Starting phenix.real_space_refine on Fri Sep 11 23:07:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5a8l_3099/09_2026/5a8l_3099.cif Found real_map, /net/cci-nas-00/data/ceres_data/5a8l_3099/09_2026/5a8l_3099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5a8l_3099/09_2026/5a8l_3099.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5a8l_3099/09_2026/5a8l_3099.cif" model { file = "/net/cci-nas-00/data/ceres_data/5a8l_3099/09_2026/5a8l_3099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5a8l_3099/09_2026/5a8l_3099.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5a8l_3099/09_2026/5a8l_3099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5a8l_3099/09_2026/5a8l_3099.map" } resolution = 3.8 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 346 5.49 5 S 18 5.16 5 C 6380 2.51 5 N 2189 2.21 5 O 3331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12264 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 5401 Classifications: {'RNAv2': 253} Modifications used: {'rna2p_pur': 24, 'rna2p_pyr': 18, 'rna3p_pur': 112, 'rna3p_pyr': 99} Link IDs: {'rna2p': 42, 'rna3p': 210} Chain breaks: 18 Chain: "B" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1423 Classifications: {'RNAv2': 67} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 27, 'rna3p_pyr': 27} Link IDs: {'rna2p': 13, 'rna3p': 53} Chain breaks: 7 Chain: "D" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 179 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "G" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1046 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 6, 'TRANS': 131} Chain: "H" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 88 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "P" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 382 Classifications: {'RNAv2': 18} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 8} Link IDs: {'rna3p': 17} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3410 Classifications: {'peptide': 431} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 421} Chain: "R" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 190 Classifications: {'RNAv2': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 6} Chain: "Z" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 145 Classifications: {'peptide': 22} Incomplete info: {'backbone_only': 6} Link IDs: {'PTRANS': 3, 'TRANS': 18} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.62, per 1000 atoms: 0.21 Number of scatterers: 12264 At special positions: 0 Unit cell: (181.602, 107.262, 139.122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 346 15.00 O 3331 8.00 N 2189 7.00 C 6380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 340.7 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 6 sheets defined 40.4% alpha, 6.7% beta 59 base pairs and 158 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'G' and resid 44 through 51 removed outlier: 3.711A pdb=" N LYS G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 84 removed outlier: 3.557A pdb=" N ILE G 81 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA G 84 " --> pdb=" O ILE G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 114 Processing helix chain 'G' and resid 115 through 119 removed outlier: 4.108A pdb=" N HIS G 118 " --> pdb=" O GLN G 115 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG G 119 " --> pdb=" O MET G 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 115 through 119' Processing helix chain 'G' and resid 127 through 132 removed outlier: 3.844A pdb=" N ILE G 132 " --> pdb=" O THR G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 139 removed outlier: 3.506A pdb=" N ALA G 136 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN G 137 " --> pdb=" O GLY G 134 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER G 138 " --> pdb=" O THR G 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 27 removed outlier: 3.561A pdb=" N ASN Q 11 " --> pdb=" O ALA Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 59 removed outlier: 3.991A pdb=" N VAL Q 48 " --> pdb=" O GLN Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 83 removed outlier: 3.503A pdb=" N LEU Q 69 " --> pdb=" O ARG Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 141 removed outlier: 4.158A pdb=" N ALA Q 138 " --> pdb=" O GLU Q 134 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU Q 139 " --> pdb=" O ALA Q 135 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER Q 141 " --> pdb=" O THR Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 186 through 213 removed outlier: 4.148A pdb=" N PHE Q 190 " --> pdb=" O SER Q 186 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL Q 205 " --> pdb=" O TYR Q 201 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA Q 206 " --> pdb=" O VAL Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 231 through 238 removed outlier: 3.601A pdb=" N GLN Q 238 " --> pdb=" O THR Q 234 " (cutoff:3.500A) Processing helix chain 'Q' and resid 245 through 250 removed outlier: 3.584A pdb=" N VAL Q 250 " --> pdb=" O GLN Q 247 " (cutoff:3.500A) Processing helix chain 'Q' and resid 259 through 296 removed outlier: 3.926A pdb=" N GLU Q 269 " --> pdb=" O ASN Q 265 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR Q 290 " --> pdb=" O LEU Q 286 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN Q 296 " --> pdb=" O ASP Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 314 removed outlier: 4.060A pdb=" N LYS Q 310 " --> pdb=" O GLU Q 306 " (cutoff:3.500A) Processing helix chain 'Q' and resid 347 through 354 Processing helix chain 'Q' and resid 355 through 357 No H-bonds generated for 'chain 'Q' and resid 355 through 357' Processing helix chain 'Q' and resid 373 through 380 Processing helix chain 'Q' and resid 396 through 405 removed outlier: 3.701A pdb=" N GLN Q 401 " --> pdb=" O GLN Q 397 " (cutoff:3.500A) Processing helix chain 'Q' and resid 421 through 436 removed outlier: 3.852A pdb=" N GLN Q 425 " --> pdb=" O GLY Q 421 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE Q 432 " --> pdb=" O ASP Q 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 20 removed outlier: 3.922A pdb=" N LEU Z 14 " --> pdb=" O LYS Z 10 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU Z 15 " --> pdb=" O LEU Z 11 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=QA, first strand: chain 'Q' and resid 35 through 39 Processing sheet with id=QB, first strand: chain 'Q' and resid 101 through 102 Processing sheet with id=QC, first strand: chain 'Q' and resid 148 through 151 removed outlier: 6.823A pdb=" N ALA Q 156 " --> pdb=" O LYS Q 171 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS Q 171 " --> pdb=" O ALA Q 156 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE Q 158 " --> pdb=" O LEU Q 169 " (cutoff:3.500A) Processing sheet with id=QD, first strand: chain 'Q' and resid 302 through 303 Processing sheet with id=QE, first strand: chain 'Q' and resid 332 through 334 171 hydrogen bonds defined for protein. 474 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 59 basepair parallelities 158 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2578 1.34 - 1.46: 4702 1.46 - 1.58: 5215 1.58 - 1.69: 664 1.69 - 1.81: 29 Bond restraints: 13188 Sorted by residual: bond pdb=" CA PRO Q 40 " pdb=" C PRO Q 40 " ideal model delta sigma weight residual 1.514 1.561 -0.047 5.50e-03 3.31e+04 7.21e+01 bond pdb=" CA PRO Q 89 " pdb=" C PRO Q 89 " ideal model delta sigma weight residual 1.514 1.555 -0.041 5.50e-03 3.31e+04 5.54e+01 bond pdb=" CA PRO G 88 " pdb=" C PRO G 88 " ideal model delta sigma weight residual 1.517 1.585 -0.068 9.30e-03 1.16e+04 5.30e+01 bond pdb=" CA PRO Z 21 " pdb=" C PRO Z 21 " ideal model delta sigma weight residual 1.517 1.573 -0.056 9.30e-03 1.16e+04 3.66e+01 bond pdb=" CA ILE Z 20 " pdb=" CB ILE Z 20 " ideal model delta sigma weight residual 1.539 1.564 -0.025 5.40e-03 3.43e+04 2.12e+01 ... (remaining 13183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 17586 1.61 - 3.21: 1498 3.21 - 4.82: 282 4.82 - 6.43: 39 6.43 - 8.04: 11 Bond angle restraints: 19416 Sorted by residual: angle pdb=" C VAL Q 88 " pdb=" N PRO Q 89 " pdb=" CA PRO Q 89 " ideal model delta sigma weight residual 119.66 126.82 -7.16 7.30e-01 1.88e+00 9.62e+01 angle pdb=" C ILE Q 39 " pdb=" N PRO Q 40 " pdb=" CA PRO Q 40 " ideal model delta sigma weight residual 119.66 126.53 -6.87 7.30e-01 1.88e+00 8.85e+01 angle pdb=" C VAL G 74 " pdb=" N PRO G 75 " pdb=" CA PRO G 75 " ideal model delta sigma weight residual 119.78 127.63 -7.85 1.03e+00 9.43e-01 5.81e+01 angle pdb=" C LEU Q 176 " pdb=" N PRO Q 177 " pdb=" CA PRO Q 177 " ideal model delta sigma weight residual 119.28 126.36 -7.08 1.10e+00 8.26e-01 4.14e+01 angle pdb=" C PRO Q 40 " pdb=" N PRO Q 41 " pdb=" CA PRO Q 41 " ideal model delta sigma weight residual 119.78 125.89 -6.11 1.03e+00 9.43e-01 3.52e+01 ... (remaining 19411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.16: 6391 32.16 - 64.31: 633 64.31 - 96.47: 62 96.47 - 128.63: 0 128.63 - 160.78: 1 Dihedral angle restraints: 7087 sinusoidal: 5322 harmonic: 1765 Sorted by residual: dihedral pdb=" C4' A A3878 " pdb=" C3' A A3878 " pdb=" C2' A A3878 " pdb=" C1' A A3878 " ideal model delta sinusoidal sigma weight residual 36.34 -36.19 72.53 1 3.10e+00 1.04e-01 6.99e+02 dihedral pdb=" C4' C B1247 " pdb=" C3' C B1247 " pdb=" C2' C B1247 " pdb=" C1' C B1247 " ideal model delta sinusoidal sigma weight residual 36.35 -36.11 72.46 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" C4' A A4412 " pdb=" C3' A A4412 " pdb=" C2' A A4412 " pdb=" C1' A A4412 " ideal model delta sinusoidal sigma weight residual 36.35 -35.95 72.29 1 3.10e+00 1.04e-01 6.95e+02 ... (remaining 7084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1944 0.081 - 0.161: 68 0.161 - 0.242: 343 0.242 - 0.322: 117 0.322 - 0.403: 1 Chirality restraints: 2473 Sorted by residual: chirality pdb=" P A A3731 " pdb=" OP1 A A3731 " pdb=" OP2 A A3731 " pdb=" O5' A A3731 " both_signs ideal model delta sigma weight residual True 2.17 -2.58 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" C2' U A3730 " pdb=" C3' U A3730 " pdb=" O2' U A3730 " pdb=" C1' U A3730 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C2' A B 628 " pdb=" C3' A B 628 " pdb=" O2' A B 628 " pdb=" C1' A B 628 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2470 not shown) Planarity restraints: 1204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE Z 20 " 0.043 5.00e-02 4.00e+02 6.24e-02 6.22e+00 pdb=" N PRO Z 21 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO Z 21 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO Z 21 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR Q 347 " -0.035 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO Q 348 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO Q 348 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO Q 348 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 87 " -0.026 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO G 88 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO G 88 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 88 " -0.020 5.00e-02 4.00e+02 ... (remaining 1201 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 3 2.13 - 2.82: 3352 2.82 - 3.51: 14928 3.51 - 4.21: 33002 4.21 - 4.90: 45121 Nonbonded interactions: 96406 Sorted by model distance: nonbonded pdb=" O3' A P 76 " pdb=" C PRO Z 22 " model vdw 1.435 3.270 nonbonded pdb=" O SER Z 13 " pdb=" OG1 THR Z 16 " model vdw 1.901 3.040 nonbonded pdb=" O LEU Z 15 " pdb=" CD LYS Z 18 " model vdw 2.044 3.440 nonbonded pdb=" O ALA Z 8 " pdb=" CB SER Z 12 " model vdw 2.133 3.440 nonbonded pdb=" O GLU Q 269 " pdb=" OG1 THR Q 272 " model vdw 2.148 3.040 ... (remaining 96401 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 group one per residue 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: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 13.600 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4329 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 : 0.004 0.068 13188 Z= 0.300 Angle : 0.987 8.035 19416 Z= 0.547 Chirality : 0.108 0.403 2473 Planarity : 0.004 0.062 1204 Dihedral : 18.719 160.783 5959 Min Nonbonded Distance : 1.435 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 2.93 % Allowed : 10.26 % Favored : 86.81 % Rotamer: Outliers : 0.95 % Allowed : 1.90 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.06 (0.33), residues: 614 helix: -2.62 (0.20), residues: 211 sheet: -2.61 (0.57), residues: 70 loop : 0.01 (0.39), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 198 TYR 0.014 0.001 TYR D 139 PHE 0.015 0.001 PHE Q 242 TRP 0.004 0.001 TRP Q 377 HIS 0.005 0.001 HIS Q 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.30 (13188) covalent geometry : angle 0.98738 / 0.55 (19416) hydrogen bonds : bond 0.15562 / 7.80 ( 311) hydrogen bonds : angle 11.51911 / 4.63 ( 688) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 168 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 164 ASN cc_start: 0.3938 (t0) cc_final: 0.3716 (t0) REVERT: Z 18 LYS cc_start: 0.5523 (OUTLIER) cc_final: 0.4829 (pptt) outliers start: 5 outliers final: 2 residues processed: 173 average time/residue: 0.1379 time to fit residues: 32.5596 Evaluate side-chains 87 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 18 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 0.0170 chunk 74 optimal weight: 7.9990 overall best weight: 2.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 162 GLN Q 200 ASN ** Q 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 266 GLN ** Q 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 296 GLN ** Q 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 366 HIS Q 381 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.168472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.156319 restraints weight = 48777.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.157956 restraints weight = 22581.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.159010 restraints weight = 12996.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.159686 restraints weight = 8560.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.160107 restraints weight = 6317.040| |-----------------------------------------------------------------------------| r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5558 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 13188 Z= 0.268 Angle : 1.481 21.337 19416 Z= 0.590 Chirality : 0.126 1.387 2473 Planarity : 0.006 0.093 1204 Dihedral : 18.067 179.666 4758 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 1.63 % Allowed : 7.33 % Favored : 91.04 % Rotamer: Outliers : 4.36 % Allowed : 10.44 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.87 (0.32), residues: 614 helix: -0.99 (0.29), residues: 224 sheet: -2.33 (0.58), residues: 66 loop : -1.08 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 128 TYR 0.016 0.002 TYR D 130 PHE 0.015 0.002 PHE Q 131 TRP 0.018 0.002 TRP Q 377 HIS 0.004 0.001 HIS Q 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.27 (13188) covalent geometry : angle 1.48066 / 0.59 (19416) hydrogen bonds : bond 0.06257 / 3.18 ( 311) hydrogen bonds : angle 6.23003 / 2.50 ( 688) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.275 Fit side-chains REVERT: Q 243 ASP cc_start: 0.5714 (m-30) cc_final: 0.5446 (m-30) REVERT: Q 374 LEU cc_start: 0.6012 (tt) cc_final: 0.5529 (tt) REVERT: Z 7 SER cc_start: 0.6710 (OUTLIER) cc_final: 0.6456 (m) outliers start: 23 outliers final: 7 residues processed: 113 average time/residue: 0.1161 time to fit residues: 18.8510 Evaluate side-chains 86 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 234 THR Chi-restraints excluded: chain Q residue 266 GLN Chi-restraints excluded: chain Q residue 322 VAL Chi-restraints excluded: chain Z residue 7 SER Chi-restraints excluded: chain Z residue 10 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 75 optimal weight: 10.0000 chunk 6 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 70 GLN Q 121 ASN Q 162 GLN Q 265 ASN Q 334 HIS ** Q 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.163553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.151183 restraints weight = 48590.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.152807 restraints weight = 22634.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.153826 restraints weight = 12981.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.154553 restraints weight = 8726.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.154880 restraints weight = 6434.181| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5798 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 13188 Z= 0.230 Angle : 1.197 14.089 19416 Z= 0.492 Chirality : 0.089 0.789 2473 Planarity : 0.005 0.049 1204 Dihedral : 18.757 167.114 4750 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 1.47 % Allowed : 7.49 % Favored : 91.04 % Rotamer: Outliers : 4.36 % Allowed : 13.28 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.72 (0.32), residues: 614 helix: -0.28 (0.33), residues: 230 sheet: -2.23 (0.55), residues: 65 loop : -1.53 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 47 TYR 0.024 0.003 TYR Q 125 PHE 0.019 0.003 PHE Q 146 TRP 0.003 0.001 TRP Q 377 HIS 0.006 0.002 HIS Q 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 (13188) covalent geometry : angle 1.19746 / 0.49 (19416) hydrogen bonds : bond 0.06969 / 3.53 ( 311) hydrogen bonds : angle 5.76103 / 2.32 ( 688) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 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: 23 poor density : 85 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 161 LEU cc_start: 0.7237 (tt) cc_final: 0.6586 (mm) REVERT: Q 245 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.4768 (ptp-170) REVERT: Q 403 VAL cc_start: 0.6184 (t) cc_final: 0.5968 (t) outliers start: 23 outliers final: 10 residues processed: 95 average time/residue: 0.1082 time to fit residues: 14.9145 Evaluate side-chains 79 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain Q residue 149 ILE Chi-restraints excluded: chain Q residue 229 SER Chi-restraints excluded: chain Q residue 234 THR Chi-restraints excluded: chain Q residue 245 ARG Chi-restraints excluded: chain Q residue 317 VAL Chi-restraints excluded: chain Q residue 322 VAL Chi-restraints excluded: chain Q residue 324 GLU Chi-restraints excluded: chain Z residue 10 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 89 optimal weight: 7.9990 chunk 61 optimal weight: 30.0000 chunk 90 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 70 GLN G 95 GLN Q 266 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.158743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.147764 restraints weight = 47569.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.148583 restraints weight = 26164.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.149273 restraints weight = 18481.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.149538 restraints weight = 12999.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.149581 restraints weight = 9727.249| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13188 Z= 0.252 Angle : 1.236 14.429 19416 Z= 0.505 Chirality : 0.091 0.832 2473 Planarity : 0.005 0.051 1204 Dihedral : 19.018 169.560 4750 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 1.30 % Allowed : 7.82 % Favored : 90.88 % Rotamer: Outliers : 4.17 % Allowed : 14.61 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.92 (0.32), residues: 614 helix: -0.32 (0.32), residues: 230 sheet: -2.13 (0.50), residues: 81 loop : -1.75 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 47 TYR 0.023 0.003 TYR D 130 PHE 0.025 0.003 PHE Q 432 TRP 0.008 0.002 TRP G 53 HIS 0.008 0.002 HIS Q 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.25 (13188) covalent geometry : angle 1.23625 / 0.51 (19416) hydrogen bonds : bond 0.07107 / 3.60 ( 311) hydrogen bonds : angle 5.73713 / 2.30 ( 688) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 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: 22 poor density : 85 time to evaluate : 0.198 Fit side-chains REVERT: G 125 LEU cc_start: 0.3492 (OUTLIER) cc_final: 0.3159 (tp) REVERT: Q 199 HIS cc_start: 0.5735 (t70) cc_final: 0.5181 (t70) REVERT: Q 324 GLU cc_start: 0.5063 (OUTLIER) cc_final: 0.4595 (pt0) outliers start: 22 outliers final: 12 residues processed: 100 average time/residue: 0.1074 time to fit residues: 15.4128 Evaluate side-chains 83 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 160 THR Chi-restraints excluded: chain Q residue 229 SER Chi-restraints excluded: chain Q residue 234 THR Chi-restraints excluded: chain Q residue 314 MET Chi-restraints excluded: chain Q residue 317 VAL Chi-restraints excluded: chain Q residue 322 VAL Chi-restraints excluded: chain Q residue 324 GLU Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 17 CYS Chi-restraints excluded: chain Z residue 19 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 50 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.159441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.147037 restraints weight = 47566.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.148694 restraints weight = 21974.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.149707 restraints weight = 12394.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.150374 restraints weight = 8226.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.150746 restraints weight = 6095.583| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13188 Z= 0.180 Angle : 1.090 14.379 19416 Z= 0.446 Chirality : 0.081 0.861 2473 Planarity : 0.005 0.056 1204 Dihedral : 19.130 166.023 4750 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 1.30 % Allowed : 7.49 % Favored : 91.21 % Rotamer: Outliers : 4.74 % Allowed : 17.46 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.75 (0.33), residues: 614 helix: 0.02 (0.33), residues: 236 sheet: -2.21 (0.49), residues: 75 loop : -1.84 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 81 TYR 0.018 0.002 TYR D 130 PHE 0.024 0.002 PHE Q 131 TRP 0.009 0.002 TRP Q 15 HIS 0.004 0.001 HIS Q 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (13188) covalent geometry : angle 1.08964 / 0.45 (19416) hydrogen bonds : bond 0.06653 / 3.36 ( 311) hydrogen bonds : angle 5.42384 / 2.18 ( 688) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.275 Fit side-chains REVERT: G 125 LEU cc_start: 0.3908 (OUTLIER) cc_final: 0.3548 (tp) REVERT: Q 178 LYS cc_start: 0.5769 (pttt) cc_final: 0.5379 (pttp) REVERT: Q 198 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6329 (mpp80) REVERT: Q 199 HIS cc_start: 0.5317 (t70) cc_final: 0.5033 (t70) REVERT: Z 19 TYR cc_start: 0.6028 (OUTLIER) cc_final: 0.4856 (t80) outliers start: 25 outliers final: 15 residues processed: 96 average time/residue: 0.1034 time to fit residues: 14.4479 Evaluate side-chains 93 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 85 HIS Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 198 ARG Chi-restraints excluded: chain Q residue 229 SER Chi-restraints excluded: chain Q residue 274 VAL Chi-restraints excluded: chain Q residue 281 ILE Chi-restraints excluded: chain Q residue 305 VAL Chi-restraints excluded: chain Q residue 314 MET Chi-restraints excluded: chain Q residue 317 VAL Chi-restraints excluded: chain Q residue 322 VAL Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 17 CYS Chi-restraints excluded: chain Z residue 19 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 overall best weight: 6.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.155242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.144428 restraints weight = 47775.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.145791 restraints weight = 28604.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.145851 restraints weight = 18548.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.146267 restraints weight = 13234.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.146587 restraints weight = 9968.219| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.7378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13188 Z= 0.251 Angle : 1.223 14.040 19416 Z= 0.496 Chirality : 0.087 0.861 2473 Planarity : 0.005 0.054 1204 Dihedral : 19.441 174.421 4750 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 1.30 % Allowed : 8.47 % Favored : 90.23 % Rotamer: Outliers : 5.50 % Allowed : 17.27 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.13 (0.32), residues: 614 helix: -0.30 (0.33), residues: 242 sheet: -2.14 (0.51), residues: 76 loop : -2.16 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Q 81 TYR 0.023 0.003 TYR D 130 PHE 0.017 0.003 PHE Q 232 TRP 0.014 0.003 TRP Q 377 HIS 0.007 0.002 HIS Q 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.25 (13188) covalent geometry : angle 1.22279 / 0.50 (19416) hydrogen bonds : bond 0.08027 / 4.06 ( 311) hydrogen bonds : angle 5.68640 / 2.28 ( 688) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 178 LYS cc_start: 0.6354 (pttt) cc_final: 0.5947 (pttp) REVERT: Q 245 ARG cc_start: 0.6074 (OUTLIER) cc_final: 0.4282 (ptp-170) REVERT: Q 253 LEU cc_start: 0.6696 (mt) cc_final: 0.6421 (mt) REVERT: Q 280 PHE cc_start: 0.6713 (m-80) cc_final: 0.6002 (m-80) REVERT: Q 324 GLU cc_start: 0.5075 (OUTLIER) cc_final: 0.4846 (pp20) REVERT: Z 19 TYR cc_start: 0.6646 (OUTLIER) cc_final: 0.5904 (t80) outliers start: 29 outliers final: 22 residues processed: 101 average time/residue: 0.1072 time to fit residues: 15.8758 Evaluate side-chains 98 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 85 HIS Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 125 TYR Chi-restraints excluded: chain Q residue 160 THR Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 229 SER Chi-restraints excluded: chain Q residue 245 ARG Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 274 VAL Chi-restraints excluded: chain Q residue 281 ILE Chi-restraints excluded: chain Q residue 305 VAL Chi-restraints excluded: chain Q residue 314 MET Chi-restraints excluded: chain Q residue 317 VAL Chi-restraints excluded: chain Q residue 322 VAL Chi-restraints excluded: chain Q residue 324 GLU Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 17 CYS Chi-restraints excluded: chain Z residue 19 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 80 GLN ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 199 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.155955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.145569 restraints weight = 47886.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.146600 restraints weight = 24545.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.147633 restraints weight = 16153.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.147728 restraints weight = 10544.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.147740 restraints weight = 7679.642| |-----------------------------------------------------------------------------| r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.7683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13188 Z= 0.187 Angle : 1.109 12.821 19416 Z= 0.450 Chirality : 0.082 0.902 2473 Planarity : 0.004 0.055 1204 Dihedral : 19.358 171.527 4750 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 1.14 % Allowed : 7.65 % Favored : 91.21 % Rotamer: Outliers : 5.69 % Allowed : 19.54 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.02 (0.32), residues: 614 helix: -0.10 (0.33), residues: 244 sheet: -2.02 (0.52), residues: 76 loop : -2.25 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 414 TYR 0.018 0.002 TYR G 14 PHE 0.018 0.002 PHE Q 432 TRP 0.009 0.002 TRP Q 15 HIS 0.005 0.001 HIS Q 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (13188) covalent geometry : angle 1.10924 / 0.45 (19416) hydrogen bonds : bond 0.07113 / 3.61 ( 311) hydrogen bonds : angle 5.47275 / 2.19 ( 688) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.281 Fit side-chains REVERT: Q 178 LYS cc_start: 0.6258 (pttt) cc_final: 0.5861 (pttp) REVERT: Q 245 ARG cc_start: 0.5975 (OUTLIER) cc_final: 0.4442 (ptp-170) REVERT: Q 253 LEU cc_start: 0.6767 (mt) cc_final: 0.6517 (mt) REVERT: Z 19 TYR cc_start: 0.6527 (OUTLIER) cc_final: 0.5766 (t80) outliers start: 30 outliers final: 21 residues processed: 99 average time/residue: 0.1111 time to fit residues: 15.9774 Evaluate side-chains 99 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 85 HIS Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 125 TYR Chi-restraints excluded: chain Q residue 160 THR Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 229 SER Chi-restraints excluded: chain Q residue 245 ARG Chi-restraints excluded: chain Q residue 274 VAL Chi-restraints excluded: chain Q residue 281 ILE Chi-restraints excluded: chain Q residue 305 VAL Chi-restraints excluded: chain Q residue 317 VAL Chi-restraints excluded: chain Q residue 322 VAL Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 17 CYS Chi-restraints excluded: chain Z residue 19 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 0.0270 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 162 GLN Q 199 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.156844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.145824 restraints weight = 47846.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.147247 restraints weight = 22267.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.148176 restraints weight = 12574.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.148758 restraints weight = 8143.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.148974 restraints weight = 5924.634| |-----------------------------------------------------------------------------| r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.7997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13188 Z= 0.164 Angle : 1.065 12.605 19416 Z= 0.432 Chirality : 0.079 0.907 2473 Planarity : 0.004 0.055 1204 Dihedral : 19.239 174.326 4750 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 1.14 % Allowed : 7.98 % Favored : 90.88 % Rotamer: Outliers : 4.93 % Allowed : 20.87 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.83 (0.33), residues: 614 helix: 0.07 (0.34), residues: 246 sheet: -1.63 (0.52), residues: 77 loop : -2.27 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 81 TYR 0.017 0.002 TYR D 130 PHE 0.018 0.002 PHE Q 431 TRP 0.011 0.002 TRP Q 377 HIS 0.003 0.001 HIS D 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (13188) covalent geometry : angle 1.06516 / 0.43 (19416) hydrogen bonds : bond 0.06594 / 3.32 ( 311) hydrogen bonds : angle 5.28143 / 2.09 ( 688) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 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: 26 poor density : 82 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: Q 178 LYS cc_start: 0.6140 (pttt) cc_final: 0.5737 (pttp) REVERT: Q 198 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6342 (mpp80) REVERT: Q 245 ARG cc_start: 0.5936 (OUTLIER) cc_final: 0.3931 (ptt180) REVERT: Q 280 PHE cc_start: 0.6525 (m-80) cc_final: 0.5973 (m-80) REVERT: Z 19 TYR cc_start: 0.6421 (OUTLIER) cc_final: 0.5345 (t80) outliers start: 26 outliers final: 16 residues processed: 98 average time/residue: 0.1122 time to fit residues: 15.8289 Evaluate side-chains 97 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 85 HIS Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 125 TYR Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 198 ARG Chi-restraints excluded: chain Q residue 245 ARG Chi-restraints excluded: chain Q residue 274 VAL Chi-restraints excluded: chain Q residue 317 VAL Chi-restraints excluded: chain Q residue 322 VAL Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 17 CYS Chi-restraints excluded: chain Z residue 19 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.154616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.145597 restraints weight = 48122.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.146106 restraints weight = 29281.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.146993 restraints weight = 20788.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.146878 restraints weight = 13279.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.147106 restraints weight = 10113.825| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.8435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13188 Z= 0.217 Angle : 1.139 12.714 19416 Z= 0.460 Chirality : 0.082 0.894 2473 Planarity : 0.005 0.053 1204 Dihedral : 19.463 174.118 4750 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 1.14 % Allowed : 8.14 % Favored : 90.72 % Rotamer: Outliers : 4.17 % Allowed : 22.01 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.99 (0.32), residues: 614 helix: -0.05 (0.34), residues: 241 sheet: -1.84 (0.51), residues: 77 loop : -2.29 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 81 TYR 0.024 0.002 TYR Q 96 PHE 0.020 0.002 PHE Q 131 TRP 0.010 0.002 TRP G 53 HIS 0.009 0.002 HIS Q 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.22 (13188) covalent geometry : angle 1.13920 / 0.46 (19416) hydrogen bonds : bond 0.07555 / 3.80 ( 311) hydrogen bonds : angle 5.39104 / 2.11 ( 688) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 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: 22 poor density : 86 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: Q 63 LYS cc_start: 0.7397 (mtpp) cc_final: 0.6232 (tptm) REVERT: Q 65 ARG cc_start: 0.7689 (ttt-90) cc_final: 0.4559 (mmt180) REVERT: Q 178 LYS cc_start: 0.6265 (pttt) cc_final: 0.5863 (pttp) REVERT: Q 198 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6472 (mpp80) REVERT: Q 245 ARG cc_start: 0.5615 (OUTLIER) cc_final: 0.4103 (ptp-170) REVERT: Q 280 PHE cc_start: 0.6635 (m-80) cc_final: 0.6029 (m-80) REVERT: Z 19 TYR cc_start: 0.6487 (OUTLIER) cc_final: 0.5236 (t80) outliers start: 22 outliers final: 19 residues processed: 98 average time/residue: 0.1170 time to fit residues: 16.1749 Evaluate side-chains 101 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 85 HIS Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 125 TYR Chi-restraints excluded: chain Q residue 160 THR Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 198 ARG Chi-restraints excluded: chain Q residue 245 ARG Chi-restraints excluded: chain Q residue 274 VAL Chi-restraints excluded: chain Q residue 281 ILE Chi-restraints excluded: chain Q residue 314 MET Chi-restraints excluded: chain Q residue 317 VAL Chi-restraints excluded: chain Q residue 322 VAL Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 17 CYS Chi-restraints excluded: chain Z residue 19 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 69 optimal weight: 30.0000 chunk 74 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.156083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.145322 restraints weight = 47978.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.146757 restraints weight = 22350.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.147651 restraints weight = 12563.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.148252 restraints weight = 8247.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.148522 restraints weight = 6021.317| |-----------------------------------------------------------------------------| r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.8603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13188 Z= 0.159 Angle : 1.058 13.281 19416 Z= 0.429 Chirality : 0.079 0.918 2473 Planarity : 0.004 0.055 1204 Dihedral : 19.394 174.093 4750 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.98 % Allowed : 7.98 % Favored : 91.04 % Rotamer: Outliers : 3.98 % Allowed : 22.39 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.90 (0.32), residues: 614 helix: 0.04 (0.34), residues: 241 sheet: -1.50 (0.55), residues: 72 loop : -2.34 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 81 TYR 0.019 0.002 TYR G 14 PHE 0.040 0.002 PHE Q 431 TRP 0.009 0.002 TRP Q 15 HIS 0.003 0.001 HIS Q 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (13188) covalent geometry : angle 1.05795 / 0.43 (19416) hydrogen bonds : bond 0.06656 / 3.37 ( 311) hydrogen bonds : angle 5.32716 / 2.09 ( 688) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 63 LYS cc_start: 0.7022 (mtpp) cc_final: 0.5847 (tptm) REVERT: Q 65 ARG cc_start: 0.7694 (ttt-90) cc_final: 0.4586 (mmt180) REVERT: Q 178 LYS cc_start: 0.6225 (pttt) cc_final: 0.5879 (pttp) REVERT: Q 245 ARG cc_start: 0.5519 (OUTLIER) cc_final: 0.4002 (ptp-170) REVERT: Q 280 PHE cc_start: 0.6580 (m-80) cc_final: 0.6121 (m-80) REVERT: Q 312 LEU cc_start: 0.6186 (tt) cc_final: 0.5801 (tp) REVERT: Q 374 LEU cc_start: 0.4869 (tp) cc_final: 0.4103 (tp) REVERT: Q 425 GLN cc_start: 0.6785 (tm-30) cc_final: 0.6238 (tt0) REVERT: Z 19 TYR cc_start: 0.6258 (OUTLIER) cc_final: 0.4946 (t80) outliers start: 21 outliers final: 18 residues processed: 101 average time/residue: 0.1148 time to fit residues: 16.4577 Evaluate side-chains 103 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 85 HIS Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 125 TYR Chi-restraints excluded: chain Q residue 160 THR Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 245 ARG Chi-restraints excluded: chain Q residue 274 VAL Chi-restraints excluded: chain Q residue 281 ILE Chi-restraints excluded: chain Q residue 314 MET Chi-restraints excluded: chain Q residue 317 VAL Chi-restraints excluded: chain Q residue 322 VAL Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 17 CYS Chi-restraints excluded: chain Z residue 19 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 40 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 36 optimal weight: 0.0170 chunk 4 optimal weight: 30.0000 chunk 46 optimal weight: 8.9990 overall best weight: 5.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.154551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.145576 restraints weight = 48653.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.146115 restraints weight = 29522.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.146898 restraints weight = 20768.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.146781 restraints weight = 15297.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.147004 restraints weight = 10833.404| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.8914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13188 Z= 0.207 Angle : 1.141 13.315 19416 Z= 0.462 Chirality : 0.082 0.885 2473 Planarity : 0.005 0.053 1204 Dihedral : 19.560 174.575 4750 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.45 % Favored : 89.58 % Rotamer: Outliers : 3.80 % Allowed : 23.72 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.09 (0.32), residues: 614 helix: -0.24 (0.33), residues: 239 sheet: -1.49 (0.57), residues: 72 loop : -2.35 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 81 TYR 0.021 0.002 TYR G 14 PHE 0.048 0.003 PHE Q 431 TRP 0.011 0.002 TRP G 53 HIS 0.005 0.001 HIS Q 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.21 (13188) covalent geometry : angle 1.14101 / 0.46 (19416) hydrogen bonds : bond 0.07511 / 3.78 ( 311) hydrogen bonds : angle 5.55241 / 2.20 ( 688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2103.05 seconds wall clock time: 37 minutes 13.86 seconds (2233.86 seconds total)