Starting phenix.real_space_refine on Wed Mar 5 20:39:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eqj_28538/03_2025/8eqj_28538_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eqj_28538/03_2025/8eqj_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/cci-nas-00/data/ceres_data/8eqj_28538/03_2025/8eqj_28538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eqj_28538/03_2025/8eqj_28538.map" model { file = "/net/cci-nas-00/data/ceres_data/8eqj_28538/03_2025/8eqj_28538_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eqj_28538/03_2025/8eqj_28538_neut.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3232 Number of models: 1 Model: "" Number of chains: 2 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: "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 Restraints were copied for chains: B Time building chain proxies: 2.65, per 1000 atoms: 0.82 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 - 3.00 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: 0.90 Conformation dependent library (CDL) restraints added in 380.8 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... Secondary structure from input PDB file: 10 helices and 4 sheets defined 49.5% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 43 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 67 through 100 Processing helix chain 'A' and resid 105 through 134 Processing helix chain 'A' and resid 136 through 141 removed outlier: 3.598A pdb=" N LEU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'B' and resid 43 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 67 through 100 Processing helix chain 'B' and resid 105 through 134 Processing helix chain 'B' and resid 136 through 141 removed outlier: 3.598A pdb=" N LEU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 Processing sheet with id=AA1, 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: 5.510A pdb=" N LEU A 214 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASN A 234 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 216 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 229 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 186 Processing sheet with id=AA3, 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: 5.510A pdb=" N LEU B 214 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASN B 234 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER B 216 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 229 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 186 198 hydrogen bonds defined for protein. 582 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: 0.83 Time building geometry restraints manager: 1.06 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: 0.00 - 3.38: 4468 3.38 - 6.75: 34 6.75 - 10.13: 11 10.13 - 13.50: 3 13.50 - 16.88: 4 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: 433 2.75 - 3.29: 3209 3.29 - 3.83: 5428 3.83 - 4.36: 6101 4.36 - 4.90: 10714 Nonbonded interactions: 25885 Sorted by model distance: nonbonded pdb=" OG1 THR A 151 " pdb=" O TYR A 154 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR B 151 " pdb=" O TYR B 154 " model vdw 2.219 3.040 nonbonded pdb=" OG SER A 205 " pdb=" O THR A 208 " model vdw 2.286 3.040 nonbonded pdb=" OG SER B 205 " pdb=" O THR B 208 " model vdw 2.287 3.040 nonbonded pdb=" ND2 ASN B 137 " pdb=" O CYS B 157 " model vdw 2.309 3.120 ... (remaining 25880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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: 0.650 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.640 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.040 ------------------------------------------------------------------------------- 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= 0.337 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 to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.319 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: 0.5089 time to fit residues: 53.8967 Evaluate side-chains 60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 116 GLN B 70 GLN B 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.149175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.115570 restraints weight = 3591.530| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.51 r_work: 0.2956 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3322 Z= 0.239 Angle : 0.520 5.427 4520 Z= 0.273 Chirality : 0.041 0.134 506 Planarity : 0.004 0.033 534 Dihedral : 25.854 140.790 490 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.57 % Allowed : 14.08 % Favored : 85.34 % 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: 1.38 (0.41), residues: 376 helix: 2.44 (0.37), residues: 178 sheet: 0.66 (0.57), residues: 68 loop : -1.18 (0.47), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 193 HIS 0.001 0.000 HIS B 78 PHE 0.008 0.001 PHE A 146 TYR 0.014 0.001 TYR A 215 ARG 0.004 0.001 ARG B 68 *********************** 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 64 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.373 Fit side-chains REVERT: A 68 ARG cc_start: 0.7628 (ttt-90) cc_final: 0.6768 (ttp-170) REVERT: A 131 TRP cc_start: 0.8291 (t60) cc_final: 0.8021 (t60) REVERT: A 198 LYS cc_start: 0.8170 (mmmm) cc_final: 0.7849 (mtpt) REVERT: B 68 ARG cc_start: 0.7621 (ttt-90) cc_final: 0.6758 (ttp-170) REVERT: B 131 TRP cc_start: 0.8284 (t60) cc_final: 0.8011 (t60) REVERT: B 198 LYS cc_start: 0.8184 (mmmm) cc_final: 0.7864 (mtpt) outliers start: 2 outliers final: 0 residues processed: 62 average time/residue: 0.8711 time to fit residues: 56.1749 Evaluate side-chains 50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 36 optimal weight: 0.0980 chunk 6 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.2976 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.139873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.106920 restraints weight = 3657.498| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.53 r_work: 0.2958 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3322 Z= 0.154 Angle : 0.498 6.099 4520 Z= 0.248 Chirality : 0.039 0.127 506 Planarity : 0.004 0.033 534 Dihedral : 20.238 125.419 490 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.30 % Allowed : 16.67 % Favored : 81.03 % 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: 1.75 (0.42), residues: 376 helix: 2.88 (0.37), residues: 178 sheet: 0.75 (0.58), residues: 68 loop : -1.18 (0.48), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 193 HIS 0.001 0.000 HIS B 204 PHE 0.006 0.001 PHE A 146 TYR 0.009 0.001 TYR A 215 ARG 0.002 0.001 ARG B 68 *********************** 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 62 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.413 Fit side-chains REVERT: A 68 ARG cc_start: 0.7648 (ttt-90) cc_final: 0.6877 (ttp-170) REVERT: A 198 LYS cc_start: 0.8155 (mmmm) cc_final: 0.7902 (mtpt) REVERT: B 68 ARG cc_start: 0.7653 (ttt-90) cc_final: 0.6879 (ttp-170) REVERT: B 198 LYS cc_start: 0.8156 (mmmm) cc_final: 0.7894 (mtpt) outliers start: 8 outliers final: 2 residues processed: 56 average time/residue: 0.8345 time to fit residues: 48.8690 Evaluate side-chains 50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.132079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.098077 restraints weight = 3676.751| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.58 r_work: 0.2888 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3650 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= 0.220 Angle : 0.474 5.031 4520 Z= 0.248 Chirality : 0.039 0.123 506 Planarity : 0.004 0.036 534 Dihedral : 18.558 135.036 490 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.30 % Allowed : 16.67 % Favored : 81.03 % 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: 1.67 (0.42), residues: 376 helix: 2.81 (0.38), residues: 178 sheet: 0.51 (0.58), residues: 68 loop : -1.06 (0.49), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 149 HIS 0.002 0.000 HIS B 204 PHE 0.007 0.001 PHE B 146 TYR 0.012 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 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.319 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 0.5653 time to fit residues: 31.2768 Evaluate side-chains 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 155 ASP 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 19 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 20 optimal weight: 0.7980 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 = 0.3450 r_free = 0.3450 target = 0.130091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.096317 restraints weight = 3650.668| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.56 r_work: 0.2835 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3991 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= 0.213 Angle : 0.460 4.373 4520 Z= 0.244 Chirality : 0.039 0.123 506 Planarity : 0.004 0.037 534 Dihedral : 17.895 153.796 490 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.72 % Allowed : 20.40 % Favored : 77.87 % 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: 1.55 (0.43), residues: 376 helix: 2.78 (0.37), residues: 178 sheet: -0.08 (0.57), residues: 72 loop : -0.92 (0.50), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 149 HIS 0.001 0.000 HIS B 204 PHE 0.008 0.001 PHE B 230 TYR 0.012 0.001 TYR B 154 ARG 0.001 0.000 ARG B 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 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.319 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.5793 time to fit residues: 32.7316 Evaluate side-chains 46 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 197 VAL 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 19 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 25 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 0.0980 chunk 31 optimal weight: 0.5980 overall best weight: 0.2858 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.132990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.100152 restraints weight = 3671.873| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.51 r_work: 0.2894 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3322 Z= 0.152 Angle : 0.433 4.327 4520 Z= 0.232 Chirality : 0.039 0.123 506 Planarity : 0.004 0.036 534 Dihedral : 17.200 152.166 490 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.30 % Allowed : 20.98 % Favored : 76.72 % 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: 1.70 (0.43), residues: 376 helix: 2.94 (0.37), residues: 178 sheet: 0.35 (0.58), residues: 68 loop : -1.11 (0.49), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.001 0.000 HIS A 150 PHE 0.005 0.001 PHE B 56 TYR 0.012 0.001 TYR B 154 ARG 0.001 0.000 ARG B 68 *********************** 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 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.305 Fit side-chains REVERT: A 68 ARG cc_start: 0.7622 (ttt-90) cc_final: 0.6826 (ttp-170) REVERT: B 68 ARG cc_start: 0.7597 (ttt-90) cc_final: 0.6815 (ttp-170) outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 0.6848 time to fit residues: 39.5881 Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 197 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.129921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.096667 restraints weight = 3669.820| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.54 r_work: 0.2846 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3322 Z= 0.192 Angle : 0.450 4.508 4520 Z= 0.240 Chirality : 0.039 0.123 506 Planarity : 0.004 0.036 534 Dihedral : 17.133 157.389 490 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: 1.67 (0.43), residues: 376 helix: 2.96 (0.37), residues: 178 sheet: 0.13 (0.58), residues: 68 loop : -1.08 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.001 0.000 HIS A 150 PHE 0.006 0.001 PHE B 146 TYR 0.012 0.001 TYR A 154 ARG 0.001 0.000 ARG B 68 *********************** 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 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.325 Fit side-chains REVERT: A 68 ARG cc_start: 0.7609 (ttt-90) cc_final: 0.6802 (ttp-170) REVERT: B 68 ARG cc_start: 0.7584 (ttt-90) cc_final: 0.6785 (ttp-170) outliers start: 8 outliers final: 5 residues processed: 53 average time/residue: 0.7733 time to fit residues: 42.9256 Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 155 ASP 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 1 optimal weight: 0.8980 chunk 16 optimal weight: 0.0670 chunk 29 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.132693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.102014 restraints weight = 3566.403| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.33 r_work: 0.2858 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3322 Z= 0.211 Angle : 0.459 5.888 4520 Z= 0.241 Chirality : 0.039 0.125 506 Planarity : 0.004 0.036 534 Dihedral : 17.108 158.803 490 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.30 % Allowed : 19.54 % 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: 1.75 (0.43), residues: 376 helix: 3.00 (0.37), residues: 178 sheet: -0.09 (0.61), residues: 68 loop : -0.82 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 149 HIS 0.002 0.000 HIS A 150 PHE 0.006 0.001 PHE A 43 TYR 0.009 0.001 TYR A 145 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 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.334 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 0.6369 time to fit residues: 33.6916 Evaluate side-chains 48 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 197 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.0060 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 0.0030 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.4006 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.129770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.096626 restraints weight = 3701.390| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.53 r_work: 0.2847 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3322 Z= 0.180 Angle : 0.467 6.235 4520 Z= 0.240 Chirality : 0.039 0.125 506 Planarity : 0.004 0.036 534 Dihedral : 17.064 160.439 490 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.86 % Allowed : 22.41 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.43), residues: 376 helix: 3.02 (0.37), residues: 178 sheet: -0.15 (0.62), residues: 68 loop : -0.96 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 149 HIS 0.001 0.000 HIS A 150 PHE 0.006 0.001 PHE A 146 TYR 0.011 0.001 TYR B 145 ARG 0.001 0.000 ARG B 68 *********************** 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 48 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.370 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.6649 time to fit residues: 33.7432 Evaluate side-chains 46 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 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 33 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 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 = 0.3485 r_free = 0.3485 target = 0.131961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.100777 restraints weight = 3558.425| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.38 r_work: 0.2854 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3322 Z= 0.221 Angle : 0.479 5.984 4520 Z= 0.248 Chirality : 0.040 0.126 506 Planarity : 0.004 0.036 534 Dihedral : 17.129 161.821 490 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.86 % Allowed : 22.70 % 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: 1.59 (0.43), residues: 376 helix: 3.00 (0.38), residues: 178 sheet: -0.23 (0.62), residues: 68 loop : -1.07 (0.49), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 149 HIS 0.002 0.000 HIS B 150 PHE 0.007 0.001 PHE A 146 TYR 0.010 0.001 TYR B 145 ARG 0.001 0.000 ARG B 68 ********************** 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 43 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.325 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 43 average time/residue: 0.7079 time to fit residues: 32.0951 Evaluate side-chains 44 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 202 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 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.130479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.099318 restraints weight = 3603.897| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.39 r_work: 0.2833 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3322 Z= 0.258 Angle : 0.495 6.262 4520 Z= 0.256 Chirality : 0.040 0.127 506 Planarity : 0.004 0.037 534 Dihedral : 17.324 163.514 490 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.86 % Allowed : 23.56 % Favored : 75.57 % 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: 1.46 (0.43), residues: 376 helix: 2.92 (0.38), residues: 178 sheet: -0.34 (0.59), residues: 72 loop : -1.17 (0.49), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 149 HIS 0.002 0.001 HIS A 150 PHE 0.008 0.001 PHE B 146 TYR 0.011 0.001 TYR B 145 ARG 0.001 0.000 ARG A 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2358.38 seconds wall clock time: 41 minutes 15.38 seconds (2475.38 seconds total)