LEU cc_start: 0.8213 (mm) cc_final: 0.7852 (mm) REVERT: A 913 MET cc_start: 0.4084 (mmm) cc_final: 0.3674 (tpp) outliers start: 37 outliers final: 25 residues processed: 142 average time/residue: 0.1602 time to fit residues: 32.1826 Evaluate side-chains 140 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 368 ILE 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 477 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4303 r_free = 0.4303 target = 0.156673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.136479 restraints weight = 15826.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.139978 restraints weight = 9360.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.142284 restraints weight = 6531.685| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7573 Z= 0.237 Angle : 0.698 10.978 10346 Z= 0.354 Chirality : 0.045 0.221 1183 Planarity : 0.004 0.073 1236 Dihedral : 16.689 178.877 1356 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 4.75 % Allowed : 18.42 % 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 (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: -1.84 (0.28), residues: 900 helix: 0.30 (0.24), residues: 455 sheet: -2.43 (0.54), residues: 85 loop : -2.99 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP A 79 HIS 0.004 0.001 HIS A 367 PHE 0.015 0.002 PHE A 476 TYR 0.014 0.002 TYR A 116 ARG 0.004 0.000 ARG A 715 *********************** 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 148 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7529 (mp) cc_final: 0.6742 (mm) REVERT: A 50 GLN cc_start: 0.8387 (mm-40) cc_final: 0.7769 (mm-40) REVERT: A 77 VAL cc_start: 0.8568 (t) cc_final: 0.8227 (p) REVERT: A 680 GLU cc_start: 0.6576 (pt0) cc_final: 0.6360 (tt0) REVERT: A 758 MET cc_start: 0.8137 (tmm) cc_final: 0.7480 (tmm) REVERT: A 802 LEU cc_start: 0.5437 (OUTLIER) cc_final: 0.4142 (tp) REVERT: A 880 LEU cc_start: 0.8246 (mm) cc_final: 0.7881 (mm) REVERT: A 913 MET cc_start: 0.3772 (mmm) cc_final: 0.3393 (tpp) REVERT: A 996 TYR cc_start: 0.6451 (m-80) cc_final: 0.5528 (t80) outliers start: 32 outliers final: 26 residues processed: 140 average time/residue: 0.1687 time to fit residues: 33.6154 Evaluate side-chains 136 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR 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 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 455 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 64 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 77 optimal weight: 0.0070 chunk 90 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.160245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.140601 restraints weight = 15774.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.144176 restraints weight = 9297.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.146601 restraints weight = 6399.406| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.3497 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= 0.181 Angle : 0.692 11.931 10346 Z= 0.343 Chirality : 0.043 0.231 1183 Planarity : 0.004 0.075 1236 Dihedral : 16.626 177.866 1356 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.16 % Allowed : 19.76 % Favored : 76.08 % 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 (0.28), residues: 900 helix: 0.49 (0.24), residues: 457 sheet: -2.33 (0.54), residues: 86 loop : -3.01 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP A 79 HIS 0.004 0.001 HIS A 952 PHE 0.020 0.002 PHE A 476 TYR 0.015 0.001 TYR A 116 ARG 0.005 0.000 ARG A 715 *********************** 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 149 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8380 (mm-40) cc_final: 0.7789 (mm-40) REVERT: A 407 GLN cc_start: 0.7318 (mt0) cc_final: 0.6943 (mm-40) REVERT: A 650 ILE cc_start: 0.6439 (pt) cc_final: 0.6233 (pt) REVERT: A 758 MET cc_start: 0.8084 (tmm) cc_final: 0.7430 (tmm) REVERT: A 803 SER cc_start: 0.7456 (m) cc_final: 0.7107 (m) REVERT: A 880 LEU cc_start: 0.8134 (mm) cc_final: 0.7766 (mm) REVERT: A 996 TYR cc_start: 0.6344 (m-80) cc_final: 0.5513 (t80) outliers start: 28 outliers final: 23 residues processed: 142 average time/residue: 0.1633 time to fit residues: 32.6369 Evaluate side-chains 135 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 88 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 0.0050 chunk 84 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4358 r_free = 0.4358 target = 0.161204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.141715 restraints weight = 15903.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.145241 restraints weight = 9345.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.147622 restraints weight = 6439.311| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7573 Z= 0.189 Angle : 0.716 12.488 10346 Z= 0.351 Chirality : 0.044 0.242 1183 Planarity : 0.004 0.077 1236 Dihedral : 16.609 177.922 1356 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 4.01 % Allowed : 20.36 % Favored : 75.63 % 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: -1.59 (0.28), residues: 900 helix: 0.57 (0.25), residues: 457 sheet: -2.17 (0.54), residues: 86 loop : -3.03 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.003 TRP A 79 HIS 0.004 0.001 HIS A 952 PHE 0.020 0.002 PHE A 476 TYR 0.018 0.002 TYR A 700 ARG 0.004 0.000 ARG A 715 *********************** 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 149 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.785 Fit side-chains REVERT: A 50 GLN cc_start: 0.8364 (mm-40) cc_final: 0.7793 (mm-40) REVERT: A 77 VAL cc_start: 0.8481 (t) cc_final: 0.8138 (p) REVERT: A 542 TYR cc_start: 0.6523 (OUTLIER) cc_final: 0.6138 (t80) REVERT: A 650 ILE cc_start: 0.6433 (pt) cc_final: 0.6206 (pt) REVERT: A 758 MET cc_start: 0.8067 (tmm) cc_final: 0.7380 (tmm) REVERT: A 803 SER cc_start: 0.7377 (m) cc_final: 0.7026 (m) REVERT: A 996 TYR cc_start: 0.6363 (m-80) cc_final: 0.5518 (t80) outliers start: 27 outliers final: 22 residues processed: 143 average time/residue: 0.1699 time to fit residues: 34.0085 Evaluate side-chains 138 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR 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 516 VAL Chi-restraints excluded: chain A residue 542 TYR Chi-restraints excluded: chain A residue 588 VAL 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 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 37 optimal weight: 1.9990 chunk 51 optimal weight: 0.0050 chunk 17 optimal weight: 0.0470 chunk 58 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.5694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4381 r_free = 0.4381 target = 0.163197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.143842 restraints weight = 15953.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.147421 restraints weight = 9320.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.149894 restraints weight = 6396.417| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.3851 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= 0.183 Angle : 0.712 12.548 10346 Z= 0.355 Chirality : 0.045 0.242 1183 Planarity : 0.004 0.080 1236 Dihedral : 16.543 177.610 1356 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 3.71 % Allowed : 21.69 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.28), residues: 900 helix: 0.62 (0.24), residues: 458 sheet: -2.14 (0.54), residues: 86 loop : -2.97 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP A 79 HIS 0.003 0.001 HIS A 126 PHE 0.017 0.002 PHE A 783 TYR 0.021 0.002 TYR A 995 ARG 0.006 0.001 ARG A 439 ********************** 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 145 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8412 (mm-40) cc_final: 0.7829 (mm-40) REVERT: A 77 VAL cc_start: 0.8416 (t) cc_final: 0.8066 (p) REVERT: A 304 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.5877 (pmm) REVERT: A 542 TYR cc_start: 0.6562 (OUTLIER) cc_final: 0.6118 (t80) REVERT: A 758 MET cc_start: 0.8094 (tmm) cc_final: 0.7343 (tmm) REVERT: A 803 SER cc_start: 0.7484 (m) cc_final: 0.7210 (m) outliers start: 25 outliers final: 21 residues processed: 138 average time/residue: 0.1821 time to fit residues: 34.9721 Evaluate side-chains 140 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 407 GLN 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 542 TYR Chi-restraints excluded: chain A residue 588 VAL 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 668 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 854 LEU 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.3832 > 50: distance: 15 - 151: 33.008 distance: 31 - 135: 32.674 distance: 34 - 132: 37.262 distance: 92 - 107: 33.927 distance: 104 - 107: 35.308 distance: 107 - 108: 69.521 distance: 108 - 109: 39.097 distance: 109 - 110: 57.303 distance: 112 - 113: 39.377 distance: 113 - 116: 38.965 distance: 114 - 115: 56.801 distance: 114 - 117: 38.630 distance: 117 - 118: 40.767 distance: 118 - 119: 56.130 distance: 118 - 121: 40.596 distance: 119 - 120: 55.637 distance: 119 - 122: 56.846 distance: 122 - 123: 40.038 distance: 123 - 124: 40.661 distance: 123 - 126: 55.609 distance: 124 - 127: 55.496 distance: 127 - 128: 56.470 distance: 128 - 129: 57.397 distance: 128 - 131: 56.929 distance: 129 - 130: 40.959 distance: 129 - 132: 56.380 distance: 133 - 134: 41.463 distance: 133 - 136: 39.914 distance: 134 - 135: 69.755 distance: 134 - 140: 39.887 distance: 136 - 137: 56.680 distance: 137 - 138: 39.691 distance: 137 - 139: 70.322 distance: 141 - 142: 39.562 distance: 141 - 144: 55.025 distance: 142 - 143: 57.061 distance: 142 - 148: 38.898 distance: 144 - 145: 38.544 distance: 145 - 146: 57.522 distance: 148 - 149: 41.296 distance: 149 - 150: 39.227 distance: 150 - 151: 57.204 distance: 150 - 159: 39.261 distance: 152 - 153: 40.147 distance: 154 - 156: 55.304 distance: 155 - 157: 40.182 distance: 156 - 158: 39.346 distance: 157 - 158: 56.538 distance: 159 - 160: 41.396 distance: 159 - 165: 56.759 distance: 160 - 163: 40.354 distance: 161 - 162: 56.798 distance: 161 - 166: 39.168 distance: 166 - 167: 57.537 distance: 167 - 168: 39.628 distance: 167 - 170: 39.426 distance: 168 - 172: 34.231