Starting phenix.real_space_refine on Fri May 9 19:28:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eqj_28538/05_2025/8eqj_28538_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eqj_28538/05_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_28538/05_2025/8eqj_28538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eqj_28538/05_2025/8eqj_28538.map" model { file = "/net/cci-nas-00/data/ceres_data/8eqj_28538/05_2025/8eqj_28538_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eqj_28538/05_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-5687/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: 2.68, per 1000 atoms: 0.83 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: 1.63 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.29 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: 0.72 Time building geometry restraints manager: 0.93 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: 0.01 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: 1.090 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.590 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- 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= 0.255 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 Details of bonding type rmsd hydrogen bonds : bond 0.13998 ( 198) hydrogen bonds : angle 7.18371 ( 582) covalent geometry : bond 0.00506 ( 3322) covalent geometry : angle 0.93972 ( 4520) *********************** 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 : 0.344 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: 0.5371 time to fit residues: 56.8528 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 : 0.349 ------------------------------------------------------------------------------- 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: 0.4980 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: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.152037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117933 restraints weight = 3609.959| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.57 r_work: 0.3082 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3322 Z= 0.144 Angle : 0.524 5.378 4520 Z= 0.271 Chirality : 0.041 0.133 506 Planarity : 0.004 0.034 534 Dihedral : 25.613 139.542 490 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.57 % Allowed : 14.66 % Favored : 84.77 % 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: 2.43 (0.37), residues: 178 sheet: 0.67 (0.58), residues: 68 loop : -1.17 (0.47), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 193 HIS 0.001 0.000 HIS A 204 PHE 0.008 0.001 PHE A 146 TYR 0.013 0.001 TYR A 215 ARG 0.004 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.03031 ( 198) hydrogen bonds : angle 4.65452 ( 582) covalent geometry : bond 0.00352 ( 3322) covalent geometry : angle 0.52412 ( 4520) *********************** 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 : 0.328 Fit side-chains REVERT: A 68 ARG cc_start: 0.7681 (ttt-90) cc_final: 0.6876 (ttp-170) REVERT: A 131 TRP cc_start: 0.8323 (t60) cc_final: 0.8072 (t60) REVERT: A 198 LYS cc_start: 0.8227 (mmmm) cc_final: 0.7974 (mtpt) REVERT: B 68 ARG cc_start: 0.7671 (ttt-90) cc_final: 0.6859 (ttp-170) REVERT: B 131 TRP cc_start: 0.8323 (t60) cc_final: 0.8092 (t60) REVERT: B 198 LYS cc_start: 0.8237 (mmmm) cc_final: 0.7979 (mtpt) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.8396 time to fit residues: 54.1446 Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain B residue 155 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.137156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.102409 restraints weight = 3659.151| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.62 r_work: 0.2950 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3011 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= 0.132 Angle : 0.503 6.138 4520 Z= 0.259 Chirality : 0.040 0.129 506 Planarity : 0.004 0.035 534 Dihedral : 21.457 120.674 490 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.87 % Allowed : 16.09 % 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: 1.71 (0.42), residues: 376 helix: 2.78 (0.38), residues: 178 sheet: 0.53 (0.59), residues: 64 loop : -0.91 (0.48), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 193 HIS 0.003 0.001 HIS B 204 PHE 0.009 0.001 PHE A 146 TYR 0.012 0.001 TYR B 215 ARG 0.003 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.02838 ( 198) hydrogen bonds : angle 4.54098 ( 582) covalent geometry : bond 0.00321 ( 3322) covalent geometry : angle 0.50334 ( 4520) *********************** 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: 10 poor density : 52 time to evaluate : 0.317 Fit side-chains REVERT: A 68 ARG cc_start: 0.7748 (ttt-90) cc_final: 0.6964 (ttp-170) REVERT: A 198 LYS cc_start: 0.8210 (mmmm) cc_final: 0.7941 (mtpt) REVERT: B 68 ARG cc_start: 0.7735 (ttt-90) cc_final: 0.6964 (ttp-170) REVERT: B 198 LYS cc_start: 0.8209 (mmmm) cc_final: 0.7932 (mtpt) outliers start: 10 outliers final: 4 residues processed: 58 average time/residue: 0.8959 time to fit residues: 53.9677 Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.0040 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 218 GLN B 70 GLN B 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.132129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.098245 restraints weight = 3710.942| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.55 r_work: 0.3024 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3517 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= 0.147 Angle : 0.485 4.723 4520 Z= 0.252 Chirality : 0.039 0.127 506 Planarity : 0.004 0.036 534 Dihedral : 18.889 132.657 490 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.30 % Allowed : 17.24 % Favored : 80.46 % 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: 1.52 (0.43), residues: 376 helix: 2.76 (0.38), residues: 178 sheet: 0.00 (0.57), residues: 72 loop : -1.01 (0.50), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 149 HIS 0.001 0.000 HIS B 204 PHE 0.007 0.001 PHE B 146 TYR 0.013 0.001 TYR A 215 ARG 0.001 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.02873 ( 198) hydrogen bonds : angle 4.48967 ( 582) covalent geometry : bond 0.00351 ( 3322) covalent geometry : angle 0.48544 ( 4520) *********************** 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 to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.345 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 54 average time/residue: 0.5644 time to fit residues: 32.4289 Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.130486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.096659 restraints weight = 3691.324| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.56 r_work: 0.2833 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3322 Z= 0.157 Angle : 0.486 4.389 4520 Z= 0.256 Chirality : 0.039 0.127 506 Planarity : 0.004 0.037 534 Dihedral : 18.103 154.173 490 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.01 % Allowed : 19.54 % Favored : 78.45 % 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: 1.42 (0.43), residues: 376 helix: 2.70 (0.38), residues: 178 sheet: -0.14 (0.58), residues: 72 loop : -1.02 (0.50), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 149 HIS 0.001 0.000 HIS B 204 PHE 0.007 0.001 PHE B 146 TYR 0.011 0.001 TYR B 215 ARG 0.001 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 198) hydrogen bonds : angle 4.56443 ( 582) covalent geometry : bond 0.00383 ( 3322) covalent geometry : angle 0.48616 ( 4520) *********************** 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 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.328 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 53 average time/residue: 0.5589 time to fit residues: 31.4760 Evaluate side-chains 44 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 73 LEU 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: 0.0980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.130868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.097685 restraints weight = 3711.281| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.52 r_work: 0.2828 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3322 Z= 0.138 Angle : 0.460 4.356 4520 Z= 0.245 Chirality : 0.039 0.122 506 Planarity : 0.004 0.038 534 Dihedral : 17.386 150.274 490 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.59 % Allowed : 20.11 % Favored : 77.30 % 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: 1.50 (0.43), residues: 376 helix: 2.84 (0.37), residues: 178 sheet: -0.16 (0.58), residues: 72 loop : -1.07 (0.50), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 149 HIS 0.001 0.000 HIS A 150 PHE 0.008 0.001 PHE A 43 TYR 0.010 0.001 TYR A 215 ARG 0.002 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02933 ( 198) hydrogen bonds : angle 4.51419 ( 582) covalent geometry : bond 0.00339 ( 3322) covalent geometry : angle 0.45985 ( 4520) *********************** 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 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.451 Fit side-chains REVERT: A 68 ARG cc_start: 0.7646 (ttt-90) cc_final: 0.6806 (ttp-170) REVERT: B 68 ARG cc_start: 0.7621 (ttt-90) cc_final: 0.6797 (ttp-170) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.7281 time to fit residues: 41.2785 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 73 LEU Chi-restraints excluded: chain B residue 97 VAL 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: 1.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.129199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.095113 restraints weight = 3671.503| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.57 r_work: 0.2816 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3322 Z= 0.151 Angle : 0.471 4.342 4520 Z= 0.251 Chirality : 0.040 0.123 506 Planarity : 0.004 0.038 534 Dihedral : 17.453 159.456 490 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.30 % Allowed : 20.11 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.43), residues: 376 helix: 2.88 (0.38), residues: 178 sheet: -0.26 (0.59), residues: 72 loop : -1.12 (0.49), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 149 HIS 0.002 0.000 HIS A 150 PHE 0.007 0.001 PHE A 146 TYR 0.012 0.001 TYR A 215 ARG 0.002 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 198) hydrogen bonds : angle 4.56149 ( 582) covalent geometry : bond 0.00372 ( 3322) covalent geometry : angle 0.47090 ( 4520) *********************** 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 61 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.365 Fit side-chains REVERT: A 68 ARG cc_start: 0.7682 (ttt-90) cc_final: 0.6891 (ttp-170) REVERT: A 150 HIS cc_start: 0.7128 (t-90) cc_final: 0.6900 (t70) REVERT: B 68 ARG cc_start: 0.7668 (ttt-90) cc_final: 0.6887 (ttp-170) outliers start: 8 outliers final: 8 residues processed: 57 average time/residue: 0.7511 time to fit residues: 44.8558 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 : 0.329 ------------------------------------------------------------------------------- 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 A residue 234 ASN Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 234 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.0070 chunk 22 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.128498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.094868 restraints weight = 3632.639| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.53 r_work: 0.2819 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 0.032 3322 Z= 0.137 Angle : 0.486 5.831 4520 Z= 0.251 Chirality : 0.040 0.125 506 Planarity : 0.004 0.037 534 Dihedral : 17.261 159.013 490 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.72 % Allowed : 22.70 % 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: 1.63 (0.43), residues: 376 helix: 3.26 (0.37), residues: 166 sheet: -0.25 (0.59), residues: 72 loop : -0.97 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 149 HIS 0.002 0.000 HIS A 150 PHE 0.007 0.001 PHE A 43 TYR 0.010 0.001 TYR B 215 ARG 0.002 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 198) hydrogen bonds : angle 4.49921 ( 582) covalent geometry : bond 0.00338 ( 3322) covalent geometry : angle 0.48624 ( 4520) *********************** 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 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.348 Fit side-chains REVERT: A 68 ARG cc_start: 0.7610 (ttt-90) cc_final: 0.6764 (ttp-170) REVERT: B 68 ARG cc_start: 0.7590 (ttt-90) cc_final: 0.6755 (ttp-170) REVERT: B 101 LEU cc_start: 0.7831 (mp) cc_final: 0.7440 (mm) outliers start: 6 outliers final: 5 residues processed: 51 average time/residue: 0.8126 time to fit residues: 43.2770 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 : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 234 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.0070 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.129285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.095824 restraints weight = 3680.438| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.52 r_work: 0.2838 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4459 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= 0.122 Angle : 0.476 6.546 4520 Z= 0.248 Chirality : 0.040 0.122 506 Planarity : 0.004 0.037 534 Dihedral : 17.177 161.243 490 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.86 % Allowed : 23.85 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.43), residues: 376 helix: 2.93 (0.38), residues: 178 sheet: -0.17 (0.61), residues: 68 loop : -0.92 (0.47), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.002 0.000 HIS A 150 PHE 0.007 0.001 PHE A 43 TYR 0.008 0.001 TYR A 109 ARG 0.002 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.02816 ( 198) hydrogen bonds : angle 4.41671 ( 582) covalent geometry : bond 0.00301 ( 3322) covalent geometry : angle 0.47579 ( 4520) *********************** 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 : 0.322 Fit side-chains REVERT: B 101 LEU cc_start: 0.7760 (mp) cc_final: 0.7345 (mm) outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.6391 time to fit residues: 32.3748 Evaluate side-chains 45 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 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 = 0.3414 r_free = 0.3414 target = 0.127427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.094134 restraints weight = 3619.151| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.48 r_work: 0.2815 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3322 Z= 0.160 Angle : 0.509 7.564 4520 Z= 0.261 Chirality : 0.041 0.125 506 Planarity : 0.004 0.038 534 Dihedral : 17.294 161.964 490 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.44 % Allowed : 23.28 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.43), residues: 376 helix: 3.27 (0.37), residues: 166 sheet: -0.40 (0.58), residues: 72 loop : -0.85 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 149 HIS 0.002 0.000 HIS A 150 PHE 0.007 0.001 PHE A 146 TYR 0.009 0.001 TYR A 109 ARG 0.003 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02967 ( 198) hydrogen bonds : angle 4.53549 ( 582) covalent geometry : bond 0.00400 ( 3322) covalent geometry : angle 0.50853 ( 4520) ********************** 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 47 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.362 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 0.6939 time to fit residues: 32.9074 Evaluate side-chains 46 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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: 0.0570 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.128820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.096234 restraints weight = 3647.988| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.45 r_work: 0.2851 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4603 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= 0.127 Angle : 0.489 7.516 4520 Z= 0.253 Chirality : 0.040 0.122 506 Planarity : 0.004 0.037 534 Dihedral : 17.241 163.374 490 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.57 % Allowed : 25.00 % Favored : 74.43 % 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 (0.42), residues: 376 helix: 3.30 (0.37), residues: 166 sheet: -0.29 (0.58), residues: 72 loop : -0.91 (0.48), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 149 HIS 0.001 0.000 HIS A 150 PHE 0.006 0.001 PHE B 146 TYR 0.009 0.001 TYR B 145 ARG 0.002 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02858 ( 198) hydrogen bonds : angle 4.46373 ( 582) covalent geometry : bond 0.00314 ( 3322) covalent geometry : angle 0.48939 ( 4520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2245.11 seconds wall clock time: 39 minutes 48.60 seconds (2388.60 seconds total)