Starting phenix.real_space_refine on Wed Sep 17 05:47:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eai_47832/09_2025/9eai_47832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eai_47832/09_2025/9eai_47832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eai_47832/09_2025/9eai_47832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eai_47832/09_2025/9eai_47832.map" model { file = "/net/cci-nas-00/data/ceres_data/9eai_47832/09_2025/9eai_47832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eai_47832/09_2025/9eai_47832.cif" } resolution = 3.1 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= 0.013 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 S 26 5.16 5 Cl 1 4.86 5 C 3653 2.51 5 N 883 2.21 5 O 991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5554 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2976 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 13, 'TRANS': 359} Chain breaks: 2 Chain: "B" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 681 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain breaks: 5 Chain: "C" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 944 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 117} Chain: "D" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'CLR': 1, 'LSN': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'Y01:plan-1': 1, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 1.30, per 1000 atoms: 0.23 Number of scatterers: 5554 At special positions: 0 Unit cell: (83.83, 91.3, 136.95, 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) Cl 1 17.00 S 26 16.00 O 991 8.00 N 883 7.00 C 3653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 89 " 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=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 158.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1294 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 9 sheets defined 47.6% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 29 through 56 removed outlier: 3.504A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 90 Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 97 through 132 removed outlier: 3.543A pdb=" N SER A 105 " --> pdb=" O CYS A 101 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 160 removed outlier: 3.739A pdb=" N GLY A 157 " --> pdb=" O TRP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 204 through 244 Processing helix chain 'A' and resid 247 through 267 removed outlier: 3.600A pdb=" N VAL A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 306 Processing helix chain 'A' and resid 309 through 326 removed outlier: 4.218A pdb=" N LYS A 320 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 340 Processing helix chain 'A' and resid 1238 through 1253 Processing helix chain 'A' and resid 1253 through 1268 Processing helix chain 'A' and resid 1273 through 1291 Proline residue: A1285 - end of helix Processing helix chain 'A' and resid 1293 through 1305 Proline residue: A1299 - end of helix removed outlier: 3.848A pdb=" N TYR A1302 " --> pdb=" O ASN A1298 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A1303 " --> pdb=" O PRO A1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.785A pdb=" N THR C 94 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.874A pdb=" N TRP C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 removed outlier: 4.154A pdb=" N VAL D 98 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171 removed outlier: 3.681A pdb=" N VAL B 91 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET B 33 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY B 49 " --> pdb=" O MET B 33 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP B 35 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 171 removed outlier: 3.690A pdb=" N TYR B 92 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.609A pdb=" N THR B 67 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA5, first strand: chain 'C' and resid 20 through 23 Processing sheet with id=AA6, first strand: chain 'C' and resid 61 through 63 removed outlier: 6.760A pdb=" N TRP C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TYR C 53 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 14 removed outlier: 3.540A pdb=" N TYR D 87 " --> pdb=" O THR D 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 47 through 49 removed outlier: 6.515A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 888 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: 0.66 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1041 1.33 - 1.45: 1495 1.45 - 1.57: 3122 1.57 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 5697 Sorted by residual: bond pdb=" C17 LSN A1401 " pdb="CL LSN A1401 " ideal model delta sigma weight residual 1.717 1.783 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C15 LSN A1401 " pdb=" N5 LSN A1401 " ideal model delta sigma weight residual 1.379 1.317 0.062 2.00e-02 2.50e+03 9.70e+00 bond pdb=" N1 LSN A1401 " pdb=" N2 LSN A1401 " ideal model delta sigma weight residual 1.290 1.352 -0.062 2.00e-02 2.50e+03 9.46e+00 bond pdb=" C1 LSN A1401 " pdb=" C2 LSN A1401 " ideal model delta sigma weight residual 1.466 1.525 -0.059 2.00e-02 2.50e+03 8.74e+00 bond pdb=" C7 LSN A1401 " pdb=" C8 LSN A1401 " ideal model delta sigma weight residual 1.479 1.531 -0.052 2.00e-02 2.50e+03 6.64e+00 ... (remaining 5692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 7563 1.31 - 2.62: 151 2.62 - 3.93: 25 3.93 - 5.25: 16 5.25 - 6.56: 3 Bond angle restraints: 7758 Sorted by residual: angle pdb=" N VAL C 67 " pdb=" CA VAL C 67 " pdb=" C VAL C 67 " ideal model delta sigma weight residual 113.20 109.56 3.64 9.60e-01 1.09e+00 1.44e+01 angle pdb=" N2 LSN A1401 " pdb=" N3 LSN A1401 " pdb=" N4 LSN A1401 " ideal model delta sigma weight residual 114.47 107.91 6.56 3.00e+00 1.11e-01 4.78e+00 angle pdb=" CA LEU A 161 " pdb=" C LEU A 161 " pdb=" N PRO A 162 " ideal model delta sigma weight residual 118.44 121.90 -3.46 1.59e+00 3.96e-01 4.73e+00 angle pdb=" N LEU A 161 " pdb=" CA LEU A 161 " pdb=" C LEU A 161 " ideal model delta sigma weight residual 109.81 114.50 -4.69 2.21e+00 2.05e-01 4.51e+00 angle pdb=" C1 LSN A1401 " pdb=" N4 LSN A1401 " pdb=" N3 LSN A1401 " ideal model delta sigma weight residual 101.68 108.00 -6.32 3.00e+00 1.11e-01 4.44e+00 ... (remaining 7753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.31: 3229 15.31 - 30.62: 171 30.62 - 45.92: 46 45.92 - 61.23: 15 61.23 - 76.54: 2 Dihedral angle restraints: 3463 sinusoidal: 1450 harmonic: 2013 Sorted by residual: dihedral pdb=" CA ASP D 71 " pdb=" CB ASP D 71 " pdb=" CG ASP D 71 " pdb=" OD1 ASP D 71 " ideal model delta sinusoidal sigma weight residual -30.00 -86.19 56.19 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" N LEU A 191 " pdb=" CA LEU A 191 " pdb=" CB LEU A 191 " pdb=" CG LEU A 191 " ideal model delta sinusoidal sigma weight residual -180.00 -121.97 -58.03 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA LYS A 329 " pdb=" CB LYS A 329 " pdb=" CG LYS A 329 " pdb=" CD LYS A 329 " ideal model delta sinusoidal sigma weight residual 180.00 122.04 57.96 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 561 0.029 - 0.059: 214 0.059 - 0.088: 73 0.088 - 0.118: 35 0.118 - 0.147: 3 Chirality restraints: 886 Sorted by residual: chirality pdb=" CA ILE D 49 " pdb=" N ILE D 49 " pdb=" C ILE D 49 " pdb=" CB ILE D 49 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE D 76 " pdb=" N ILE D 76 " pdb=" C ILE D 76 " pdb=" CB ILE D 76 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE A1238 " pdb=" N ILE A1238 " pdb=" C ILE A1238 " pdb=" CB ILE A1238 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 883 not shown) Planarity restraints: 936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 108 " -0.029 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO C 109 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 109 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 109 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 94 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO A 95 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 44 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO D 45 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 45 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 45 " -0.018 5.00e-02 4.00e+02 ... (remaining 933 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 944 2.77 - 3.30: 5341 3.30 - 3.83: 9272 3.83 - 4.37: 11071 4.37 - 4.90: 19655 Nonbonded interactions: 46283 Sorted by model distance: nonbonded pdb=" OE1 GLN A 296 " pdb=" OG1 THR A 322 " model vdw 2.233 3.040 nonbonded pdb=" OG SER C 55 " pdb=" OH TYR C 104 " model vdw 2.266 3.040 nonbonded pdb=" O TYR D 50 " pdb=" OH TYR D 92 " model vdw 2.274 3.040 nonbonded pdb=" O GLY A 196 " pdb=" ND2 ASN A 200 " model vdw 2.286 3.120 nonbonded pdb=" N ASN B 98 " pdb=" OD1 ASN B 98 " model vdw 2.290 3.120 ... (remaining 46278 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: 2.690 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.910 Find NCS groups from input model: 0.020 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:0.920 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.003 0.066 5701 Z= 0.164 Angle : 0.512 6.558 7766 Z= 0.254 Chirality : 0.038 0.147 886 Planarity : 0.003 0.043 936 Dihedral : 10.650 76.538 2157 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.37 % Allowed : 6.51 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.13 (0.34), residues: 665 helix: 1.55 (0.31), residues: 301 sheet: -1.19 (0.45), residues: 145 loop : -0.96 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 126 TYR 0.014 0.001 TYR D 92 PHE 0.014 0.001 PHE A 286 TRP 0.015 0.001 TRP A 232 HIS 0.002 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 5697) covalent geometry : angle 0.51047 ( 7758) SS BOND : bond 0.00159 ( 4) SS BOND : angle 1.19482 ( 8) hydrogen bonds : bond 0.16733 ( 302) hydrogen bonds : angle 6.75640 ( 888) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.197 Fit side-chains REVERT: A 101 CYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8204 (t) REVERT: A 216 THR cc_start: 0.8026 (m) cc_final: 0.7790 (m) REVERT: A 237 ASP cc_start: 0.7034 (m-30) cc_final: 0.6777 (m-30) REVERT: A 283 MET cc_start: 0.7985 (tpp) cc_final: 0.7640 (tpt) REVERT: D 5 MET cc_start: 0.8516 (mmm) cc_final: 0.7920 (mmt) REVERT: D 110 ARG cc_start: 0.5481 (mtt180) cc_final: 0.3055 (ptt-90) outliers start: 8 outliers final: 6 residues processed: 82 average time/residue: 0.0618 time to fit residues: 7.0187 Evaluate side-chains 73 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 125 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.0270 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0370 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A1235 ASN D 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.183241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144480 restraints weight = 5970.141| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.07 r_work: 0.3423 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5701 Z= 0.114 Angle : 0.483 4.937 7766 Z= 0.250 Chirality : 0.039 0.148 886 Planarity : 0.004 0.045 936 Dihedral : 6.470 63.209 968 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.23 % Allowed : 8.73 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.43 (0.34), residues: 665 helix: 1.88 (0.30), residues: 305 sheet: -1.19 (0.43), residues: 153 loop : -0.86 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 93 TYR 0.012 0.001 TYR D 50 PHE 0.013 0.001 PHE A 286 TRP 0.015 0.001 TRP A 232 HIS 0.003 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 5697) covalent geometry : angle 0.48202 ( 7758) SS BOND : bond 0.00182 ( 4) SS BOND : angle 1.06302 ( 8) hydrogen bonds : bond 0.04334 ( 302) hydrogen bonds : angle 4.51451 ( 888) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.137 Fit side-chains REVERT: A 101 CYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8441 (t) REVERT: A 168 ASN cc_start: 0.8200 (m-40) cc_final: 0.7926 (m-40) REVERT: A 200 ASN cc_start: 0.8028 (m-40) cc_final: 0.7739 (m-40) REVERT: A 216 THR cc_start: 0.7906 (m) cc_final: 0.7681 (m) REVERT: A 237 ASP cc_start: 0.6898 (m-30) cc_final: 0.6590 (m-30) REVERT: A 283 MET cc_start: 0.7919 (tpp) cc_final: 0.7576 (tpt) REVERT: B 103 SER cc_start: 0.7626 (t) cc_final: 0.6981 (p) REVERT: D 110 ARG cc_start: 0.5470 (mtt180) cc_final: 0.2927 (ptt-90) outliers start: 13 outliers final: 7 residues processed: 77 average time/residue: 0.0575 time to fit residues: 6.2225 Evaluate side-chains 70 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 296 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.181259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.142422 restraints weight = 5933.262| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.14 r_work: 0.3466 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5701 Z= 0.143 Angle : 0.505 7.473 7766 Z= 0.256 Chirality : 0.039 0.143 886 Planarity : 0.004 0.044 936 Dihedral : 6.370 58.245 964 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.57 % Allowed : 9.25 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.42 (0.34), residues: 665 helix: 1.86 (0.30), residues: 304 sheet: -1.18 (0.43), residues: 153 loop : -0.82 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 90 TYR 0.015 0.001 TYR D 50 PHE 0.015 0.001 PHE A 286 TRP 0.014 0.001 TRP A 232 HIS 0.003 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5697) covalent geometry : angle 0.50316 ( 7758) SS BOND : bond 0.00172 ( 4) SS BOND : angle 1.27377 ( 8) hydrogen bonds : bond 0.04285 ( 302) hydrogen bonds : angle 4.30400 ( 888) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.215 Fit side-chains REVERT: A 100 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7529 (mp) REVERT: A 168 ASN cc_start: 0.8102 (m-40) cc_final: 0.7841 (m-40) REVERT: A 216 THR cc_start: 0.8189 (m) cc_final: 0.7932 (m) REVERT: A 237 ASP cc_start: 0.7124 (m-30) cc_final: 0.6908 (m-30) REVERT: A 283 MET cc_start: 0.7935 (tpp) cc_final: 0.7653 (tpt) REVERT: D 77 SER cc_start: 0.7776 (m) cc_final: 0.7323 (p) REVERT: D 110 ARG cc_start: 0.5787 (mtt180) cc_final: 0.3369 (ptt-90) outliers start: 15 outliers final: 13 residues processed: 77 average time/residue: 0.0625 time to fit residues: 6.7519 Evaluate side-chains 79 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 57 optimal weight: 0.0030 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 296 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.181495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.142483 restraints weight = 5986.926| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.15 r_work: 0.3377 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5701 Z= 0.138 Angle : 0.492 6.353 7766 Z= 0.251 Chirality : 0.039 0.140 886 Planarity : 0.004 0.044 936 Dihedral : 6.299 58.580 963 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.40 % Allowed : 9.93 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.46 (0.34), residues: 665 helix: 1.88 (0.30), residues: 304 sheet: -1.14 (0.44), residues: 145 loop : -0.84 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 93 TYR 0.014 0.001 TYR D 50 PHE 0.015 0.001 PHE A 286 TRP 0.014 0.001 TRP A 232 HIS 0.002 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5697) covalent geometry : angle 0.49088 ( 7758) SS BOND : bond 0.00170 ( 4) SS BOND : angle 1.17565 ( 8) hydrogen bonds : bond 0.04131 ( 302) hydrogen bonds : angle 4.16281 ( 888) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.215 Fit side-chains REVERT: A 100 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7259 (mp) REVERT: A 168 ASN cc_start: 0.8308 (m-40) cc_final: 0.7943 (m-40) REVERT: A 200 ASN cc_start: 0.8072 (m-40) cc_final: 0.7806 (m-40) REVERT: A 216 THR cc_start: 0.7902 (m) cc_final: 0.7656 (m) REVERT: A 237 ASP cc_start: 0.7003 (m-30) cc_final: 0.6678 (m-30) REVERT: A 283 MET cc_start: 0.7865 (tpp) cc_final: 0.7499 (tpt) REVERT: D 77 SER cc_start: 0.7819 (m) cc_final: 0.7258 (p) REVERT: D 110 ARG cc_start: 0.5486 (mtt180) cc_final: 0.2921 (ptt-90) outliers start: 14 outliers final: 11 residues processed: 80 average time/residue: 0.0602 time to fit residues: 6.9073 Evaluate side-chains 80 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 52 optimal weight: 0.0470 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A1295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.182236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143329 restraints weight = 6064.252| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.21 r_work: 0.3416 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5701 Z= 0.116 Angle : 0.470 5.608 7766 Z= 0.240 Chirality : 0.038 0.143 886 Planarity : 0.003 0.046 936 Dihedral : 6.028 58.077 959 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.74 % Allowed : 10.62 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.65 (0.34), residues: 665 helix: 2.04 (0.30), residues: 304 sheet: -1.04 (0.43), residues: 145 loop : -0.76 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 93 TYR 0.012 0.001 TYR D 50 PHE 0.013 0.001 PHE A 286 TRP 0.013 0.001 TRP A 232 HIS 0.002 0.001 HIS A1256 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 5697) covalent geometry : angle 0.46918 ( 7758) SS BOND : bond 0.00158 ( 4) SS BOND : angle 1.07422 ( 8) hydrogen bonds : bond 0.03896 ( 302) hydrogen bonds : angle 4.00818 ( 888) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.252 Fit side-chains REVERT: A 100 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7489 (mp) REVERT: A 101 CYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8255 (t) REVERT: A 168 ASN cc_start: 0.8137 (m-40) cc_final: 0.7874 (m-40) REVERT: A 200 ASN cc_start: 0.8105 (m-40) cc_final: 0.7789 (m-40) REVERT: A 216 THR cc_start: 0.8118 (m) cc_final: 0.7856 (m) REVERT: A 237 ASP cc_start: 0.7085 (m-30) cc_final: 0.6849 (m-30) REVERT: A 283 MET cc_start: 0.7913 (tpp) cc_final: 0.7610 (tpt) REVERT: A 1293 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.6810 (m-80) REVERT: D 77 SER cc_start: 0.7777 (m) cc_final: 0.7298 (p) REVERT: D 110 ARG cc_start: 0.5710 (mtt180) cc_final: 0.3254 (ptt-90) outliers start: 16 outliers final: 11 residues processed: 79 average time/residue: 0.0677 time to fit residues: 7.3746 Evaluate side-chains 81 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 1293 PHE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 62 optimal weight: 0.0670 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 23 optimal weight: 0.0570 chunk 51 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.182414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.143465 restraints weight = 5975.872| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.19 r_work: 0.3445 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5701 Z= 0.107 Angle : 0.476 9.644 7766 Z= 0.237 Chirality : 0.038 0.143 886 Planarity : 0.003 0.046 936 Dihedral : 5.969 58.489 959 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.08 % Allowed : 10.96 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.71 (0.34), residues: 665 helix: 2.10 (0.30), residues: 305 sheet: -0.98 (0.43), residues: 145 loop : -0.79 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 93 TYR 0.011 0.001 TYR D 50 PHE 0.013 0.001 PHE A 286 TRP 0.014 0.001 TRP A 232 HIS 0.002 0.001 HIS A1256 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 5697) covalent geometry : angle 0.47509 ( 7758) SS BOND : bond 0.00158 ( 4) SS BOND : angle 1.00453 ( 8) hydrogen bonds : bond 0.03736 ( 302) hydrogen bonds : angle 3.89722 ( 888) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.201 Fit side-chains REVERT: A 51 ILE cc_start: 0.8205 (mt) cc_final: 0.7688 (mp) REVERT: A 55 PHE cc_start: 0.7494 (m-10) cc_final: 0.7144 (m-10) REVERT: A 100 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7509 (mp) REVERT: A 101 CYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8231 (t) REVERT: A 216 THR cc_start: 0.8136 (m) cc_final: 0.7846 (m) REVERT: A 237 ASP cc_start: 0.7088 (m-30) cc_final: 0.6859 (m-30) REVERT: A 283 MET cc_start: 0.7903 (tpp) cc_final: 0.7657 (tpt) REVERT: A 339 ASP cc_start: 0.7272 (t0) cc_final: 0.6919 (t70) REVERT: A 1243 MET cc_start: 0.8002 (tpt) cc_final: 0.7581 (ttm) REVERT: A 1293 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.6787 (m-80) REVERT: D 5 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7537 (mmt) REVERT: D 77 SER cc_start: 0.7764 (m) cc_final: 0.7291 (p) REVERT: D 110 ARG cc_start: 0.5830 (mtt180) cc_final: 0.3336 (ptt-90) outliers start: 18 outliers final: 12 residues processed: 78 average time/residue: 0.0629 time to fit residues: 6.8171 Evaluate side-chains 82 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 1293 PHE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 57 optimal weight: 0.0870 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.0020 chunk 14 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.3166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.182783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143918 restraints weight = 6064.454| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.21 r_work: 0.3397 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5701 Z= 0.101 Angle : 0.451 4.983 7766 Z= 0.230 Chirality : 0.038 0.143 886 Planarity : 0.003 0.047 936 Dihedral : 5.951 59.709 959 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.42 % Allowed : 11.30 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.81 (0.34), residues: 665 helix: 2.17 (0.30), residues: 305 sheet: -0.75 (0.43), residues: 141 loop : -0.88 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 93 TYR 0.011 0.001 TYR D 50 PHE 0.012 0.001 PHE A 286 TRP 0.014 0.001 TRP A 232 HIS 0.002 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 5697) covalent geometry : angle 0.45003 ( 7758) SS BOND : bond 0.00161 ( 4) SS BOND : angle 1.00235 ( 8) hydrogen bonds : bond 0.03644 ( 302) hydrogen bonds : angle 3.83915 ( 888) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.211 Fit side-chains REVERT: A 51 ILE cc_start: 0.8105 (mt) cc_final: 0.7584 (mp) REVERT: A 55 PHE cc_start: 0.7485 (m-10) cc_final: 0.7111 (m-10) REVERT: A 100 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7440 (mp) REVERT: A 101 CYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8238 (t) REVERT: A 216 THR cc_start: 0.8106 (m) cc_final: 0.7827 (m) REVERT: A 237 ASP cc_start: 0.7052 (m-30) cc_final: 0.6803 (m-30) REVERT: A 283 MET cc_start: 0.7886 (tpp) cc_final: 0.7627 (tpt) REVERT: A 1243 MET cc_start: 0.7955 (tpt) cc_final: 0.7623 (ttm) REVERT: D 5 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7433 (mmt) REVERT: D 77 SER cc_start: 0.7763 (m) cc_final: 0.7270 (p) REVERT: D 110 ARG cc_start: 0.5701 (mtt180) cc_final: 0.3251 (ptt-90) outliers start: 20 outliers final: 12 residues processed: 76 average time/residue: 0.0678 time to fit residues: 6.9543 Evaluate side-chains 77 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 30 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.180216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140921 restraints weight = 5973.651| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.19 r_work: 0.3352 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5701 Z= 0.148 Angle : 0.507 9.579 7766 Z= 0.255 Chirality : 0.040 0.137 886 Planarity : 0.004 0.046 936 Dihedral : 6.067 59.173 959 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.08 % Allowed : 11.99 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.60 (0.34), residues: 665 helix: 2.01 (0.30), residues: 304 sheet: -0.98 (0.43), residues: 145 loop : -0.88 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 41 TYR 0.016 0.001 TYR D 50 PHE 0.015 0.001 PHE A 286 TRP 0.011 0.001 TRP A 232 HIS 0.004 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5697) covalent geometry : angle 0.50541 ( 7758) SS BOND : bond 0.00197 ( 4) SS BOND : angle 1.24316 ( 8) hydrogen bonds : bond 0.04047 ( 302) hydrogen bonds : angle 3.98063 ( 888) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.199 Fit side-chains REVERT: A 55 PHE cc_start: 0.7486 (m-10) cc_final: 0.7100 (m-10) REVERT: A 100 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7482 (mp) REVERT: A 168 ASN cc_start: 0.8165 (m-40) cc_final: 0.7797 (m-40) REVERT: A 237 ASP cc_start: 0.7131 (m-30) cc_final: 0.6873 (m-30) REVERT: A 283 MET cc_start: 0.7905 (tpp) cc_final: 0.7639 (tpt) REVERT: A 1243 MET cc_start: 0.8017 (tpt) cc_final: 0.7610 (ttm) REVERT: A 1293 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.6814 (m-80) REVERT: D 5 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7551 (mmt) REVERT: D 77 SER cc_start: 0.7785 (m) cc_final: 0.7265 (p) REVERT: D 110 ARG cc_start: 0.5682 (mtt180) cc_final: 0.3218 (ptt-90) outliers start: 18 outliers final: 14 residues processed: 78 average time/residue: 0.0710 time to fit residues: 7.5365 Evaluate side-chains 81 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 1293 PHE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 7 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 61 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 296 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.181041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.141795 restraints weight = 6042.305| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.22 r_work: 0.3362 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5701 Z= 0.122 Angle : 0.477 5.009 7766 Z= 0.244 Chirality : 0.039 0.141 886 Planarity : 0.003 0.047 936 Dihedral : 6.061 59.678 959 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.42 % Allowed : 12.33 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.68 (0.34), residues: 665 helix: 2.06 (0.30), residues: 304 sheet: -0.81 (0.43), residues: 141 loop : -0.94 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 93 TYR 0.013 0.001 TYR D 50 PHE 0.014 0.001 PHE A 286 TRP 0.013 0.001 TRP A 232 HIS 0.014 0.002 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5697) covalent geometry : angle 0.47572 ( 7758) SS BOND : bond 0.00169 ( 4) SS BOND : angle 1.13754 ( 8) hydrogen bonds : bond 0.03888 ( 302) hydrogen bonds : angle 3.88678 ( 888) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.203 Fit side-chains REVERT: A 51 ILE cc_start: 0.8091 (mt) cc_final: 0.7575 (mp) REVERT: A 55 PHE cc_start: 0.7492 (m-10) cc_final: 0.7115 (m-10) REVERT: A 100 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7467 (mp) REVERT: A 101 CYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8268 (t) REVERT: A 237 ASP cc_start: 0.7057 (m-30) cc_final: 0.6791 (m-30) REVERT: A 283 MET cc_start: 0.7878 (tpp) cc_final: 0.7608 (tpt) REVERT: A 339 ASP cc_start: 0.7263 (t0) cc_final: 0.6868 (t70) REVERT: A 1243 MET cc_start: 0.8005 (tpt) cc_final: 0.7616 (ttm) REVERT: A 1293 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.6792 (m-80) REVERT: D 5 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7467 (mmt) REVERT: D 77 SER cc_start: 0.7758 (m) cc_final: 0.7241 (p) REVERT: D 110 ARG cc_start: 0.5681 (mtt180) cc_final: 0.3221 (ptt-90) outliers start: 20 outliers final: 14 residues processed: 78 average time/residue: 0.0718 time to fit residues: 7.6672 Evaluate side-chains 82 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 1293 PHE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 52 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.180916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141561 restraints weight = 6072.474| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.23 r_work: 0.3364 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5701 Z= 0.129 Angle : 0.476 5.030 7766 Z= 0.245 Chirality : 0.039 0.139 886 Planarity : 0.003 0.047 936 Dihedral : 6.079 59.657 959 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.42 % Allowed : 11.99 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.65 (0.34), residues: 665 helix: 2.04 (0.30), residues: 304 sheet: -0.91 (0.43), residues: 143 loop : -0.87 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 41 TYR 0.014 0.001 TYR D 50 PHE 0.014 0.001 PHE A 286 TRP 0.013 0.001 TRP A 232 HIS 0.002 0.001 HIS A1256 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5697) covalent geometry : angle 0.47494 ( 7758) SS BOND : bond 0.00179 ( 4) SS BOND : angle 1.14884 ( 8) hydrogen bonds : bond 0.03904 ( 302) hydrogen bonds : angle 3.90610 ( 888) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.223 Fit side-chains REVERT: A 51 ILE cc_start: 0.8015 (mt) cc_final: 0.7511 (mp) REVERT: A 55 PHE cc_start: 0.7515 (m-10) cc_final: 0.7164 (m-10) REVERT: A 57 MET cc_start: 0.6828 (ttt) cc_final: 0.6606 (tmm) REVERT: A 100 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7378 (mp) REVERT: A 101 CYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8295 (t) REVERT: A 237 ASP cc_start: 0.6987 (m-30) cc_final: 0.6705 (m-30) REVERT: A 282 GLU cc_start: 0.6019 (OUTLIER) cc_final: 0.4209 (tm-30) REVERT: A 283 MET cc_start: 0.7862 (tpp) cc_final: 0.7489 (tpt) REVERT: A 1243 MET cc_start: 0.7947 (tpt) cc_final: 0.7555 (ttm) REVERT: A 1293 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.6723 (m-80) REVERT: D 5 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.7499 (mmt) REVERT: D 110 ARG cc_start: 0.5603 (mtt180) cc_final: 0.3148 (ptt-90) outliers start: 20 outliers final: 14 residues processed: 80 average time/residue: 0.0710 time to fit residues: 7.6086 Evaluate side-chains 83 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 1293 PHE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 26 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 296 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.180380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.141068 restraints weight = 5954.124| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.18 r_work: 0.3356 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5701 Z= 0.141 Angle : 0.488 5.073 7766 Z= 0.251 Chirality : 0.040 0.138 886 Planarity : 0.004 0.047 936 Dihedral : 6.117 59.704 959 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.60 % Allowed : 12.16 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.61 (0.34), residues: 665 helix: 1.99 (0.30), residues: 304 sheet: -0.91 (0.43), residues: 143 loop : -0.89 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 323 TYR 0.015 0.001 TYR D 50 PHE 0.015 0.001 PHE A 286 TRP 0.013 0.001 TRP A 232 HIS 0.007 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 5697) covalent geometry : angle 0.48702 ( 7758) SS BOND : bond 0.00185 ( 4) SS BOND : angle 1.20639 ( 8) hydrogen bonds : bond 0.04007 ( 302) hydrogen bonds : angle 3.95756 ( 888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1613.47 seconds wall clock time: 28 minutes 24.15 seconds (1704.15 seconds total)