Starting phenix.real_space_refine on Thu Jan 18 02:06:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/01_2024/6w62_21551.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/01_2024/6w62_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/01_2024/6w62_21551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/01_2024/6w62_21551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/01_2024/6w62_21551.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/01_2024/6w62_21551.pdb" } 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 Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A GLU 680": "OE1" <-> "OE2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "A GLU 840": "OE1" <-> "OE2" Residue "A GLU 894": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 4.81, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 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: 3.10 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 2.54 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: 2.33 Time building geometry restraints manager: 3.28 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: 100.10 - 106.89: 298 106.89 - 113.67: 4252 113.67 - 120.46: 2925 120.46 - 127.24: 2771 127.24 - 134.03: 100 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: 4486 35.75 - 71.50: 117 71.50 - 107.25: 15 107.25 - 142.99: 0 142.99 - 178.74: 2 Dihedral angle restraints: 4620 sinusoidal: 1946 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 4617 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 2.440 nonbonded pdb=" O2' G B 1 " pdb=" O5' C B 2 " model vdw 2.064 2.440 nonbonded pdb=" N VAL A 686 " pdb=" OD1 ASP A 696 " model vdw 2.198 2.520 nonbonded pdb=" O SER A 798 " pdb=" N SER A 800 " model vdw 2.201 2.520 nonbonded pdb=" OH TYR A 473 " pdb=" O LYS A 619 " model vdw 2.204 2.440 ... (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 ========== 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: 0.310 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: 1.760 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.680 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.940 ------------------------------------------------------------------------------- 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 : 15.871 178.742 2886 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 fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.744 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: 0.1759 time to fit residues: 33.1333 Evaluate side-chains 111 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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: 0.9980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 459 HIS A 477 ASN A 592 GLN A 600 GLN A 771 HIS A 993 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.1617 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= 0.258 Angle : 0.695 8.530 10346 Z= 0.359 Chirality : 0.044 0.177 1183 Planarity : 0.004 0.059 1236 Dihedral : 16.620 179.506 1336 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.67 % Favored : 89.11 % Rotamer: Outliers : 2.23 % Allowed : 10.10 % Favored : 87.67 % 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: -1.92 (0.27), residues: 900 helix: 0.34 (0.24), residues: 450 sheet: -2.28 (0.56), residues: 80 loop : -3.17 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 79 HIS 0.006 0.001 HIS A 662 PHE 0.031 0.003 PHE A1047 TYR 0.014 0.002 TYR A 996 ARG 0.003 0.000 ARG A 715 *********************** 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 141 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8151 (mm-40) REVERT: A 77 VAL cc_start: 0.8263 (t) cc_final: 0.8025 (p) REVERT: A 80 PHE cc_start: 0.7980 (m-80) cc_final: 0.7747 (m-80) REVERT: A 758 MET cc_start: 0.7487 (tmm) cc_final: 0.7204 (tmm) REVERT: A 880 LEU cc_start: 0.8205 (mm) cc_final: 0.7963 (mm) outliers start: 15 outliers final: 13 residues processed: 133 average time/residue: 0.2015 time to fit residues: 36.5524 Evaluate side-chains 120 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN 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 Chi-restraints excluded: chain A residue 1057 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 477 ASN A 862 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7573 Z= 0.234 Angle : 0.669 8.191 10346 Z= 0.346 Chirality : 0.044 0.244 1183 Planarity : 0.004 0.065 1236 Dihedral : 16.642 179.729 1336 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.56 % Favored : 89.33 % Rotamer: Outliers : 4.31 % Allowed : 14.12 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.27), residues: 900 helix: 0.29 (0.24), residues: 455 sheet: -2.32 (0.56), residues: 81 loop : -3.21 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 79 HIS 0.009 0.001 HIS A 367 PHE 0.023 0.002 PHE A1047 TYR 0.018 0.002 TYR A 116 ARG 0.003 0.000 ARG A 652 *********************** 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 150 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8017 (mm-40) REVERT: A 80 PHE cc_start: 0.7919 (m-80) cc_final: 0.7657 (m-80) REVERT: A 650 ILE cc_start: 0.6545 (pt) cc_final: 0.6305 (pt) REVERT: A 758 MET cc_start: 0.7611 (tmm) cc_final: 0.7089 (tmm) REVERT: A 880 LEU cc_start: 0.8152 (mm) cc_final: 0.7866 (mm) outliers start: 29 outliers final: 19 residues processed: 137 average time/residue: 0.1379 time to fit residues: 27.3847 Evaluate side-chains 126 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 372 ASN 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 1057 ASP 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 83 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 7573 Z= 0.429 Angle : 0.830 7.537 10346 Z= 0.436 Chirality : 0.050 0.214 1183 Planarity : 0.005 0.073 1236 Dihedral : 16.911 176.273 1336 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 25.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 5.79 % Allowed : 14.86 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.26), residues: 900 helix: -0.35 (0.23), residues: 458 sheet: -2.62 (0.54), residues: 77 loop : -3.34 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 79 HIS 0.015 0.002 HIS A 367 PHE 0.020 0.002 PHE A1003 TYR 0.020 0.003 TYR A 656 ARG 0.005 0.001 ARG A 918 *********************** 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 152 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 113 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7374 (mp) cc_final: 0.6518 (mm) REVERT: A 50 GLN cc_start: 0.8453 (mm-40) cc_final: 0.7944 (mm-40) REVERT: A 77 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8102 (p) REVERT: A 80 PHE cc_start: 0.8015 (m-80) cc_final: 0.7800 (m-80) REVERT: A 466 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.7846 (tt) REVERT: A 487 LYS cc_start: 0.5308 (pttt) cc_final: 0.5067 (ptmt) REVERT: A 758 MET cc_start: 0.8192 (tmm) cc_final: 0.7446 (tmm) REVERT: A 802 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.5285 (pp) REVERT: A 880 LEU cc_start: 0.8294 (mm) cc_final: 0.7950 (mm) REVERT: A 968 PRO cc_start: 0.8272 (Cg_exo) cc_final: 0.8060 (Cg_endo) outliers start: 39 outliers final: 24 residues processed: 136 average time/residue: 0.1699 time to fit residues: 32.6373 Evaluate side-chains 132 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 162 ILE 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 370 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 429 LEU 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 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 684 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1057 ASP 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 74 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.3039 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= 0.190 Angle : 0.659 10.330 10346 Z= 0.336 Chirality : 0.043 0.201 1183 Planarity : 0.004 0.065 1236 Dihedral : 16.636 178.812 1336 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 4.46 % Allowed : 17.24 % Favored : 78.31 % 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 (0.28), residues: 900 helix: 0.24 (0.24), residues: 459 sheet: -2.43 (0.55), residues: 82 loop : -3.21 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 79 HIS 0.010 0.001 HIS A 367 PHE 0.020 0.002 PHE A 476 TYR 0.015 0.002 TYR A 995 ARG 0.006 0.000 ARG A 918 *********************** 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 151 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7291 (mp) cc_final: 0.6485 (mm) REVERT: A 50 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7882 (mm-40) REVERT: A 80 PHE cc_start: 0.7891 (m-80) cc_final: 0.7686 (m-80) REVERT: A 476 PHE cc_start: 0.6810 (m-80) cc_final: 0.6607 (m-80) REVERT: A 758 MET cc_start: 0.8127 (tmm) cc_final: 0.7469 (tmm) REVERT: A 820 HIS cc_start: 0.4765 (m-70) cc_final: 0.4399 (m-70) REVERT: A 880 LEU cc_start: 0.8219 (mm) cc_final: 0.7915 (mm) REVERT: A 913 MET cc_start: 0.4000 (mmm) cc_final: 0.3579 (tpp) outliers start: 30 outliers final: 17 residues processed: 142 average time/residue: 0.1678 time to fit residues: 33.1751 Evaluate side-chains 124 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 384 HIS 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 651 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 839 ASP 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 30 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7573 Z= 0.218 Angle : 0.690 10.411 10346 Z= 0.348 Chirality : 0.044 0.232 1183 Planarity : 0.004 0.070 1236 Dihedral : 16.610 179.515 1336 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 5.20 % Allowed : 18.57 % 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 (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: -1.87 (0.28), residues: 900 helix: 0.33 (0.24), residues: 457 sheet: -2.35 (0.57), residues: 80 loop : -3.11 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 79 HIS 0.010 0.001 HIS A 367 PHE 0.015 0.002 PHE A 476 TYR 0.017 0.002 TYR A 995 ARG 0.006 0.001 ARG A 779 *********************** 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 145 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 110 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 19 MET cc_start: 0.6572 (tpt) cc_final: 0.6331 (tpt) REVERT: A 20 ILE cc_start: 0.7368 (mp) cc_final: 0.6502 (mm) REVERT: A 50 GLN cc_start: 0.8444 (mm-40) cc_final: 0.7937 (mm-40) REVERT: A 78 ASN cc_start: 0.7269 (OUTLIER) cc_final: 0.7027 (t0) REVERT: A 542 TYR cc_start: 0.6604 (OUTLIER) cc_final: 0.6301 (t80) REVERT: A 650 ILE cc_start: 0.6598 (pt) cc_final: 0.6353 (pt) REVERT: A 680 GLU cc_start: 0.6379 (pt0) cc_final: 0.6100 (tt0) REVERT: A 758 MET cc_start: 0.8034 (tmm) cc_final: 0.7354 (tmm) REVERT: A 880 LEU cc_start: 0.8183 (mm) cc_final: 0.7835 (mm) REVERT: A 913 MET cc_start: 0.4072 (mmm) cc_final: 0.3646 (tpp) outliers start: 35 outliers final: 27 residues processed: 135 average time/residue: 0.1693 time to fit residues: 31.9225 Evaluate side-chains 136 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 384 HIS 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 507 ASP 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 666 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 993 ASN Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1057 ASP 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 86 optimal weight: 0.2980 chunk 10 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 477 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7573 Z= 0.175 Angle : 0.658 11.503 10346 Z= 0.329 Chirality : 0.043 0.203 1183 Planarity : 0.004 0.068 1236 Dihedral : 16.511 178.284 1336 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % 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 (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: 459 sheet: -2.09 (0.56), residues: 90 loop : -3.11 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 79 HIS 0.007 0.001 HIS A 367 PHE 0.013 0.002 PHE A 804 TYR 0.014 0.001 TYR A 995 ARG 0.005 0.000 ARG A 779 *********************** 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 149 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8433 (mm-40) cc_final: 0.7882 (mm-40) REVERT: A 78 ASN cc_start: 0.7096 (OUTLIER) cc_final: 0.6780 (t0) REVERT: A 650 ILE cc_start: 0.6511 (pt) cc_final: 0.6240 (pt) REVERT: A 758 MET cc_start: 0.8091 (tmm) cc_final: 0.7447 (tmm) REVERT: A 820 HIS cc_start: 0.4531 (m-70) cc_final: 0.4112 (m-70) REVERT: A 913 MET cc_start: 0.3839 (mmm) cc_final: 0.3460 (tpp) outliers start: 32 outliers final: 25 residues processed: 141 average time/residue: 0.1658 time to fit residues: 32.8322 Evaluate side-chains 136 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 110 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 384 HIS 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 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 839 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 993 ASN Chi-restraints excluded: chain A residue 1046 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 0.0060 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 81 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- 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 407 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.3548 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= 0.194 Angle : 0.668 12.021 10346 Z= 0.333 Chirality : 0.043 0.228 1183 Planarity : 0.004 0.070 1236 Dihedral : 16.493 178.805 1336 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 4.61 % Allowed : 20.51 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.28), residues: 900 helix: 0.58 (0.24), residues: 458 sheet: -2.15 (0.54), residues: 93 loop : -3.07 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 79 HIS 0.009 0.001 HIS A 367 PHE 0.019 0.002 PHE A 80 TYR 0.023 0.002 TYR A 700 ARG 0.006 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 140 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 109 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8454 (mm-40) cc_final: 0.7923 (mm-40) REVERT: A 542 TYR cc_start: 0.6499 (OUTLIER) cc_final: 0.6189 (t80) REVERT: A 650 ILE cc_start: 0.6532 (pt) cc_final: 0.6299 (pt) REVERT: A 758 MET cc_start: 0.8074 (tmm) cc_final: 0.7394 (tmm) REVERT: A 880 LEU cc_start: 0.8113 (mm) cc_final: 0.7784 (mm) REVERT: A 913 MET cc_start: 0.3904 (mmm) cc_final: 0.3554 (tpp) outliers start: 31 outliers final: 25 residues processed: 133 average time/residue: 0.1493 time to fit residues: 28.2686 Evaluate side-chains 130 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN 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 377 TRP Chi-restraints excluded: chain A residue 383 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 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 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 839 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 993 ASN 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 78 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 407 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.3670 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= 0.195 Angle : 0.690 12.004 10346 Z= 0.347 Chirality : 0.044 0.223 1183 Planarity : 0.004 0.072 1236 Dihedral : 16.466 178.781 1336 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 4.75 % Allowed : 20.95 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.28), residues: 900 helix: 0.48 (0.24), residues: 460 sheet: -2.10 (0.54), residues: 93 loop : -3.06 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP A 79 HIS 0.007 0.001 HIS A 367 PHE 0.018 0.002 PHE A 718 TYR 0.021 0.002 TYR A 995 ARG 0.005 0.001 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 143 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 111 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7895 (mm-40) REVERT: A 507 ASP cc_start: 0.4709 (OUTLIER) cc_final: 0.4188 (m-30) REVERT: A 542 TYR cc_start: 0.6481 (OUTLIER) cc_final: 0.6109 (t80) REVERT: A 650 ILE cc_start: 0.6566 (pt) cc_final: 0.6303 (pt) REVERT: A 758 MET cc_start: 0.8036 (tmm) cc_final: 0.7282 (tmm) REVERT: A 880 LEU cc_start: 0.8035 (mm) cc_final: 0.7779 (mm) REVERT: A 913 MET cc_start: 0.3888 (mmm) cc_final: 0.3522 (tpp) outliers start: 32 outliers final: 27 residues processed: 133 average time/residue: 0.1682 time to fit residues: 31.8552 Evaluate side-chains 134 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 384 HIS 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 507 ASP 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 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 839 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 993 ASN 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 53 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 477 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.3821 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= 0.215 Angle : 0.699 11.920 10346 Z= 0.355 Chirality : 0.044 0.220 1183 Planarity : 0.004 0.074 1236 Dihedral : 16.444 179.135 1336 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 4.61 % Allowed : 20.95 % Favored : 74.44 % 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: -1.69 (0.28), residues: 900 helix: 0.44 (0.24), residues: 463 sheet: -2.07 (0.55), residues: 93 loop : -3.10 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.003 TRP A 79 HIS 0.007 0.001 HIS A 367 PHE 0.027 0.002 PHE A 783 TYR 0.019 0.002 TYR A 995 ARG 0.007 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 138 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8483 (mm-40) cc_final: 0.7895 (mm-40) REVERT: A 77 VAL cc_start: 0.8396 (t) cc_final: 0.8018 (p) REVERT: A 542 TYR cc_start: 0.6501 (OUTLIER) cc_final: 0.6111 (t80) REVERT: A 650 ILE cc_start: 0.6634 (pt) cc_final: 0.6379 (pt) REVERT: A 758 MET cc_start: 0.8008 (tmm) cc_final: 0.7322 (tmm) REVERT: A 913 MET cc_start: 0.3862 (mmm) cc_final: 0.3495 (tpp) outliers start: 31 outliers final: 27 residues processed: 130 average time/residue: 0.1569 time to fit residues: 29.1548 Evaluate side-chains 133 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 384 HIS 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 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 666 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 993 ASN 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 22 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 0.1980 chunk 75 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.157806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.138379 restraints weight = 15802.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.141760 restraints weight = 9397.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.144030 restraints weight = 6537.275| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 7573 Z= 0.264 Angle : 1.018 59.200 10346 Z= 0.592 Chirality : 0.046 0.400 1183 Planarity : 0.004 0.072 1236 Dihedral : 16.453 179.134 1336 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 4.16 % Allowed : 21.99 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.28), residues: 900 helix: 0.44 (0.24), residues: 463 sheet: -2.05 (0.55), residues: 93 loop : -3.10 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.004 TRP A 79 HIS 0.006 0.001 HIS A 367 PHE 0.023 0.002 PHE A 718 TYR 0.017 0.002 TYR A 995 ARG 0.005 0.000 ARG A 779 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1562.84 seconds wall clock time: 32 minutes 53.58 seconds (1973.58 seconds total)