Starting phenix.real_space_refine on Tue Feb 13 05:02:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqj_28538/02_2024/8eqj_28538_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqj_28538/02_2024/8eqj_28538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqj_28538/02_2024/8eqj_28538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqj_28538/02_2024/8eqj_28538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqj_28538/02_2024/8eqj_28538_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqj_28538/02_2024/8eqj_28538_neut_updated.pdb" } resolution = 3.0 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 4 5.49 5 S 16 5.16 5 C 2140 2.51 5 N 492 2.21 5 O 580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3232 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1571 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 1 Chain: "B" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1571 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 1 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 57 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 57 Time building chain proxies: 2.41, per 1000 atoms: 0.75 Number of scatterers: 3232 At special positions: 0 Unit cell: (64.988, 61.612, 91.152, 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 16 16.00 P 4 15.00 O 580 8.00 N 492 7.00 C 2140 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: 1.28 Conformation dependent library (CDL) restraints added in 582.2 milliseconds 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 732 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 10 helices and 4 sheets defined 45.3% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 44 through 61 removed outlier: 3.592A pdb=" N LYS A 61 " --> pdb=" O GLN A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 99 Processing helix chain 'A' and resid 106 through 133 Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'B' and resid 44 through 61 removed outlier: 3.591A pdb=" N LYS B 61 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 99 Processing helix chain 'B' and resid 106 through 133 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 220 through 223 No H-bonds generated for 'chain 'B' and resid 220 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 155 through 160 removed outlier: 5.922A pdb=" N HIS A 150 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS A 200 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE A 232 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR A 217 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE A 230 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 229 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 183 through 186 Processing sheet with id= C, first strand: chain 'B' and resid 155 through 160 removed outlier: 5.922A pdb=" N HIS B 150 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS B 200 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE B 232 " --> pdb=" O TYR B 215 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR B 217 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE B 230 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 229 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 183 through 186 186 hydrogen bonds defined for protein. 534 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: 0.85 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 470 1.31 - 1.43: 1028 1.43 - 1.56: 1798 1.56 - 1.68: 8 1.68 - 1.81: 18 Bond restraints: 3322 Sorted by residual: bond pdb=" C30 PEE A 401 " pdb=" O3 PEE A 401 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C30 PEE B 401 " pdb=" O3 PEE B 401 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C30 PEE B 402 " pdb=" O3 PEE B 402 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C30 PEE A 402 " pdb=" O3 PEE A 402 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C10 PEE B 402 " pdb=" O2 PEE B 402 " ideal model delta sigma weight residual 1.332 1.403 -0.071 2.00e-02 2.50e+03 1.24e+01 ... (remaining 3317 not shown) Histogram of bond angle deviations from ideal: 100.88 - 107.53: 92 107.53 - 114.18: 1906 114.18 - 120.83: 1481 120.83 - 127.48: 999 127.48 - 134.13: 42 Bond angle restraints: 4520 Sorted by residual: angle pdb=" O3P PEE B 402 " pdb=" P PEE B 402 " pdb=" O4P PEE B 402 " ideal model delta sigma weight residual 92.91 109.79 -16.88 3.00e+00 1.11e-01 3.16e+01 angle pdb=" O3P PEE A 402 " pdb=" P PEE A 402 " pdb=" O4P PEE A 402 " ideal model delta sigma weight residual 92.91 109.79 -16.88 3.00e+00 1.11e-01 3.16e+01 angle pdb=" O3P PEE A 401 " pdb=" P PEE A 401 " pdb=" O4P PEE A 401 " ideal model delta sigma weight residual 92.91 109.75 -16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" O3P PEE B 401 " pdb=" P PEE B 401 " pdb=" O4P PEE B 401 " ideal model delta sigma weight residual 92.91 109.74 -16.83 3.00e+00 1.11e-01 3.15e+01 angle pdb=" O1P PEE A 402 " pdb=" P PEE A 402 " pdb=" O2P PEE A 402 " ideal model delta sigma weight residual 119.43 109.11 10.32 3.00e+00 1.11e-01 1.18e+01 ... (remaining 4515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 1826 34.91 - 69.82: 36 69.82 - 104.73: 16 104.73 - 139.64: 10 139.64 - 174.54: 10 Dihedral angle restraints: 1898 sinusoidal: 754 harmonic: 1144 Sorted by residual: dihedral pdb=" C3 PEE A 401 " pdb=" C1 PEE A 401 " pdb=" C2 PEE A 401 " pdb=" O3P PEE A 401 " ideal model delta sinusoidal sigma weight residual 62.73 -111.81 174.54 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C2 PEE B 401 " pdb=" O3P PEE B 401 " ideal model delta sinusoidal sigma weight residual 62.73 -111.79 174.52 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C2 PEE B 401 " pdb=" O3P PEE B 401 " ideal model delta sinusoidal sigma weight residual 300.04 129.14 170.90 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 1895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 362 0.037 - 0.073: 100 0.073 - 0.110: 36 0.110 - 0.146: 2 0.146 - 0.183: 6 Chirality restraints: 506 Sorted by residual: chirality pdb=" C2 PEE A 401 " pdb=" C1 PEE A 401 " pdb=" C3 PEE A 401 " pdb=" O2 PEE A 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.51 0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" C2 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C3 PEE B 401 " pdb=" O2 PEE B 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.51 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" C2 PEE B 402 " pdb=" C1 PEE B 402 " pdb=" C3 PEE B 402 " pdb=" O2 PEE B 402 " both_signs ideal model delta sigma weight residual False -2.33 -2.50 0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 503 not shown) Planarity restraints: 534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 87 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C PHE A 87 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE A 87 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A 88 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 87 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C PHE B 87 " 0.032 2.00e-02 2.50e+03 pdb=" O PHE B 87 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B 88 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 84 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C LEU B 84 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU B 84 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU B 85 " -0.009 2.00e-02 2.50e+03 ... (remaining 531 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 443 2.75 - 3.29: 3213 3.29 - 3.83: 5449 3.83 - 4.36: 6110 4.36 - 4.90: 10718 Nonbonded interactions: 25933 Sorted by model distance: nonbonded pdb=" OG1 THR A 151 " pdb=" O TYR A 154 " model vdw 2.219 2.440 nonbonded pdb=" OG1 THR B 151 " pdb=" O TYR B 154 " model vdw 2.219 2.440 nonbonded pdb=" OG SER A 205 " pdb=" O THR A 208 " model vdw 2.286 2.440 nonbonded pdb=" OG SER B 205 " pdb=" O THR B 208 " model vdw 2.287 2.440 nonbonded pdb=" ND2 ASN B 137 " pdb=" O CYS B 157 " model vdw 2.309 2.520 ... (remaining 25928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic 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: 0.710 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: 3.490 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.880 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 3322 Z= 0.326 Angle : 0.940 16.875 4520 Z= 0.385 Chirality : 0.043 0.183 506 Planarity : 0.005 0.029 534 Dihedral : 24.650 174.544 1166 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.19 (0.41), residues: 376 helix: 0.56 (0.38), residues: 174 sheet: 0.33 (0.51), residues: 88 loop : -1.44 (0.51), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 193 HIS 0.001 0.000 HIS B 78 PHE 0.006 0.001 PHE A 146 TYR 0.016 0.001 TYR B 107 ARG 0.001 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.359 Fit side-chains REVERT: A 131 TRP cc_start: 0.7835 (t60) cc_final: 0.7447 (t60) REVERT: A 147 LEU cc_start: 0.7854 (tp) cc_final: 0.7291 (tm) REVERT: A 154 TYR cc_start: 0.7156 (t80) cc_final: 0.6951 (t80) REVERT: A 185 GLN cc_start: 0.8176 (pp30) cc_final: 0.7914 (pp30) REVERT: A 192 LYS cc_start: 0.8250 (ttmt) cc_final: 0.7848 (mtpp) REVERT: A 198 LYS cc_start: 0.7426 (mmmm) cc_final: 0.6927 (mtpt) REVERT: A 202 VAL cc_start: 0.7707 (m) cc_final: 0.7404 (p) REVERT: A 210 ASP cc_start: 0.7522 (m-30) cc_final: 0.7186 (m-30) REVERT: A 222 ASP cc_start: 0.7900 (t0) cc_final: 0.7699 (t0) REVERT: B 131 TRP cc_start: 0.7837 (t60) cc_final: 0.7447 (t60) REVERT: B 147 LEU cc_start: 0.7845 (tp) cc_final: 0.7282 (tm) REVERT: B 154 TYR cc_start: 0.7138 (t80) cc_final: 0.6934 (t80) REVERT: B 185 GLN cc_start: 0.8186 (pp30) cc_final: 0.7928 (pp30) REVERT: B 192 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7853 (mtpp) REVERT: B 198 LYS cc_start: 0.7415 (mmmm) cc_final: 0.6911 (mtpt) REVERT: B 202 VAL cc_start: 0.7705 (m) cc_final: 0.7402 (p) REVERT: B 210 ASP cc_start: 0.7518 (m-30) cc_final: 0.7182 (m-30) REVERT: B 222 ASP cc_start: 0.7899 (t0) cc_final: 0.7698 (t0) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.5309 time to fit residues: 56.2030 Evaluate side-chains 60 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 19 optimal weight: 0.0970 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 overall best weight: 0.2716 ------------------------------------------------------------------------------- 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: 0.7025 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3322 Z= 0.160 Angle : 0.467 5.559 4520 Z= 0.238 Chirality : 0.039 0.127 506 Planarity : 0.004 0.029 534 Dihedral : 26.194 142.484 490 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.57 % Allowed : 12.93 % Favored : 86.49 % 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: 1.45 (0.41), residues: 376 helix: 2.55 (0.36), residues: 176 sheet: 0.61 (0.58), residues: 68 loop : -1.12 (0.46), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 193 HIS 0.002 0.000 HIS A 78 PHE 0.007 0.001 PHE A 146 TYR 0.014 0.001 TYR A 215 ARG 0.002 0.001 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.347 Fit side-chains REVERT: A 68 ARG cc_start: 0.6701 (ttt-90) cc_final: 0.5785 (ttp-170) REVERT: A 131 TRP cc_start: 0.7908 (t60) cc_final: 0.7525 (t60) REVERT: A 185 GLN cc_start: 0.8285 (pp30) cc_final: 0.7927 (pp30) REVERT: A 192 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7915 (mtpp) REVERT: A 198 LYS cc_start: 0.7284 (mmmm) cc_final: 0.6849 (mtpt) REVERT: A 210 ASP cc_start: 0.7464 (m-30) cc_final: 0.7133 (m-30) REVERT: A 222 ASP cc_start: 0.7889 (t0) cc_final: 0.7667 (t0) REVERT: B 68 ARG cc_start: 0.6692 (ttt-90) cc_final: 0.5777 (ttp-170) REVERT: B 131 TRP cc_start: 0.7908 (t60) cc_final: 0.7523 (t60) REVERT: B 185 GLN cc_start: 0.8298 (pp30) cc_final: 0.7943 (pp30) REVERT: B 192 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7917 (mtpp) REVERT: B 198 LYS cc_start: 0.7270 (mmmm) cc_final: 0.6832 (mtpt) REVERT: B 210 ASP cc_start: 0.7460 (m-30) cc_final: 0.7130 (m-30) REVERT: B 222 ASP cc_start: 0.7873 (t0) cc_final: 0.7650 (t0) outliers start: 2 outliers final: 0 residues processed: 60 average time/residue: 0.8901 time to fit residues: 55.5897 Evaluate side-chains 52 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.0980 chunk 11 optimal weight: 0.0770 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 0.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3322 Z= 0.137 Angle : 0.465 4.676 4520 Z= 0.230 Chirality : 0.038 0.125 506 Planarity : 0.003 0.027 534 Dihedral : 19.615 125.462 490 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.57 % Allowed : 15.52 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.42), residues: 376 helix: 3.12 (0.37), residues: 176 sheet: 0.30 (0.52), residues: 84 loop : -1.19 (0.50), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 193 HIS 0.001 0.000 HIS A 204 PHE 0.006 0.001 PHE A 146 TYR 0.011 0.001 TYR A 154 ARG 0.003 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.367 Fit side-chains REVERT: A 68 ARG cc_start: 0.6816 (ttt-90) cc_final: 0.5861 (ttp-170) REVERT: A 185 GLN cc_start: 0.8348 (pp30) cc_final: 0.8089 (pp30) REVERT: A 192 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7918 (mtpp) REVERT: A 210 ASP cc_start: 0.7302 (m-30) cc_final: 0.7046 (m-30) REVERT: B 68 ARG cc_start: 0.6809 (ttt-90) cc_final: 0.5855 (ttp-170) REVERT: B 185 GLN cc_start: 0.8357 (pp30) cc_final: 0.8101 (pp30) REVERT: B 192 LYS cc_start: 0.8317 (ttmt) cc_final: 0.7920 (mtpp) REVERT: B 210 ASP cc_start: 0.7305 (m-30) cc_final: 0.7065 (m-30) outliers start: 2 outliers final: 0 residues processed: 58 average time/residue: 0.8916 time to fit residues: 53.7560 Evaluate side-chains 52 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.0000 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN B 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3322 Z= 0.192 Angle : 0.440 4.340 4520 Z= 0.229 Chirality : 0.038 0.131 506 Planarity : 0.003 0.026 534 Dihedral : 17.690 137.341 490 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.30 % Allowed : 14.66 % Favored : 83.05 % 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: 1.73 (0.43), residues: 376 helix: 3.05 (0.37), residues: 176 sheet: -0.05 (0.57), residues: 72 loop : -0.91 (0.49), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 149 HIS 0.002 0.001 HIS B 78 PHE 0.008 0.001 PHE B 146 TYR 0.016 0.001 TYR A 215 ARG 0.002 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 LYS cc_start: 0.8243 (ttmt) cc_final: 0.7940 (mtpp) REVERT: A 210 ASP cc_start: 0.7495 (m-30) cc_final: 0.7144 (m-30) REVERT: B 192 LYS cc_start: 0.8243 (ttmt) cc_final: 0.7942 (mtpp) REVERT: B 210 ASP cc_start: 0.7479 (m-30) cc_final: 0.7133 (m-30) outliers start: 8 outliers final: 6 residues processed: 56 average time/residue: 0.5280 time to fit residues: 31.6495 Evaluate side-chains 52 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 197 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 12 optimal weight: 0.2980 chunk 33 optimal weight: 0.0670 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.0570 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN B 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3322 Z= 0.131 Angle : 0.402 4.350 4520 Z= 0.212 Chirality : 0.037 0.123 506 Planarity : 0.003 0.027 534 Dihedral : 17.428 145.258 490 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.45 % Allowed : 15.23 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.42), residues: 376 helix: 3.03 (0.37), residues: 176 sheet: 0.32 (0.58), residues: 68 loop : -1.05 (0.48), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 149 HIS 0.001 0.000 HIS A 150 PHE 0.005 0.001 PHE B 146 TYR 0.012 0.001 TYR A 154 ARG 0.002 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7962 (mtpp) REVERT: A 210 ASP cc_start: 0.7438 (m-30) cc_final: 0.7197 (m-30) REVERT: B 43 PHE cc_start: 0.6912 (m-80) cc_final: 0.6608 (t80) REVERT: B 192 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7964 (mtpp) REVERT: B 210 ASP cc_start: 0.7412 (m-30) cc_final: 0.7186 (m-30) outliers start: 12 outliers final: 6 residues processed: 55 average time/residue: 0.5017 time to fit residues: 29.8015 Evaluate side-chains 52 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 197 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7144 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3322 Z= 0.279 Angle : 0.467 4.310 4520 Z= 0.244 Chirality : 0.039 0.132 506 Planarity : 0.003 0.029 534 Dihedral : 17.504 147.095 490 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.45 % Allowed : 16.38 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.42), residues: 376 helix: 2.85 (0.37), residues: 176 sheet: -0.38 (0.58), residues: 68 loop : -0.99 (0.48), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 149 HIS 0.002 0.001 HIS A 78 PHE 0.007 0.001 PHE A 56 TYR 0.015 0.002 TYR B 215 ARG 0.002 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.361 Fit side-chains REVERT: A 192 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7920 (mtpp) REVERT: A 210 ASP cc_start: 0.7579 (m-30) cc_final: 0.7211 (m-30) REVERT: B 43 PHE cc_start: 0.6911 (m-80) cc_final: 0.6438 (t80) REVERT: B 192 LYS cc_start: 0.8312 (ttmt) cc_final: 0.7917 (mtpp) REVERT: B 210 ASP cc_start: 0.7587 (m-30) cc_final: 0.7221 (m-30) outliers start: 12 outliers final: 10 residues processed: 56 average time/residue: 0.7018 time to fit residues: 41.2484 Evaluate side-chains 52 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 202 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3322 Z= 0.212 Angle : 0.441 4.942 4520 Z= 0.229 Chirality : 0.039 0.122 506 Planarity : 0.003 0.029 534 Dihedral : 17.274 151.913 490 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 3.45 % Allowed : 16.67 % Favored : 79.89 % 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: 1.44 (0.42), residues: 376 helix: 2.88 (0.36), residues: 176 sheet: -0.46 (0.55), residues: 72 loop : -0.98 (0.49), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 149 HIS 0.005 0.001 HIS B 150 PHE 0.007 0.001 PHE A 43 TYR 0.016 0.001 TYR B 154 ARG 0.001 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.351 Fit side-chains REVERT: A 68 ARG cc_start: 0.6974 (ttt-90) cc_final: 0.5882 (ttp-170) REVERT: A 150 HIS cc_start: 0.7232 (m90) cc_final: 0.6648 (m-70) REVERT: A 192 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7931 (mtpp) REVERT: A 210 ASP cc_start: 0.7572 (m-30) cc_final: 0.7270 (m-30) REVERT: A 219 LEU cc_start: 0.7917 (mt) cc_final: 0.7572 (mm) REVERT: B 68 ARG cc_start: 0.6965 (ttt-90) cc_final: 0.5875 (ttp-170) REVERT: B 150 HIS cc_start: 0.7232 (m90) cc_final: 0.6641 (m-70) REVERT: B 192 LYS cc_start: 0.8332 (ttmt) cc_final: 0.7932 (mtpp) REVERT: B 210 ASP cc_start: 0.7569 (m-30) cc_final: 0.7252 (m-30) outliers start: 12 outliers final: 8 residues processed: 56 average time/residue: 0.6687 time to fit residues: 39.4542 Evaluate side-chains 52 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 197 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3322 Z= 0.231 Angle : 0.450 5.460 4520 Z= 0.235 Chirality : 0.039 0.124 506 Planarity : 0.003 0.029 534 Dihedral : 17.185 154.282 490 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.74 % Allowed : 17.24 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.41), residues: 376 helix: 2.90 (0.37), residues: 176 sheet: -0.38 (0.58), residues: 68 loop : -0.92 (0.46), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 149 HIS 0.002 0.001 HIS B 78 PHE 0.015 0.001 PHE A 43 TYR 0.016 0.001 TYR A 154 ARG 0.001 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.345 Fit side-chains REVERT: A 68 ARG cc_start: 0.6990 (ttt-90) cc_final: 0.5881 (ttp-170) REVERT: A 192 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7880 (mtpp) REVERT: A 210 ASP cc_start: 0.7597 (m-30) cc_final: 0.7278 (m-30) REVERT: B 68 ARG cc_start: 0.6981 (ttt-90) cc_final: 0.5873 (ttp-170) REVERT: B 155 ASP cc_start: 0.7895 (m-30) cc_final: 0.7539 (OUTLIER) REVERT: B 192 LYS cc_start: 0.8299 (ttmt) cc_final: 0.7880 (mtpp) REVERT: B 210 ASP cc_start: 0.7591 (m-30) cc_final: 0.7246 (m-30) REVERT: B 218 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7754 (mm110) outliers start: 13 outliers final: 11 residues processed: 55 average time/residue: 0.6784 time to fit residues: 39.2506 Evaluate side-chains 51 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 202 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7178 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3322 Z= 0.243 Angle : 0.459 5.295 4520 Z= 0.240 Chirality : 0.039 0.124 506 Planarity : 0.003 0.030 534 Dihedral : 17.110 157.334 490 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.59 % Allowed : 19.25 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.45 (0.42), residues: 376 helix: 2.86 (0.37), residues: 176 sheet: -0.41 (0.58), residues: 68 loop : -0.96 (0.46), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 149 HIS 0.004 0.001 HIS B 150 PHE 0.017 0.001 PHE A 43 TYR 0.014 0.001 TYR A 154 ARG 0.004 0.001 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.354 Fit side-chains REVERT: A 68 ARG cc_start: 0.6975 (ttt-90) cc_final: 0.6035 (ttp-170) REVERT: A 192 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7938 (mtpp) REVERT: A 210 ASP cc_start: 0.7591 (m-30) cc_final: 0.7277 (m-30) REVERT: B 68 ARG cc_start: 0.6968 (ttt-90) cc_final: 0.6029 (ttp-170) REVERT: B 192 LYS cc_start: 0.8306 (ttmt) cc_final: 0.7941 (mtpp) REVERT: B 210 ASP cc_start: 0.7551 (m-30) cc_final: 0.7219 (m-30) outliers start: 9 outliers final: 8 residues processed: 49 average time/residue: 0.7343 time to fit residues: 37.8534 Evaluate side-chains 45 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.0470 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.0270 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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: 0.7152 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3322 Z= 0.165 Angle : 0.423 4.823 4520 Z= 0.222 Chirality : 0.038 0.116 506 Planarity : 0.003 0.029 534 Dihedral : 16.935 158.963 490 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.30 % Allowed : 20.69 % Favored : 77.01 % 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: 1.58 (0.42), residues: 376 helix: 2.98 (0.37), residues: 176 sheet: -0.26 (0.60), residues: 68 loop : -0.98 (0.46), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 149 HIS 0.003 0.001 HIS B 150 PHE 0.021 0.001 PHE A 43 TYR 0.009 0.001 TYR B 215 ARG 0.002 0.001 ARG A 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.411 Fit side-chains REVERT: A 68 ARG cc_start: 0.6975 (ttt-90) cc_final: 0.5886 (ttp-170) REVERT: A 192 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7887 (mtpp) REVERT: A 210 ASP cc_start: 0.7642 (m-30) cc_final: 0.7296 (m-30) REVERT: B 68 ARG cc_start: 0.6966 (ttt-90) cc_final: 0.5883 (ttp-170) REVERT: B 192 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7896 (mtpp) REVERT: B 210 ASP cc_start: 0.7665 (m-30) cc_final: 0.7321 (m-30) outliers start: 8 outliers final: 8 residues processed: 50 average time/residue: 0.6775 time to fit residues: 35.7280 Evaluate side-chains 47 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.131030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.097708 restraints weight = 3689.911| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.53 r_work: 0.2831 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3322 Z= 0.216 Angle : 0.444 5.301 4520 Z= 0.233 Chirality : 0.039 0.124 506 Planarity : 0.003 0.029 534 Dihedral : 17.008 159.599 490 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.87 % Allowed : 20.69 % Favored : 76.44 % 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: 1.53 (0.42), residues: 376 helix: 2.96 (0.37), residues: 176 sheet: -0.24 (0.60), residues: 68 loop : -1.05 (0.46), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 149 HIS 0.002 0.001 HIS B 150 PHE 0.023 0.001 PHE A 43 TYR 0.011 0.001 TYR B 215 ARG 0.002 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1511.79 seconds wall clock time: 27 minutes 47.51 seconds (1667.51 seconds total)