Starting phenix.real_space_refine on Wed Sep 17 23:27:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5a8l_3099/09_2025/5a8l_3099.cif Found real_map, /net/cci-nas-00/data/ceres_data/5a8l_3099/09_2025/5a8l_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 { model { file = "/net/cci-nas-00/data/ceres_data/5a8l_3099/09_2025/5a8l_3099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5a8l_3099/09_2025/5a8l_3099.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5a8l_3099/09_2025/5a8l_3099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5a8l_3099/09_2025/5a8l_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-2.0-5805/lib/python3.9/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: {'RNA': 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: {'RNA': 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 Inner-chain residues flagged as termini: ['pdbres=" C P 74 "'] Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 8} Link IDs: {'rna3p': 17} 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: {'RNA': 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: 3.21, per 1000 atoms: 0.26 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: 1.22 Conformation dependent library (CDL) restraints added in 382.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 2.07 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: 3.12 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 18624 1.61 - 3.21: 646 3.21 - 4.82: 112 4.82 - 6.43: 23 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 - 35.52: 7467 35.52 - 71.05: 715 71.05 - 106.57: 94 106.57 - 142.10: 0 142.10 - 177.62: 7 Dihedral angle restraints: 8283 sinusoidal: 6518 harmonic: 1765 Sorted by residual: dihedral pdb=" O4' C A1576 " pdb=" C1' C A1576 " pdb=" N1 C A1576 " pdb=" C2 C A1576 " ideal model delta sinusoidal sigma weight residual 200.00 46.74 153.26 1 1.50e+01 4.44e-03 8.08e+01 dihedral pdb=" O4' U B1242 " pdb=" C1' U B1242 " pdb=" N1 U B1242 " pdb=" C2 U B1242 " ideal model delta sinusoidal sigma weight residual -128.00 49.62 -177.62 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 627 " pdb=" C1' U B 627 " pdb=" N1 U B 627 " pdb=" C2 U B 627 " ideal model delta sinusoidal sigma weight residual -128.00 48.92 -176.92 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 8280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2253 0.035 - 0.071: 125 0.071 - 0.106: 71 0.106 - 0.142: 21 0.142 - 0.177: 3 Chirality restraints: 2473 Sorted by residual: chirality pdb=" C3' U A3730 " pdb=" C4' U A3730 " pdb=" O3' U A3730 " pdb=" C2' U A3730 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.18 2.00e-01 2.50e+01 7.85e-01 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 2.41 -2.58 -0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CA LEU Z 15 " pdb=" N LEU Z 15 " pdb=" C LEU Z 15 " pdb=" CB LEU Z 15 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.12e-01 ... (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: 7.890 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.220 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: 0.010 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4253 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= 0.284 Angle : 0.671 8.035 19416 Z= 0.470 Chirality : 0.025 0.177 2473 Planarity : 0.004 0.062 1204 Dihedral : 21.127 177.623 7155 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 aren 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 covalent geometry : bond 0.00379 (13188) covalent geometry : angle 0.67141 (19416) hydrogen bonds : bond 0.15562 ( 311) hydrogen bonds : angle 11.51911 ( 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 : 0.277 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: 0.1450 time to fit residues: 33.9272 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 : 0.272 ------------------------------------------------------------------------------- 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: 30.0000 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: 6.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 162 GLN Q 200 ASN Q 265 ASN Q 266 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.167360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.156462 restraints weight = 48374.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.157465 restraints weight = 27324.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.157833 restraints weight = 16824.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.158155 restraints weight = 12084.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.158216 restraints weight = 10055.442| |-----------------------------------------------------------------------------| r_work (final): 0.4438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5511 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13188 Z= 0.159 Angle : 0.654 14.836 19416 Z= 0.325 Chirality : 0.034 0.240 2473 Planarity : 0.005 0.045 1204 Dihedral : 22.410 177.507 5954 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 1.63 % Allowed : 7.33 % Favored : 91.04 % Rotamer: Outliers : 3.80 % Allowed : 10.63 % Favored : 85.58 % 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 aren not related in a simple way. whole: -1.85 (0.32), residues: 614 helix: -0.97 (0.29), residues: 225 sheet: -2.30 (0.58), residues: 66 loop : -1.08 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 198 TYR 0.021 0.002 TYR D 130 PHE 0.014 0.002 PHE Q 146 TRP 0.016 0.002 TRP Q 377 HIS 0.004 0.001 HIS Q 199 Details of bonding type rmsd covalent geometry : bond 0.00329 (13188) covalent geometry : angle 0.65427 (19416) hydrogen bonds : bond 0.05811 ( 311) hydrogen bonds : angle 6.15652 ( 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: 20 poor density : 106 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: Q 243 ASP cc_start: 0.6026 (m-30) cc_final: 0.5753 (m-30) REVERT: Q 246 LEU cc_start: 0.4537 (OUTLIER) cc_final: 0.4335 (mp) REVERT: Q 374 LEU cc_start: 0.6059 (tt) cc_final: 0.5518 (tt) REVERT: Q 425 GLN cc_start: 0.6794 (tm-30) cc_final: 0.6530 (tm-30) outliers start: 20 outliers final: 8 residues processed: 115 average time/residue: 0.1220 time to fit residues: 19.9906 Evaluate side-chains 91 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 246 LEU Chi-restraints excluded: chain Q residue 266 GLN Chi-restraints excluded: chain Q residue 322 VAL Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 18 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 75 optimal weight: 7.9990 chunk 6 optimal weight: 40.0000 chunk 87 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 74 optimal weight: 50.0000 chunk 16 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 41 optimal weight: 0.0870 overall best weight: 3.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 70 GLN Q 121 ASN Q 356 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.163242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.150226 restraints weight = 48095.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.151823 restraints weight = 22101.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.152858 restraints weight = 12690.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.153530 restraints weight = 8548.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.153806 restraints weight = 6385.294| |-----------------------------------------------------------------------------| r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5711 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13188 Z= 0.158 Angle : 0.627 12.337 19416 Z= 0.322 Chirality : 0.034 0.223 2473 Planarity : 0.005 0.064 1204 Dihedral : 22.491 178.222 5950 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 1.47 % Allowed : 7.98 % Favored : 90.55 % Rotamer: Outliers : 4.17 % Allowed : 14.04 % Favored : 81.78 % 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 aren not related in a simple way. whole: -1.75 (0.32), residues: 614 helix: -0.27 (0.33), residues: 230 sheet: -2.16 (0.53), residues: 71 loop : -1.57 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 330 TYR 0.025 0.003 TYR Q 125 PHE 0.024 0.002 PHE Q 146 TRP 0.003 0.001 TRP G 53 HIS 0.004 0.001 HIS Q 180 Details of bonding type rmsd covalent geometry : bond 0.00314 (13188) covalent geometry : angle 0.62724 (19416) hydrogen bonds : bond 0.05590 ( 311) hydrogen bonds : angle 5.60100 ( 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 113 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 161 LEU cc_start: 0.7195 (tt) cc_final: 0.6491 (mm) REVERT: Q 245 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.4438 (ptp-170) REVERT: Q 403 VAL cc_start: 0.6162 (t) cc_final: 0.5951 (t) outliers start: 22 outliers final: 13 residues processed: 101 average time/residue: 0.1246 time to fit residues: 17.8013 Evaluate side-chains 89 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 81 ILE 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 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 Chi-restraints excluded: chain Z residue 18 LYS Chi-restraints excluded: chain Z residue 19 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 89 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 27 optimal weight: 30.0000 chunk 31 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 76 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 70 GLN Q 266 GLN Q 334 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.159173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.146333 restraints weight = 47652.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.147983 restraints weight = 21089.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.149000 restraints weight = 11781.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.149495 restraints weight = 7761.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.149949 restraints weight = 5977.893| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5870 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 13188 Z= 0.172 Angle : 0.654 15.542 19416 Z= 0.333 Chirality : 0.036 0.388 2473 Planarity : 0.005 0.044 1204 Dihedral : 22.711 179.024 5950 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 1.14 % Allowed : 7.98 % Favored : 90.88 % Rotamer: Outliers : 4.55 % Allowed : 14.61 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.77 (0.32), residues: 614 helix: -0.05 (0.33), residues: 230 sheet: -2.21 (0.49), residues: 83 loop : -1.73 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 81 TYR 0.022 0.002 TYR D 130 PHE 0.015 0.002 PHE Q 432 TRP 0.006 0.001 TRP G 53 HIS 0.005 0.002 HIS Q 356 Details of bonding type rmsd covalent geometry : bond 0.00336 (13188) covalent geometry : angle 0.65394 (19416) hydrogen bonds : bond 0.05860 ( 311) hydrogen bonds : angle 5.53750 ( 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 108 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 125 LEU cc_start: 0.3750 (OUTLIER) cc_final: 0.3389 (tp) REVERT: Q 161 LEU cc_start: 0.7001 (tt) cc_final: 0.6586 (mm) REVERT: Q 194 ARG cc_start: 0.6364 (tmm160) cc_final: 0.5783 (ttt-90) REVERT: Q 199 HIS cc_start: 0.5503 (t70) cc_final: 0.5089 (t70) outliers start: 24 outliers final: 11 residues processed: 101 average time/residue: 0.1273 time to fit residues: 18.1921 Evaluate side-chains 81 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 229 SER Chi-restraints excluded: chain Q residue 234 THR 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 18 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 95 GLN G 97 ASN ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 266 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.154884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.144172 restraints weight = 47959.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.145090 restraints weight = 25107.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.145317 restraints weight = 16448.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.145510 restraints weight = 13257.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.145384 restraints weight = 10501.785| |-----------------------------------------------------------------------------| r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13188 Z= 0.212 Angle : 0.720 7.890 19416 Z= 0.371 Chirality : 0.038 0.259 2473 Planarity : 0.006 0.061 1204 Dihedral : 23.132 179.436 5950 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 1.30 % Allowed : 7.82 % Favored : 90.88 % Rotamer: Outliers : 5.12 % Allowed : 17.84 % Favored : 77.04 % 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 aren not related in a simple way. whole: -1.96 (0.32), residues: 614 helix: -0.25 (0.33), residues: 228 sheet: -1.93 (0.50), residues: 81 loop : -1.93 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.002 ARG Q 194 TYR 0.023 0.002 TYR D 130 PHE 0.024 0.002 PHE Q 280 TRP 0.011 0.002 TRP G 53 HIS 0.010 0.002 HIS Q 180 Details of bonding type rmsd covalent geometry : bond 0.00417 (13188) covalent geometry : angle 0.72036 (19416) hydrogen bonds : bond 0.07410 ( 311) hydrogen bonds : angle 5.65958 ( 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 109 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.307 Fit side-chains REVERT: D 135 ARG cc_start: 0.7121 (mtm180) cc_final: 0.6916 (mtm180) REVERT: G 125 LEU cc_start: 0.3465 (OUTLIER) cc_final: 0.3207 (tp) REVERT: Q 161 LEU cc_start: 0.7489 (tt) cc_final: 0.6900 (mm) REVERT: Q 178 LYS cc_start: 0.6109 (pttt) cc_final: 0.5113 (pttp) REVERT: Q 198 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6852 (mpp80) REVERT: Q 280 PHE cc_start: 0.6818 (m-80) cc_final: 0.6546 (m-80) REVERT: Q 324 GLU cc_start: 0.5182 (OUTLIER) cc_final: 0.4925 (pt0) REVERT: Q 425 GLN cc_start: 0.6611 (tm-30) cc_final: 0.6191 (tt0) REVERT: Z 10 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6973 (ttmm) outliers start: 27 outliers final: 16 residues processed: 100 average time/residue: 0.1303 time to fit residues: 18.2355 Evaluate side-chains 91 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 ILE 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 48 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 122 THR 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 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 18 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 40 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 45 optimal weight: 0.0670 chunk 84 optimal weight: 5.9990 overall best weight: 6.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.153591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.141163 restraints weight = 47570.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.142765 restraints weight = 21249.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.143695 restraints weight = 11994.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.144300 restraints weight = 7957.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.144549 restraints weight = 5888.950| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.6744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13188 Z= 0.199 Angle : 0.687 7.738 19416 Z= 0.352 Chirality : 0.038 0.283 2473 Planarity : 0.005 0.062 1204 Dihedral : 23.230 179.281 5950 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 1.47 % Allowed : 7.82 % Favored : 90.72 % Rotamer: Outliers : 6.45 % Allowed : 18.41 % Favored : 75.14 % 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 aren not related in a simple way. whole: -2.10 (0.31), residues: 614 helix: -0.30 (0.33), residues: 235 sheet: -1.79 (0.51), residues: 80 loop : -2.20 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG Q 194 TYR 0.019 0.002 TYR D 130 PHE 0.010 0.002 PHE Q 264 TRP 0.012 0.003 TRP Q 377 HIS 0.007 0.002 HIS Q 180 Details of bonding type rmsd covalent geometry : bond 0.00394 (13188) covalent geometry : angle 0.68687 (19416) hydrogen bonds : bond 0.06871 ( 311) hydrogen bonds : angle 5.53594 ( 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 118 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: D 135 ARG cc_start: 0.7131 (mtm180) cc_final: 0.6910 (mtm180) REVERT: G 125 LEU cc_start: 0.3515 (OUTLIER) cc_final: 0.3244 (tp) REVERT: Q 178 LYS cc_start: 0.6630 (pttt) cc_final: 0.6302 (pttp) REVERT: Q 196 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7423 (mm-30) REVERT: Q 235 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6306 (pm20) REVERT: Q 245 ARG cc_start: 0.6048 (OUTLIER) cc_final: 0.4223 (ptp-170) REVERT: Q 280 PHE cc_start: 0.6845 (m-80) cc_final: 0.6202 (m-80) REVERT: Q 324 GLU cc_start: 0.5662 (OUTLIER) cc_final: 0.5411 (pt0) outliers start: 34 outliers final: 24 residues processed: 106 average time/residue: 0.1189 time to fit residues: 18.2846 Evaluate side-chains 99 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 121 LEU 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 60 SER Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 125 TYR Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 229 SER Chi-restraints excluded: chain Q residue 235 GLU 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 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 18 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.151167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.139077 restraints weight = 48146.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.140530 restraints weight = 22364.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.141427 restraints weight = 12965.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.141996 restraints weight = 8715.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.142228 restraints weight = 6662.887| |-----------------------------------------------------------------------------| r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.7575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13188 Z= 0.221 Angle : 0.756 12.225 19416 Z= 0.384 Chirality : 0.040 0.304 2473 Planarity : 0.005 0.059 1204 Dihedral : 23.501 177.451 5950 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 1.30 % Allowed : 9.45 % Favored : 89.25 % Rotamer: Outliers : 7.02 % Allowed : 19.92 % Favored : 73.06 % 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 aren not related in a simple way. whole: -2.35 (0.31), residues: 614 helix: -0.45 (0.33), residues: 242 sheet: -1.91 (0.49), residues: 80 loop : -2.43 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 194 TYR 0.022 0.002 TYR D 130 PHE 0.021 0.002 PHE Q 146 TRP 0.011 0.003 TRP Q 377 HIS 0.008 0.002 HIS Q 180 Details of bonding type rmsd covalent geometry : bond 0.00432 (13188) covalent geometry : angle 0.75642 (19416) hydrogen bonds : bond 0.07766 ( 311) hydrogen bonds : angle 5.52269 ( 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 122 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.313 Fit side-chains REVERT: D 135 ARG cc_start: 0.7157 (mtm180) cc_final: 0.6912 (mtm180) REVERT: Q 65 ARG cc_start: 0.7414 (ttt-90) cc_final: 0.4371 (mmt180) REVERT: Q 198 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6244 (mpp80) REVERT: Q 199 HIS cc_start: 0.5336 (t70) cc_final: 0.5131 (t70) REVERT: Q 245 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5497 (ptt-90) REVERT: Q 280 PHE cc_start: 0.6561 (m-80) cc_final: 0.5971 (m-80) REVERT: Q 318 GLU cc_start: 0.4658 (tt0) cc_final: 0.4203 (mt-10) REVERT: Q 324 GLU cc_start: 0.5641 (OUTLIER) cc_final: 0.5370 (pt0) REVERT: Q 425 GLN cc_start: 0.6406 (tm-30) cc_final: 0.6023 (tt0) outliers start: 37 outliers final: 28 residues processed: 109 average time/residue: 0.1218 time to fit residues: 19.0683 Evaluate side-chains 102 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 71 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 121 LEU 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 12 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 72 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 174 VAL Chi-restraints excluded: chain Q residue 198 ARG 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 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 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 18 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 51 optimal weight: 0.0370 chunk 32 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 overall best weight: 3.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 80 GLN Q 200 ASN ** Q 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.152837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.140971 restraints weight = 47892.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.142536 restraints weight = 21483.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.143460 restraints weight = 11976.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.144016 restraints weight = 7862.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.144277 restraints weight = 5856.975| |-----------------------------------------------------------------------------| r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.7647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13188 Z= 0.139 Angle : 0.636 8.605 19416 Z= 0.324 Chirality : 0.035 0.302 2473 Planarity : 0.005 0.061 1204 Dihedral : 23.262 179.639 5950 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 1.14 % Allowed : 8.79 % Favored : 90.07 % Rotamer: Outliers : 6.07 % Allowed : 22.77 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.10 (0.32), residues: 614 helix: -0.25 (0.34), residues: 242 sheet: -1.83 (0.49), residues: 80 loop : -2.28 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 81 TYR 0.018 0.002 TYR G 14 PHE 0.013 0.002 PHE Q 213 TRP 0.010 0.002 TRP Q 377 HIS 0.003 0.001 HIS D 133 Details of bonding type rmsd covalent geometry : bond 0.00275 (13188) covalent geometry : angle 0.63553 (19416) hydrogen bonds : bond 0.06114 ( 311) hydrogen bonds : angle 5.23612 ( 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 111 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.300 Fit side-chains REVERT: Q 196 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7137 (mm-30) REVERT: Q 198 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6154 (mpp80) REVERT: Q 200 ASN cc_start: 0.6026 (OUTLIER) cc_final: 0.5575 (m-40) REVERT: Q 245 ARG cc_start: 0.5749 (OUTLIER) cc_final: 0.5463 (ptt180) REVERT: Q 280 PHE cc_start: 0.6340 (m-80) cc_final: 0.5798 (m-80) REVERT: Q 312 LEU cc_start: 0.6200 (tt) cc_final: 0.5850 (tp) REVERT: Q 318 GLU cc_start: 0.4570 (tt0) cc_final: 0.4091 (mt-10) outliers start: 32 outliers final: 23 residues processed: 98 average time/residue: 0.1244 time to fit residues: 17.3915 Evaluate side-chains 97 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 121 LEU 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 72 LEU Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 125 TYR Chi-restraints excluded: chain Q residue 149 ILE Chi-restraints excluded: chain Q residue 160 THR Chi-restraints excluded: chain Q residue 198 ARG Chi-restraints excluded: chain Q residue 200 ASN 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 18 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 6 optimal weight: 30.0000 chunk 92 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 overall best weight: 6.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 200 ASN ** Q 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.150533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.138303 restraints weight = 47672.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.139856 restraints weight = 21940.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.140797 restraints weight = 12568.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.141388 restraints weight = 8444.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.141663 restraints weight = 6336.462| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 moved from start: 0.8072 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= 0.204 Angle : 0.728 10.752 19416 Z= 0.370 Chirality : 0.038 0.289 2473 Planarity : 0.005 0.060 1204 Dihedral : 23.446 177.981 5950 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 1.14 % Allowed : 9.12 % Favored : 89.74 % Rotamer: Outliers : 6.64 % Allowed : 22.77 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.17 (0.33), residues: 614 helix: -0.39 (0.34), residues: 235 sheet: -1.92 (0.50), residues: 80 loop : -2.17 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 81 TYR 0.022 0.002 TYR G 14 PHE 0.012 0.002 PHE Q 264 TRP 0.011 0.002 TRP Q 377 HIS 0.010 0.002 HIS Q 199 Details of bonding type rmsd covalent geometry : bond 0.00397 (13188) covalent geometry : angle 0.72806 (19416) hydrogen bonds : bond 0.07357 ( 311) hydrogen bonds : angle 5.46183 ( 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 111 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 89 GLN cc_start: 0.2585 (tp-100) cc_final: 0.2318 (tp40) REVERT: Q 65 ARG cc_start: 0.7658 (ttt-90) cc_final: 0.4438 (mmt180) REVERT: Q 198 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6208 (mpp80) REVERT: Q 245 ARG cc_start: 0.5740 (OUTLIER) cc_final: 0.5488 (ptt180) REVERT: Q 280 PHE cc_start: 0.6362 (m-80) cc_final: 0.5865 (m-80) REVERT: Q 318 GLU cc_start: 0.4732 (tt0) cc_final: 0.4222 (mt-10) REVERT: Q 324 GLU cc_start: 0.5212 (pt0) cc_final: 0.5007 (pp20) outliers start: 35 outliers final: 29 residues processed: 96 average time/residue: 0.1353 time to fit residues: 18.0488 Evaluate side-chains 105 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 121 LEU 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 12 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 125 TYR Chi-restraints excluded: chain Q residue 149 ILE 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 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 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 18 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 69 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 65 optimal weight: 0.0470 chunk 15 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 overall best weight: 5.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.150906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.138739 restraints weight = 47971.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.140340 restraints weight = 21435.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.141291 restraints weight = 12232.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.141781 restraints weight = 8225.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.142243 restraints weight = 6276.564| |-----------------------------------------------------------------------------| r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.8331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13188 Z= 0.172 Angle : 0.674 8.169 19416 Z= 0.342 Chirality : 0.036 0.301 2473 Planarity : 0.005 0.061 1204 Dihedral : 23.400 179.694 5950 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 1.14 % Allowed : 9.61 % Favored : 89.25 % Rotamer: Outliers : 6.07 % Allowed : 23.53 % Favored : 70.40 % 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 aren not related in a simple way. whole: -2.24 (0.32), residues: 614 helix: -0.42 (0.34), residues: 233 sheet: -2.00 (0.54), residues: 75 loop : -2.23 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 81 TYR 0.027 0.002 TYR D 130 PHE 0.012 0.002 PHE Q 264 TRP 0.011 0.002 TRP Q 377 HIS 0.004 0.001 HIS Q 180 Details of bonding type rmsd covalent geometry : bond 0.00336 (13188) covalent geometry : angle 0.67418 (19416) hydrogen bonds : bond 0.06536 ( 311) hydrogen bonds : angle 5.33596 ( 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: 32 poor density : 78 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 65 ARG cc_start: 0.7847 (ttt-90) cc_final: 0.4448 (mmt180) REVERT: Q 241 MET cc_start: 0.4747 (ptp) cc_final: 0.3995 (ptp) REVERT: Q 280 PHE cc_start: 0.6175 (m-80) cc_final: 0.5755 (m-80) REVERT: Q 318 GLU cc_start: 0.5063 (tt0) cc_final: 0.4425 (mt-10) REVERT: Q 425 GLN cc_start: 0.6392 (tm-30) cc_final: 0.5900 (tt0) outliers start: 32 outliers final: 27 residues processed: 98 average time/residue: 0.1444 time to fit residues: 19.3953 Evaluate side-chains 102 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 121 LEU 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 72 LEU Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 125 TYR Chi-restraints excluded: chain Q residue 149 ILE Chi-restraints excluded: chain Q residue 160 THR Chi-restraints excluded: chain Q residue 173 THR 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 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 18 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 40 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 50 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 4 optimal weight: 40.0000 chunk 46 optimal weight: 10.0000 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 129 ASN Q 199 HIS ** Q 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.149162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.137227 restraints weight = 47844.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.138750 restraints weight = 22066.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.139690 restraints weight = 12744.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.140239 restraints weight = 8534.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.140561 restraints weight = 6535.724| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.8815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13188 Z= 0.215 Angle : 0.763 9.025 19416 Z= 0.386 Chirality : 0.040 0.292 2473 Planarity : 0.006 0.060 1204 Dihedral : 23.651 178.371 5950 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 1.30 % Allowed : 10.91 % Favored : 87.79 % Rotamer: Outliers : 5.69 % Allowed : 23.91 % Favored : 70.40 % 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 aren not related in a simple way. whole: -2.31 (0.32), residues: 614 helix: -0.41 (0.33), residues: 220 sheet: -2.12 (0.53), residues: 75 loop : -2.23 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 81 TYR 0.023 0.003 TYR G 14 PHE 0.020 0.002 PHE Q 431 TRP 0.021 0.003 TRP Q 377 HIS 0.008 0.002 HIS Q 180 Details of bonding type rmsd covalent geometry : bond 0.00418 (13188) covalent geometry : angle 0.76253 (19416) hydrogen bonds : bond 0.07807 ( 311) hydrogen bonds : angle 5.57038 ( 688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2324.51 seconds wall clock time: 41 minutes 6.55 seconds (2466.55 seconds total)