Starting phenix.real_space_refine on Mon Sep 23 11:31:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgn_10499/09_2024/6tgn_10499.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgn_10499/09_2024/6tgn_10499.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/6tgn_10499/09_2024/6tgn_10499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgn_10499/09_2024/6tgn_10499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgn_10499/09_2024/6tgn_10499.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tgn_10499/09_2024/6tgn_10499.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= 1.000 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: 4 Type Number sf(0) Gaussians S 1 5.16 5 C 425 2.51 5 N 115 2.21 5 O 131 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 672 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 672 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Time building chain proxies: 1.01, per 1000 atoms: 1.50 Number of scatterers: 672 At special positions: 0 Unit cell: (38.808, 48.51, 51.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 1 16.00 O 131 8.00 N 115 7.00 C 425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.14 Conformation dependent library (CDL) restraints added in 79.9 milliseconds 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 164 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 2 sheets defined 22.7% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 34 through 46 removed outlier: 3.859A pdb=" N GLU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.864A pdb=" N ASN A 79 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.553A pdb=" N VAL A 17 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 14 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.553A pdb=" N VAL A 17 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 14 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 13 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 89 " --> pdb=" O SER A 13 " (cutoff:3.500A) 17 hydrogen bonds defined for protein. 42 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.13 Time building geometry restraints manager: 0.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 124 1.32 - 1.44: 153 1.44 - 1.56: 399 1.56 - 1.68: 0 1.68 - 1.80: 2 Bond restraints: 678 Sorted by residual: bond pdb=" C TYR A 58 " pdb=" O TYR A 58 " ideal model delta sigma weight residual 1.234 1.197 0.037 1.16e-02 7.43e+03 1.01e+01 bond pdb=" CA ILE A 87 " pdb=" CB ILE A 87 " ideal model delta sigma weight residual 1.537 1.505 0.032 1.26e-02 6.30e+03 6.49e+00 bond pdb=" N ALA A 5 " pdb=" CA ALA A 5 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.31e+00 bond pdb=" C LEU A 56 " pdb=" O LEU A 56 " ideal model delta sigma weight residual 1.236 1.209 0.026 1.21e-02 6.83e+03 4.72e+00 bond pdb=" C ILE A 87 " pdb=" O ILE A 87 " ideal model delta sigma weight residual 1.238 1.214 0.024 1.10e-02 8.26e+03 4.64e+00 ... (remaining 673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 622 1.53 - 3.07: 215 3.07 - 4.60: 66 4.60 - 6.13: 10 6.13 - 7.66: 3 Bond angle restraints: 916 Sorted by residual: angle pdb=" C ASN A 88 " pdb=" CA ASN A 88 " pdb=" CB ASN A 88 " ideal model delta sigma weight residual 109.53 102.18 7.35 1.65e+00 3.67e-01 1.98e+01 angle pdb=" O GLY A 15 " pdb=" C GLY A 15 " pdb=" N GLY A 16 " ideal model delta sigma weight residual 122.57 126.54 -3.97 9.10e-01 1.21e+00 1.90e+01 angle pdb=" N ILE A 87 " pdb=" CA ILE A 87 " pdb=" C ILE A 87 " ideal model delta sigma weight residual 107.75 113.41 -5.66 1.46e+00 4.69e-01 1.50e+01 angle pdb=" CA LYS A 11 " pdb=" C LYS A 11 " pdb=" O LYS A 11 " ideal model delta sigma weight residual 120.32 116.14 4.18 1.10e+00 8.26e-01 1.44e+01 angle pdb=" N LEU A 85 " pdb=" CA LEU A 85 " pdb=" CB LEU A 85 " ideal model delta sigma weight residual 110.29 105.20 5.09 1.52e+00 4.33e-01 1.12e+01 ... (remaining 911 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 10.12: 333 10.12 - 20.23: 57 20.23 - 30.34: 15 30.34 - 40.45: 4 40.45 - 50.55: 3 Dihedral angle restraints: 412 sinusoidal: 159 harmonic: 253 Sorted by residual: dihedral pdb=" CA ASP A 62 " pdb=" C ASP A 62 " pdb=" N GLY A 63 " pdb=" CA GLY A 63 " ideal model delta harmonic sigma weight residual 180.00 152.99 27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ALA A 5 " pdb=" C ALA A 5 " pdb=" N ASN A 6 " pdb=" CA ASN A 6 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" C ASN A 88 " pdb=" N ASN A 88 " pdb=" CA ASN A 88 " pdb=" CB ASN A 88 " ideal model delta harmonic sigma weight residual -122.60 -112.69 -9.91 0 2.50e+00 1.60e-01 1.57e+01 ... (remaining 409 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.058: 41 0.058 - 0.115: 36 0.115 - 0.172: 17 0.172 - 0.229: 10 0.229 - 0.286: 6 Chirality restraints: 110 Sorted by residual: chirality pdb=" CA VAL A 66 " pdb=" N VAL A 66 " pdb=" C VAL A 66 " pdb=" CB VAL A 66 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ARG A 81 " pdb=" N ARG A 81 " pdb=" C ARG A 81 " pdb=" CB ARG A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA TYR A 58 " pdb=" N TYR A 58 " pdb=" C TYR A 58 " pdb=" CB TYR A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 107 not shown) Planarity restraints: 120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 14 " 0.042 2.00e-02 2.50e+03 2.17e-02 9.38e+00 pdb=" CG TYR A 14 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 14 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 14 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 14 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 14 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 14 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 14 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 58 " -0.030 2.00e-02 2.50e+03 1.63e-02 5.33e+00 pdb=" CG TYR A 58 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 58 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 58 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 58 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 58 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 58 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR A 58 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 46 " 0.001 2.00e-02 2.50e+03 1.71e-02 5.12e+00 pdb=" CG PHE A 46 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 46 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 46 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 46 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 46 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 46 " -0.019 2.00e-02 2.50e+03 ... (remaining 117 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 41 2.71 - 3.26: 598 3.26 - 3.80: 901 3.80 - 4.35: 1146 4.35 - 4.90: 1881 Nonbonded interactions: 4567 Sorted by model distance: nonbonded pdb=" OD1 ASP A 60 " pdb=" N GLU A 61 " model vdw 2.161 3.120 nonbonded pdb=" N ASP A 60 " pdb=" O ASP A 60 " model vdw 2.548 2.496 nonbonded pdb=" N ARG A 19 " pdb=" O ARG A 19 " model vdw 2.602 2.496 nonbonded pdb=" N GLU A 34 " pdb=" OE1 GLU A 34 " model vdw 2.607 3.120 nonbonded pdb=" O ARG A 19 " pdb=" CA ARG A 20 " model vdw 2.627 2.776 ... (remaining 4562 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: 0.120 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: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 8.180 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 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 : 0.010 0.044 678 Z= 0.599 Angle : 1.727 7.656 916 Z= 1.087 Chirality : 0.118 0.286 110 Planarity : 0.008 0.022 120 Dihedral : 11.933 50.555 248 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.39 % Allowed : 2.78 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.57 (0.75), residues: 86 helix: -4.95 (0.26), residues: 18 sheet: -1.43 (0.99), residues: 28 loop : -1.61 (0.75), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.008 PHE A 46 TYR 0.042 0.016 TYR A 14 ARG 0.022 0.006 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: A 17 VAL cc_start: 0.9635 (t) cc_final: 0.9428 (p) REVERT: A 22 ARG cc_start: 0.9505 (mtp-110) cc_final: 0.9078 (mpt180) REVERT: A 34 GLU cc_start: 0.9286 (pm20) cc_final: 0.8982 (mp0) REVERT: A 35 MET cc_start: 0.8809 (mmm) cc_final: 0.7750 (mmm) REVERT: A 59 SER cc_start: 0.9144 (m) cc_final: 0.8752 (t) REVERT: A 62 ASP cc_start: 0.8422 (p0) cc_final: 0.8135 (p0) REVERT: A 70 ASP cc_start: 0.8954 (p0) cc_final: 0.8753 (p0) outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.1508 time to fit residues: 5.9279 Evaluate side-chains 34 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 overall best weight: 6.7490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 678 Z= 0.224 Angle : 0.654 5.395 916 Z= 0.334 Chirality : 0.044 0.131 110 Planarity : 0.003 0.014 120 Dihedral : 7.513 41.908 97 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.17 % Allowed : 18.06 % Favored : 77.78 % 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: -2.55 (0.78), residues: 86 helix: -2.99 (0.83), residues: 20 sheet: -1.14 (1.01), residues: 28 loop : -1.16 (0.78), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE A 46 TYR 0.012 0.002 TYR A 58 ARG 0.001 0.000 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.073 Fit side-chains REVERT: A 22 ARG cc_start: 0.9532 (mtp-110) cc_final: 0.9241 (mpt180) REVERT: A 34 GLU cc_start: 0.9038 (pm20) cc_final: 0.8660 (tm-30) REVERT: A 35 MET cc_start: 0.8302 (mmm) cc_final: 0.8091 (mmm) outliers start: 3 outliers final: 2 residues processed: 33 average time/residue: 0.1647 time to fit residues: 5.7633 Evaluate side-chains 33 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 74 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 overall best weight: 8.2490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 678 Z= 0.271 Angle : 0.703 8.507 916 Z= 0.335 Chirality : 0.044 0.130 110 Planarity : 0.003 0.009 120 Dihedral : 7.331 43.117 97 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 8.33 % Allowed : 22.22 % Favored : 69.44 % 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: -1.01 (0.96), residues: 86 helix: -1.86 (1.36), residues: 14 sheet: -0.82 (1.04), residues: 28 loop : 0.07 (1.03), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE A 46 TYR 0.011 0.002 TYR A 58 ARG 0.001 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.079 Fit side-chains REVERT: A 22 ARG cc_start: 0.9555 (mtp-110) cc_final: 0.9251 (mpt180) REVERT: A 34 GLU cc_start: 0.9017 (pm20) cc_final: 0.8632 (tm-30) REVERT: A 60 ASP cc_start: 0.7490 (t0) cc_final: 0.7139 (t0) outliers start: 6 outliers final: 4 residues processed: 35 average time/residue: 0.1603 time to fit residues: 6.0101 Evaluate side-chains 33 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 74 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 overall best weight: 4.7490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 678 Z= 0.170 Angle : 0.646 8.728 916 Z= 0.299 Chirality : 0.042 0.121 110 Planarity : 0.002 0.013 120 Dihedral : 7.034 43.650 97 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 6.94 % Allowed : 23.61 % Favored : 69.44 % 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: -0.37 (1.01), residues: 86 helix: -1.25 (1.56), residues: 14 sheet: -0.97 (0.94), residues: 34 loop : 1.26 (1.17), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE A 46 TYR 0.011 0.002 TYR A 58 ARG 0.001 0.000 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.132 Fit side-chains REVERT: A 21 PHE cc_start: 0.9318 (p90) cc_final: 0.8762 (p90) REVERT: A 22 ARG cc_start: 0.9541 (mtp-110) cc_final: 0.9249 (mpt180) REVERT: A 34 GLU cc_start: 0.8972 (pm20) cc_final: 0.8660 (tm-30) REVERT: A 60 ASP cc_start: 0.7741 (t0) cc_final: 0.7391 (t0) outliers start: 5 outliers final: 3 residues processed: 34 average time/residue: 0.1649 time to fit residues: 5.9504 Evaluate side-chains 34 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 overall best weight: 6.2490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 678 Z= 0.209 Angle : 0.641 7.400 916 Z= 0.305 Chirality : 0.042 0.119 110 Planarity : 0.002 0.007 120 Dihedral : 7.140 44.063 97 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 6.94 % Allowed : 26.39 % Favored : 66.67 % 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: -0.13 (1.03), residues: 86 helix: -1.24 (1.54), residues: 14 sheet: -0.71 (0.97), residues: 34 loop : 1.38 (1.19), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE A 46 TYR 0.010 0.002 TYR A 58 ARG 0.000 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.076 Fit side-chains REVERT: A 21 PHE cc_start: 0.9263 (p90) cc_final: 0.8808 (p90) REVERT: A 22 ARG cc_start: 0.9490 (mtp-110) cc_final: 0.9218 (mpt180) REVERT: A 34 GLU cc_start: 0.9027 (pm20) cc_final: 0.8730 (tm-30) REVERT: A 60 ASP cc_start: 0.7671 (t0) cc_final: 0.7300 (t0) REVERT: A 71 ASP cc_start: 0.8789 (t0) cc_final: 0.8528 (t0) outliers start: 5 outliers final: 4 residues processed: 36 average time/residue: 0.1573 time to fit residues: 6.0027 Evaluate side-chains 36 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 overall best weight: 5.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 678 Z= 0.188 Angle : 0.694 9.441 916 Z= 0.329 Chirality : 0.043 0.119 110 Planarity : 0.002 0.006 120 Dihedral : 6.889 43.824 97 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 6.94 % Allowed : 29.17 % Favored : 63.89 % 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: -0.23 (1.01), residues: 86 helix: -0.95 (1.33), residues: 20 sheet: -0.59 (0.96), residues: 34 loop : 1.36 (1.24), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE A 46 TYR 0.010 0.001 TYR A 58 ARG 0.001 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.084 Fit side-chains REVERT: A 21 PHE cc_start: 0.9185 (p90) cc_final: 0.8721 (p90) REVERT: A 22 ARG cc_start: 0.9493 (mtp-110) cc_final: 0.9221 (mpt180) REVERT: A 34 GLU cc_start: 0.9028 (pm20) cc_final: 0.8806 (tm-30) REVERT: A 39 LYS cc_start: 0.9471 (mtmm) cc_final: 0.9181 (mtmm) REVERT: A 60 ASP cc_start: 0.7668 (t0) cc_final: 0.7292 (t0) REVERT: A 71 ASP cc_start: 0.9000 (t0) cc_final: 0.8788 (t0) outliers start: 5 outliers final: 4 residues processed: 35 average time/residue: 0.1606 time to fit residues: 5.9594 Evaluate side-chains 39 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 overall best weight: 6.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 678 Z= 0.218 Angle : 0.671 8.644 916 Z= 0.320 Chirality : 0.043 0.119 110 Planarity : 0.002 0.007 120 Dihedral : 6.949 43.545 97 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 9.72 % Allowed : 23.61 % Favored : 66.67 % 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: -0.15 (1.00), residues: 86 helix: -0.88 (1.34), residues: 20 sheet: -0.52 (0.94), residues: 34 loop : 1.38 (1.24), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE A 46 TYR 0.009 0.002 TYR A 58 ARG 0.001 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.078 Fit side-chains REVERT: A 22 ARG cc_start: 0.9489 (mtp-110) cc_final: 0.9195 (mpt180) REVERT: A 34 GLU cc_start: 0.9092 (pm20) cc_final: 0.8881 (tm-30) REVERT: A 39 LYS cc_start: 0.9517 (mtmm) cc_final: 0.9165 (mtmm) REVERT: A 60 ASP cc_start: 0.7599 (t0) cc_final: 0.7195 (t0) outliers start: 7 outliers final: 6 residues processed: 35 average time/residue: 0.1619 time to fit residues: 6.0025 Evaluate side-chains 38 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 77 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.0670 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7905 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 678 Z= 0.143 Angle : 0.688 8.109 916 Z= 0.313 Chirality : 0.042 0.136 110 Planarity : 0.002 0.016 120 Dihedral : 6.133 43.099 97 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.17 % Allowed : 31.94 % Favored : 63.89 % 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: 0.52 (1.01), residues: 86 helix: -1.03 (1.25), residues: 19 sheet: -0.18 (0.94), residues: 34 loop : 2.29 (1.28), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE A 75 TYR 0.008 0.001 TYR A 58 ARG 0.001 0.000 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.077 Fit side-chains REVERT: A 22 ARG cc_start: 0.9424 (mtp-110) cc_final: 0.9196 (mpt180) REVERT: A 34 GLU cc_start: 0.8853 (pm20) cc_final: 0.8598 (tm-30) REVERT: A 39 LYS cc_start: 0.9504 (mtmm) cc_final: 0.9113 (mtmm) REVERT: A 60 ASP cc_start: 0.7456 (t0) cc_final: 0.7102 (t0) outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.1418 time to fit residues: 5.1423 Evaluate side-chains 35 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 30.0000 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 678 Z= 0.261 Angle : 0.762 7.875 916 Z= 0.358 Chirality : 0.044 0.149 110 Planarity : 0.002 0.008 120 Dihedral : 4.396 11.355 93 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.56 % Allowed : 29.17 % Favored : 65.28 % 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: 0.17 (1.00), residues: 86 helix: -1.18 (1.27), residues: 20 sheet: -0.15 (0.96), residues: 34 loop : 1.76 (1.23), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE A 75 TYR 0.010 0.002 TYR A 58 ARG 0.001 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.082 Fit side-chains REVERT: A 22 ARG cc_start: 0.9487 (mtp-110) cc_final: 0.9182 (mpt180) REVERT: A 34 GLU cc_start: 0.9109 (pm20) cc_final: 0.8878 (tm-30) REVERT: A 39 LYS cc_start: 0.9566 (mtmm) cc_final: 0.9251 (mtmm) outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.1615 time to fit residues: 4.8049 Evaluate side-chains 28 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 0.0570 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 overall best weight: 2.7633 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 678 Z= 0.183 Angle : 0.782 7.512 916 Z= 0.357 Chirality : 0.043 0.137 110 Planarity : 0.001 0.008 120 Dihedral : 3.879 12.328 93 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.17 % Allowed : 33.33 % Favored : 62.50 % 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: 0.23 (0.98), residues: 86 helix: -1.37 (1.21), residues: 20 sheet: 0.06 (0.96), residues: 34 loop : 1.75 (1.19), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 75 TYR 0.009 0.001 TYR A 58 ARG 0.001 0.000 ARG A 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.077 Fit side-chains REVERT: A 22 ARG cc_start: 0.9410 (mtp-110) cc_final: 0.9146 (mpt180) REVERT: A 39 LYS cc_start: 0.9563 (mtmm) cc_final: 0.9219 (mtmm) REVERT: A 71 ASP cc_start: 0.8884 (t0) cc_final: 0.8536 (t0) outliers start: 3 outliers final: 3 residues processed: 29 average time/residue: 0.1585 time to fit residues: 4.8850 Evaluate side-chains 31 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 0.0670 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 overall best weight: 4.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.107659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.091011 restraints weight = 1464.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.093167 restraints weight = 956.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.094806 restraints weight = 723.091| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 678 Z= 0.202 Angle : 0.852 7.602 916 Z= 0.401 Chirality : 0.044 0.137 110 Planarity : 0.001 0.006 120 Dihedral : 4.371 17.362 93 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.56 % Allowed : 31.94 % Favored : 62.50 % 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: 0.31 (0.98), residues: 86 helix: -1.26 (1.24), residues: 20 sheet: 0.20 (0.96), residues: 34 loop : 1.63 (1.19), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 75 TYR 0.009 0.001 TYR A 58 ARG 0.001 0.000 ARG A 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 449.59 seconds wall clock time: 8 minutes 42.79 seconds (522.79 seconds total)