Starting phenix.real_space_refine on Tue Aug 4 16:52:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ibw_52814/08_2026/9ibw_52814.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ibw_52814/08_2026/9ibw_52814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ibw_52814/08_2026/9ibw_52814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ibw_52814/08_2026/9ibw_52814.map" model { file = "/net/cci-nas-00/data/ceres_data/9ibw_52814/08_2026/9ibw_52814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ibw_52814/08_2026/9ibw_52814.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 3247 2.51 5 N 814 2.21 5 O 888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4983 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3201 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 15, 'TRANS': 387} Chain breaks: 2 Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "H" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.29, per 1000 atoms: 0.26 Number of scatterers: 4983 At special positions: 0 Unit cell: (65.88, 79.788, 147.132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 888 8.00 N 814 7.00 C 3247 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 181 " distance=2.02 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 97 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 107.1 milliseconds 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 4 sheets defined 53.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 29 through 57 removed outlier: 3.690A pdb=" N LEU A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) Proline residue: A 47 - end of helix removed outlier: 3.624A pdb=" N LEU A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 61 Processing helix chain 'A' and resid 64 through 95 removed outlier: 3.612A pdb=" N TYR A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 100 through 135 Processing helix chain 'A' and resid 143 through 168 removed outlier: 3.758A pdb=" N THR A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 193 through 207 Processing helix chain 'A' and resid 207 through 230 Processing helix chain 'A' and resid 888 through 911 Processing helix chain 'A' and resid 913 through 934 Processing helix chain 'A' and resid 949 through 972 removed outlier: 3.624A pdb=" N LEU A 969 " --> pdb=" O ASP A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 995 removed outlier: 3.825A pdb=" N ALA A 978 " --> pdb=" O LYS A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 272 Proline residue: A 261 - end of helix Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.533A pdb=" N LYS A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 304 Proline residue: A 297 - end of helix removed outlier: 3.861A pdb=" N PHE A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.545A pdb=" N MET A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.806A pdb=" N SER H 92 " --> pdb=" O SER H 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AA2, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.514A pdb=" N LYS L 50 " --> pdb=" O GLN L 54 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 58 through 61 removed outlier: 6.581A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TRP H 51 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE H 35 " --> pdb=" O TRP H 51 " (cutoff:3.500A) 288 hydrogen bonds defined for protein. 825 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: 0.88 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 5065 1.57 - 1.91: 50 1.91 - 2.26: 0 2.26 - 2.60: 0 2.60 - 2.94: 1 Bond restraints: 5116 Sorted by residual: bond pdb=" C GLN A 230 " pdb=" N ALA A 887 " ideal model delta sigma weight residual 1.334 2.945 -1.611 1.38e-02 5.25e+03 1.36e+04 bond pdb=" C8 RET A1101 " pdb=" C9 RET A1101 " ideal model delta sigma weight residual 1.450 1.390 0.060 2.00e-02 2.50e+03 9.01e+00 bond pdb=" C10 RET A1101 " pdb=" C9 RET A1101 " ideal model delta sigma weight residual 1.359 1.411 -0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" C10 RET A1101 " pdb=" C11 RET A1101 " ideal model delta sigma weight residual 1.433 1.384 0.049 2.00e-02 2.50e+03 6.00e+00 bond pdb=" C12 RET A1101 " pdb=" C13 RET A1101 " ideal model delta sigma weight residual 1.446 1.408 0.038 2.00e-02 2.50e+03 3.65e+00 ... (remaining 5111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.27: 6930 5.27 - 10.55: 4 10.55 - 15.82: 1 15.82 - 21.09: 0 21.09 - 26.37: 1 Bond angle restraints: 6936 Sorted by residual: angle pdb=" CA GLN A 230 " pdb=" C GLN A 230 " pdb=" N ALA A 887 " ideal model delta sigma weight residual 117.30 101.57 15.73 1.16e+00 7.43e-01 1.84e+02 angle pdb=" C GLN A 230 " pdb=" N ALA A 887 " pdb=" CA ALA A 887 " ideal model delta sigma weight residual 121.18 94.81 26.37 1.98e+00 2.55e-01 1.77e+02 angle pdb=" O GLN A 230 " pdb=" C GLN A 230 " pdb=" N ALA A 887 " ideal model delta sigma weight residual 122.12 118.05 4.07 1.06e+00 8.90e-01 1.47e+01 angle pdb=" C10 RET A1101 " pdb=" C11 RET A1101 " pdb=" C12 RET A1101 " ideal model delta sigma weight residual 122.68 132.55 -9.87 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C SER L 31 " pdb=" CA SER L 31 " pdb=" CB SER L 31 " ideal model delta sigma weight residual 110.42 115.88 -5.46 1.99e+00 2.53e-01 7.53e+00 ... (remaining 6931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.05: 2447 14.05 - 28.10: 330 28.10 - 42.15: 155 42.15 - 56.20: 38 56.20 - 70.25: 11 Dihedral angle restraints: 2981 sinusoidal: 1157 harmonic: 1824 Sorted by residual: dihedral pdb=" CB CYS A 104 " pdb=" SG CYS A 104 " pdb=" SG CYS A 181 " pdb=" CB CYS A 181 " ideal model delta sinusoidal sigma weight residual -86.00 -138.38 52.38 1 1.00e+01 1.00e-02 3.74e+01 dihedral pdb=" CA THR L 73 " pdb=" C THR L 73 " pdb=" N LEU L 74 " pdb=" CA LEU L 74 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA PHE H 81 " pdb=" C PHE H 81 " pdb=" N MET H 82 " pdb=" CA MET H 82 " ideal model delta harmonic sigma weight residual 180.00 161.46 18.54 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 463 0.028 - 0.056: 189 0.056 - 0.084: 68 0.084 - 0.112: 27 0.112 - 0.140: 7 Chirality restraints: 754 Sorted by residual: chirality pdb=" CA ILE H 21 " pdb=" N ILE H 21 " pdb=" C ILE H 21 " pdb=" CB ILE H 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE A 173 " pdb=" N ILE A 173 " pdb=" C ILE A 173 " pdb=" CB ILE A 173 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE H 35 " pdb=" N ILE H 35 " pdb=" C ILE H 35 " pdb=" CB ILE H 35 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 751 not shown) Planarity restraints: 872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 230 " -0.100 2.00e-02 2.50e+03 1.74e-01 3.03e+02 pdb=" C GLN A 230 " 0.295 2.00e-02 2.50e+03 pdb=" O GLN A 230 " -0.150 2.00e-02 2.50e+03 pdb=" N ALA A 887 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET A1101 " -0.060 2.00e-02 2.50e+03 6.59e-02 5.42e+01 pdb=" C13 RET A1101 " 0.018 2.00e-02 2.50e+03 pdb=" C14 RET A1101 " 0.107 2.00e-02 2.50e+03 pdb=" C15 RET A1101 " -0.079 2.00e-02 2.50e+03 pdb=" C20 RET A1101 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 41 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C VAL A 41 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL A 41 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 42 " 0.012 2.00e-02 2.50e+03 ... (remaining 869 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 2137 2.90 - 3.40: 5088 3.40 - 3.90: 8049 3.90 - 4.40: 9218 4.40 - 4.90: 15297 Nonbonded interactions: 39789 Sorted by model distance: nonbonded pdb=" O PRO H 100 " pdb=" O ASP H 106 " model vdw 2.398 3.040 nonbonded pdb=" O PHE H 30 " pdb=" OG1 THR H 31 " model vdw 2.404 3.040 nonbonded pdb=" OD1 ASP A 965 " pdb=" OG SER H 56 " model vdw 2.450 3.040 nonbonded pdb=" O GLY L 65 " pdb=" OG SER L 66 " model vdw 2.466 3.040 nonbonded pdb=" O SER H 78 " pdb=" OG SER H 78 " model vdw 2.478 3.040 ... (remaining 39784 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 9.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.000 Find NCS groups from input model: 0.040 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 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 : 0.023 1.611 5120 Z= 1.661 Angle : 0.735 26.368 6942 Z= 0.420 Chirality : 0.038 0.140 754 Planarity : 0.008 0.174 872 Dihedral : 16.360 70.254 1802 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.56 % Allowed : 24.58 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.33), residues: 617 helix: 0.87 (0.29), residues: 310 sheet: -1.51 (0.56), residues: 67 loop : -2.13 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 889 TYR 0.013 0.001 TYR A 217 PHE 0.018 0.001 PHE H 30 TRP 0.012 0.001 TRP H 51 HIS 0.002 0.001 HIS H 60 Details of bonding type rmsd/Z covalent geometry : bond 0.02298 / 1.65 ( 5116) covalent geometry : angle 0.73496 / 0.42 ( 6936) SS BOND : bond 0.00737 / 0.36 ( 3) SS BOND : angle 0.96732 / 0.49 ( 6) hydrogen bonds : bond 0.13753 / 9.47 ( 288) hydrogen bonds : angle 7.34486 / 5.42 ( 825) Misc. bond : bond 0.16342 / 8.60 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: A 79 LEU cc_start: 0.7738 (tp) cc_final: 0.7503 (mp) REVERT: A 94 ASN cc_start: 0.6294 (m-40) cc_final: 0.5913 (t0) REVERT: A 996 TYR cc_start: 0.4990 (OUTLIER) cc_final: 0.4109 (t80) REVERT: A 247 MET cc_start: 0.7566 (ttp) cc_final: 0.7282 (tmm) REVERT: A 256 CYS cc_start: 0.7726 (t) cc_final: 0.7490 (m) REVERT: A 267 MET cc_start: 0.5947 (mmp) cc_final: 0.5553 (ptt) REVERT: L 76 ILE cc_start: 0.5732 (mm) cc_final: 0.5328 (mm) outliers start: 19 outliers final: 13 residues processed: 100 average time/residue: 0.0729 time to fit residues: 9.3904 Evaluate side-chains 80 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.0070 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN H 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.249960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.209577 restraints weight = 6228.265| |-----------------------------------------------------------------------------| r_work (start): 0.4412 rms_B_bonded: 3.24 r_work: 0.4162 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5120 Z= 0.186 Angle : 0.626 8.897 6942 Z= 0.333 Chirality : 0.042 0.145 754 Planarity : 0.005 0.040 872 Dihedral : 7.498 81.417 710 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 5.44 % Allowed : 24.02 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.34), residues: 619 helix: 1.87 (0.29), residues: 314 sheet: -1.33 (0.60), residues: 67 loop : -2.09 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 62 TYR 0.018 0.002 TYR A 217 PHE 0.023 0.002 PHE A 86 TRP 0.012 0.001 TRP H 51 HIS 0.002 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 ( 5116) covalent geometry : angle 0.62605 / 0.33 ( 6936) SS BOND : bond 0.00508 / 0.26 ( 3) SS BOND : angle 0.78241 / 0.41 ( 6) hydrogen bonds : bond 0.04327 / 3.07 ( 288) hydrogen bonds : angle 5.36710 / 3.95 ( 825) Misc. bond : bond 0.00075 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.185 Fit side-chains REVERT: A 110 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6858 (mm) REVERT: A 167 PHE cc_start: 0.6314 (m-10) cc_final: 0.6015 (m-10) REVERT: A 185 TRP cc_start: 0.6364 (m-10) cc_final: 0.5855 (m-10) REVERT: A 996 TYR cc_start: 0.5203 (OUTLIER) cc_final: 0.4263 (t80) REVERT: A 243 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.5940 (pt0) REVERT: A 244 VAL cc_start: 0.6394 (p) cc_final: 0.6120 (p) REVERT: A 247 MET cc_start: 0.7458 (ttp) cc_final: 0.6413 (tmm) REVERT: A 312 MET cc_start: 0.4932 (ppp) cc_final: 0.4350 (tpt) REVERT: L 48 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.4631 (mt) REVERT: L 84 PHE cc_start: 0.1769 (OUTLIER) cc_final: 0.0691 (m-80) outliers start: 29 outliers final: 12 residues processed: 93 average time/residue: 0.0551 time to fit residues: 7.1341 Evaluate side-chains 80 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 108 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 chunk 9 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 54 optimal weight: 0.0570 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.251165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.210999 restraints weight = 6256.242| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 3.23 r_work: 0.4171 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5120 Z= 0.133 Angle : 0.589 8.532 6942 Z= 0.306 Chirality : 0.041 0.144 754 Planarity : 0.004 0.031 872 Dihedral : 6.874 87.437 700 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.94 % Allowed : 25.89 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.35), residues: 619 helix: 2.08 (0.29), residues: 313 sheet: -0.62 (0.59), residues: 73 loop : -2.13 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 246 TYR 0.020 0.001 TYR A 217 PHE 0.018 0.001 PHE A 302 TRP 0.013 0.001 TRP H 51 HIS 0.002 0.001 HIS H 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 5116) covalent geometry : angle 0.58879 / 0.31 ( 6936) SS BOND : bond 0.00391 / 0.20 ( 3) SS BOND : angle 0.71734 / 0.38 ( 6) hydrogen bonds : bond 0.03787 / 2.71 ( 288) hydrogen bonds : angle 5.02541 / 3.68 ( 825) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.162 Fit side-chains REVERT: A 185 TRP cc_start: 0.6249 (m-10) cc_final: 0.5767 (m-10) REVERT: A 312 MET cc_start: 0.5097 (ppp) cc_final: 0.4571 (tpt) REVERT: L 48 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.4426 (mt) REVERT: L 54 GLN cc_start: 0.8397 (tt0) cc_final: 0.8073 (tp40) REVERT: L 84 PHE cc_start: 0.2022 (OUTLIER) cc_final: 0.0938 (m-80) outliers start: 21 outliers final: 12 residues processed: 85 average time/residue: 0.0593 time to fit residues: 6.8488 Evaluate side-chains 73 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 108 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 2 optimal weight: 0.0670 chunk 56 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 0.2980 chunk 13 optimal weight: 0.0000 chunk 17 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.248698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.211065 restraints weight = 6226.749| |-----------------------------------------------------------------------------| r_work (start): 0.4440 rms_B_bonded: 2.61 r_work: 0.4193 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5120 Z= 0.151 Angle : 0.609 8.998 6942 Z= 0.312 Chirality : 0.040 0.152 754 Planarity : 0.004 0.034 872 Dihedral : 6.607 89.560 695 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 6.00 % Allowed : 25.33 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.35), residues: 619 helix: 2.14 (0.29), residues: 313 sheet: -0.62 (0.58), residues: 73 loop : -2.14 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.019 0.001 TYR A 217 PHE 0.018 0.002 PHE A 167 TRP 0.013 0.001 TRP H 51 HIS 0.002 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 5116) covalent geometry : angle 0.60851 / 0.31 ( 6936) SS BOND : bond 0.00516 / 0.26 ( 3) SS BOND : angle 0.81972 / 0.43 ( 6) hydrogen bonds : bond 0.03683 / 2.63 ( 288) hydrogen bonds : angle 4.95949 / 3.64 ( 825) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.150 Fit side-chains REVERT: A 64 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.7099 (tm-30) REVERT: A 110 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6726 (mm) REVERT: A 163 ILE cc_start: 0.6646 (mt) cc_final: 0.6133 (mt) REVERT: A 185 TRP cc_start: 0.6210 (m-10) cc_final: 0.5776 (m-10) REVERT: L 48 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.4602 (mt) REVERT: L 84 PHE cc_start: 0.2580 (OUTLIER) cc_final: 0.1459 (m-80) outliers start: 32 outliers final: 22 residues processed: 86 average time/residue: 0.0579 time to fit residues: 6.8215 Evaluate side-chains 86 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 108 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 10 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 19 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.246846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.208367 restraints weight = 6257.413| |-----------------------------------------------------------------------------| r_work (start): 0.4412 rms_B_bonded: 2.61 r_work: 0.4164 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5120 Z= 0.179 Angle : 0.621 9.731 6942 Z= 0.320 Chirality : 0.041 0.155 754 Planarity : 0.004 0.041 872 Dihedral : 6.671 88.572 695 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 6.38 % Allowed : 24.77 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.35), residues: 619 helix: 2.11 (0.29), residues: 314 sheet: -0.64 (0.63), residues: 63 loop : -2.14 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 62 TYR 0.019 0.001 TYR A 217 PHE 0.022 0.002 PHE A 167 TRP 0.013 0.001 TRP H 51 HIS 0.002 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 5116) covalent geometry : angle 0.62029 / 0.32 ( 6936) SS BOND : bond 0.00624 / 0.32 ( 3) SS BOND : angle 0.94021 / 0.49 ( 6) hydrogen bonds : bond 0.03753 / 2.67 ( 288) hydrogen bonds : angle 5.06628 / 3.71 ( 825) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 65 time to evaluate : 0.123 Fit side-chains REVERT: A 64 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: A 110 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6733 (mm) REVERT: A 185 TRP cc_start: 0.6200 (m-10) cc_final: 0.5758 (m-10) REVERT: A 996 TYR cc_start: 0.5123 (OUTLIER) cc_final: 0.4260 (t80) REVERT: A 247 MET cc_start: 0.8003 (ttp) cc_final: 0.7613 (ttt) REVERT: A 312 MET cc_start: 0.4915 (ppp) cc_final: 0.4222 (tpt) outliers start: 34 outliers final: 25 residues processed: 90 average time/residue: 0.0519 time to fit residues: 6.5865 Evaluate side-chains 89 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 108 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 0.0070 chunk 47 optimal weight: 0.0470 chunk 59 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.248264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.210166 restraints weight = 6319.849| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 2.90 r_work: 0.4164 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5120 Z= 0.145 Angle : 0.595 9.113 6942 Z= 0.306 Chirality : 0.040 0.164 754 Planarity : 0.004 0.040 872 Dihedral : 6.358 84.861 693 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.44 % Allowed : 25.52 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.35), residues: 619 helix: 2.18 (0.29), residues: 314 sheet: -0.64 (0.63), residues: 63 loop : -2.16 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 129 TYR 0.019 0.001 TYR A 217 PHE 0.019 0.002 PHE A 86 TRP 0.013 0.001 TRP H 51 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 5116) covalent geometry : angle 0.59490 / 0.31 ( 6936) SS BOND : bond 0.00547 / 0.28 ( 3) SS BOND : angle 0.82236 / 0.43 ( 6) hydrogen bonds : bond 0.03527 / 2.50 ( 288) hydrogen bonds : angle 4.91768 / 3.59 ( 825) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.139 Fit side-chains REVERT: A 110 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6677 (mm) REVERT: A 185 TRP cc_start: 0.6095 (m-10) cc_final: 0.5691 (m-10) REVERT: A 996 TYR cc_start: 0.5202 (OUTLIER) cc_final: 0.4274 (t80) REVERT: A 312 MET cc_start: 0.5179 (ppp) cc_final: 0.4352 (tpt) REVERT: L 19 ARG cc_start: 0.5652 (mtp85) cc_final: 0.4284 (mtm-85) REVERT: L 48 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.4697 (mt) REVERT: L 71 ASP cc_start: 0.7167 (t0) cc_final: 0.6928 (t0) outliers start: 29 outliers final: 20 residues processed: 88 average time/residue: 0.0607 time to fit residues: 6.8920 Evaluate side-chains 84 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 58 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 890 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.244941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.205149 restraints weight = 6190.652| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 3.42 r_work: 0.4124 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5120 Z= 0.216 Angle : 0.669 10.411 6942 Z= 0.346 Chirality : 0.042 0.165 754 Planarity : 0.004 0.045 872 Dihedral : 6.803 88.730 693 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 7.69 % Allowed : 24.58 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.35), residues: 619 helix: 2.00 (0.29), residues: 314 sheet: -0.81 (0.64), residues: 63 loop : -2.20 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 63 TYR 0.019 0.002 TYR A 217 PHE 0.015 0.002 PHE H 33 TRP 0.012 0.002 TRP H 51 HIS 0.002 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.22 ( 5116) covalent geometry : angle 0.66809 / 0.35 ( 6936) SS BOND : bond 0.00785 / 0.40 ( 3) SS BOND : angle 1.14591 / 0.59 ( 6) hydrogen bonds : bond 0.03873 / 2.73 ( 288) hydrogen bonds : angle 5.14279 / 3.76 ( 825) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 66 time to evaluate : 0.131 Fit side-chains REVERT: A 110 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6778 (mm) REVERT: A 185 TRP cc_start: 0.6263 (m-10) cc_final: 0.5755 (m-10) REVERT: A 996 TYR cc_start: 0.5414 (OUTLIER) cc_final: 0.4312 (t80) REVERT: A 312 MET cc_start: 0.5268 (ppp) cc_final: 0.4345 (tpt) REVERT: L 19 ARG cc_start: 0.5774 (mtp85) cc_final: 0.4463 (mtm-85) outliers start: 41 outliers final: 34 residues processed: 95 average time/residue: 0.0567 time to fit residues: 7.2797 Evaluate side-chains 98 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 62 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN A 890 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.245848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.207942 restraints weight = 6259.829| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 2.85 r_work: 0.4156 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5120 Z= 0.179 Angle : 0.647 10.624 6942 Z= 0.333 Chirality : 0.042 0.173 754 Planarity : 0.004 0.043 872 Dihedral : 6.564 86.200 693 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 6.75 % Allowed : 25.33 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.35), residues: 619 helix: 2.07 (0.29), residues: 314 sheet: -0.96 (0.67), residues: 51 loop : -2.10 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 129 TYR 0.018 0.001 TYR A 217 PHE 0.020 0.002 PHE A 86 TRP 0.014 0.001 TRP H 51 HIS 0.002 0.001 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 5116) covalent geometry : angle 0.64677 / 0.33 ( 6936) SS BOND : bond 0.00641 / 0.33 ( 3) SS BOND : angle 0.99555 / 0.52 ( 6) hydrogen bonds : bond 0.03715 / 2.63 ( 288) hydrogen bonds : angle 5.06369 / 3.69 ( 825) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 65 time to evaluate : 0.112 Fit side-chains REVERT: A 110 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6736 (mm) REVERT: A 185 TRP cc_start: 0.6207 (m-10) cc_final: 0.5790 (m-10) REVERT: A 996 TYR cc_start: 0.5419 (OUTLIER) cc_final: 0.4337 (t80) REVERT: A 312 MET cc_start: 0.5308 (ppp) cc_final: 0.4863 (ppp) REVERT: L 19 ARG cc_start: 0.5702 (mtp85) cc_final: 0.4371 (mtm-85) outliers start: 36 outliers final: 30 residues processed: 90 average time/residue: 0.0470 time to fit residues: 5.7131 Evaluate side-chains 95 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 63 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 0.0770 chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.240862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.201806 restraints weight = 6200.050| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 3.24 r_work: 0.4078 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5120 Z= 0.166 Angle : 0.651 11.176 6942 Z= 0.335 Chirality : 0.042 0.175 754 Planarity : 0.004 0.042 872 Dihedral : 6.324 85.714 691 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 7.13 % Allowed : 24.58 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.35), residues: 619 helix: 2.10 (0.29), residues: 313 sheet: -0.78 (0.68), residues: 51 loop : -2.07 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 129 TYR 0.019 0.001 TYR A 217 PHE 0.024 0.002 PHE A 167 TRP 0.014 0.001 TRP H 51 HIS 0.001 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 5116) covalent geometry : angle 0.65030 / 0.33 ( 6936) SS BOND : bond 0.00592 / 0.30 ( 3) SS BOND : angle 0.94720 / 0.49 ( 6) hydrogen bonds : bond 0.03641 / 2.57 ( 288) hydrogen bonds : angle 5.00677 / 3.65 ( 825) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 62 time to evaluate : 0.109 Fit side-chains REVERT: A 110 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6604 (mm) REVERT: A 122 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7158 (tp) REVERT: A 185 TRP cc_start: 0.6191 (m-10) cc_final: 0.5816 (m-10) REVERT: A 977 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: A 996 TYR cc_start: 0.5418 (OUTLIER) cc_final: 0.4338 (t80) REVERT: A 312 MET cc_start: 0.5300 (ppp) cc_final: 0.4866 (ppp) REVERT: L 19 ARG cc_start: 0.5600 (mtp85) cc_final: 0.4222 (mtm-85) REVERT: L 71 ASP cc_start: 0.7352 (t0) cc_final: 0.7142 (t0) outliers start: 38 outliers final: 34 residues processed: 89 average time/residue: 0.0555 time to fit residues: 6.7619 Evaluate side-chains 99 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 61 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 977 GLU Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN A 890 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.240823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.200472 restraints weight = 6219.449| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 3.40 r_work: 0.4063 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5120 Z= 0.184 Angle : 0.661 11.391 6942 Z= 0.340 Chirality : 0.042 0.186 754 Planarity : 0.004 0.042 872 Dihedral : 6.413 86.884 691 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 7.50 % Allowed : 24.58 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.34), residues: 619 helix: 2.06 (0.29), residues: 315 sheet: -0.86 (0.67), residues: 51 loop : -2.15 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.019 0.001 TYR A 217 PHE 0.021 0.002 PHE A 86 TRP 0.013 0.002 TRP H 51 HIS 0.002 0.001 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 5116) covalent geometry : angle 0.66039 / 0.34 ( 6936) SS BOND : bond 0.00692 / 0.35 ( 3) SS BOND : angle 1.09228 / 0.56 ( 6) hydrogen bonds : bond 0.03690 / 2.62 ( 288) hydrogen bonds : angle 5.02113 / 3.65 ( 825) Misc. bond : bond 0.00025 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 67 time to evaluate : 0.105 Fit side-chains REVERT: A 110 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6648 (mm) REVERT: A 122 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7192 (tp) REVERT: A 167 PHE cc_start: 0.6235 (m-10) cc_final: 0.5920 (m-10) REVERT: A 185 TRP cc_start: 0.6268 (m-10) cc_final: 0.5863 (m-10) REVERT: A 192 TYR cc_start: 0.5598 (m-80) cc_final: 0.5154 (m-80) REVERT: A 996 TYR cc_start: 0.5469 (OUTLIER) cc_final: 0.4388 (t80) REVERT: A 312 MET cc_start: 0.5298 (ppp) cc_final: 0.4830 (ppp) REVERT: L 19 ARG cc_start: 0.5621 (mtp85) cc_final: 0.4268 (mtm-85) outliers start: 40 outliers final: 33 residues processed: 95 average time/residue: 0.0433 time to fit residues: 5.5684 Evaluate side-chains 102 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 66 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 2 optimal weight: 0.0570 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 890 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.240550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.200220 restraints weight = 6232.864| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 3.56 r_work: 0.4067 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5120 Z= 0.172 Angle : 0.661 11.287 6942 Z= 0.339 Chirality : 0.042 0.174 754 Planarity : 0.004 0.041 872 Dihedral : 6.375 85.120 691 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 6.94 % Allowed : 25.33 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.34), residues: 619 helix: 2.05 (0.29), residues: 313 sheet: -0.94 (0.66), residues: 51 loop : -2.13 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 889 TYR 0.021 0.001 TYR A 130 PHE 0.013 0.001 PHE A 302 TRP 0.014 0.001 TRP H 51 HIS 0.001 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 5116) covalent geometry : angle 0.66020 / 0.34 ( 6936) SS BOND : bond 0.00635 / 0.32 ( 3) SS BOND : angle 1.04081 / 0.54 ( 6) hydrogen bonds : bond 0.03577 / 2.54 ( 288) hydrogen bonds : angle 5.00557 / 3.64 ( 825) Misc. bond : bond 0.00021 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1391.06 seconds wall clock time: 24 minutes 32.09 seconds (1472.09 seconds total)