Starting phenix.real_space_refine on Tue Jun 10 23:49:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5a8l_3099/06_2025/5a8l_3099.cif Found real_map, /net/cci-nas-00/data/ceres_data/5a8l_3099/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5a8l_3099/06_2025/5a8l_3099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5a8l_3099/06_2025/5a8l_3099.map" model { file = "/net/cci-nas-00/data/ceres_data/5a8l_3099/06_2025/5a8l_3099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5a8l_3099/06_2025/5a8l_3099.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.67, per 1000 atoms: 0.71 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: 2.68 Conformation dependent library (CDL) restraints added in 810.0 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: 4.79 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: 5.27 Time building geometry restraints manager: 3.20 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: 8.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.940 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.840 ------------------------------------------------------------------------------- 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 : 8.96 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.004 0.001 TRP Q 377 HIS 0.005 0.001 HIS Q 132 PHE 0.015 0.001 PHE Q 242 TYR 0.014 0.001 TYR D 139 ARG 0.005 0.000 ARG Q 198 Details of bonding type rmsd hydrogen bonds : bond 0.15562 ( 311) hydrogen bonds : angle 11.51911 ( 688) covalent geometry : bond 0.00379 (13188) covalent geometry : angle 0.67141 (19416) *********************** 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 : 1.087 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: 0.3549 time to fit residues: 82.8817 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 : 0.740 ------------------------------------------------------------------------------- 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 78 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 44 optimal weight: 0.0870 chunk 54 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 overall best weight: 2.9964 ------------------------------------------------------------------------------- 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 = 0.4574 r_free = 0.4574 target = 0.167322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.156288 restraints weight = 47840.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.157084 restraints weight = 29997.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.157621 restraints weight = 17895.051| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5527 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 13188 Z= 0.156 Angle : 0.656 14.487 19416 Z= 0.328 Chirality : 0.034 0.238 2473 Planarity : 0.005 0.041 1204 Dihedral : 22.410 177.404 5954 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 1.63 % Allowed : 7.33 % Favored : 91.04 % Rotamer: Outliers : 3.80 % Allowed : 10.44 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.32), residues: 614 helix: -0.95 (0.29), residues: 225 sheet: -2.28 (0.58), residues: 66 loop : -1.16 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 377 HIS 0.005 0.001 HIS Q 199 PHE 0.014 0.002 PHE Q 146 TYR 0.020 0.002 TYR D 130 ARG 0.011 0.001 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.05801 ( 311) hydrogen bonds : angle 6.12434 ( 688) covalent geometry : bond 0.00326 (13188) covalent geometry : angle 0.65646 (19416) *********************** 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 : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 243 ASP cc_start: 0.6063 (m-30) cc_final: 0.5720 (m-30) REVERT: Q 246 LEU cc_start: 0.4714 (OUTLIER) cc_final: 0.4249 (mp) REVERT: Q 374 LEU cc_start: 0.6042 (tt) cc_final: 0.5519 (tt) outliers start: 20 outliers final: 8 residues processed: 115 average time/residue: 0.2607 time to fit residues: 42.5659 Evaluate side-chains 89 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 28 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 8 optimal weight: 20.0000 chunk 61 optimal weight: 30.0000 chunk 91 optimal weight: 40.0000 chunk 17 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 overall best weight: 9.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN ** Q 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 164 ASN Q 334 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.155518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.143173 restraints weight = 48870.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.143683 restraints weight = 26740.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.144629 restraints weight = 15467.517| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 13188 Z= 0.307 Angle : 0.929 11.589 19416 Z= 0.470 Chirality : 0.046 0.252 2473 Planarity : 0.008 0.079 1204 Dihedral : 23.451 176.385 5950 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 1.30 % Allowed : 9.45 % Favored : 89.25 % Rotamer: Outliers : 7.02 % Allowed : 13.47 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.30), residues: 614 helix: -0.92 (0.30), residues: 236 sheet: -2.37 (0.50), residues: 81 loop : -2.03 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP G 53 HIS 0.015 0.004 HIS Q 180 PHE 0.024 0.004 PHE Q 131 TYR 0.044 0.004 TYR Q 125 ARG 0.011 0.002 ARG Q 245 Details of bonding type rmsd hydrogen bonds : bond 0.09376 ( 311) hydrogen bonds : angle 6.26588 ( 688) covalent geometry : bond 0.00618 (13188) covalent geometry : angle 0.92944 (19416) *********************** 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 126 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 34 MET cc_start: 0.3291 (mtp) cc_final: 0.2637 (tmm) REVERT: Q 126 LEU cc_start: 0.7558 (tp) cc_final: 0.7250 (mt) REVERT: Q 198 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6835 (mpp80) REVERT: Q 199 HIS cc_start: 0.5512 (t70) cc_final: 0.5269 (t70) REVERT: Q 245 ARG cc_start: 0.5811 (OUTLIER) cc_final: 0.4105 (ptp-170) REVERT: Q 280 PHE cc_start: 0.6957 (m-10) cc_final: 0.6673 (m-80) REVERT: Q 324 GLU cc_start: 0.4795 (OUTLIER) cc_final: 0.4595 (pt0) REVERT: Q 403 VAL cc_start: 0.6116 (t) cc_final: 0.5908 (t) outliers start: 37 outliers final: 17 residues processed: 113 average time/residue: 0.2940 time to fit residues: 46.9658 Evaluate side-chains 89 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 110 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 247 GLN 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 7 SER Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 18 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 52 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 70 GLN G 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.154668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.143927 restraints weight = 47440.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.144635 restraints weight = 25099.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.144582 restraints weight = 18610.946| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 13188 Z= 0.204 Angle : 0.708 9.249 19416 Z= 0.365 Chirality : 0.038 0.277 2473 Planarity : 0.005 0.058 1204 Dihedral : 23.266 179.859 5950 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 1.30 % Allowed : 8.31 % Favored : 90.39 % Rotamer: Outliers : 6.07 % Allowed : 17.27 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.31), residues: 614 helix: -0.48 (0.32), residues: 239 sheet: -2.33 (0.49), residues: 82 loop : -2.11 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 53 HIS 0.007 0.002 HIS Q 180 PHE 0.015 0.002 PHE Q 264 TYR 0.019 0.003 TYR Q 301 ARG 0.005 0.001 ARG Q 203 Details of bonding type rmsd hydrogen bonds : bond 0.07169 ( 311) hydrogen bonds : angle 5.73888 ( 688) covalent geometry : bond 0.00404 (13188) covalent geometry : angle 0.70808 (19416) *********************** 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 115 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 90 PRO cc_start: 0.8299 (Cg_exo) cc_final: 0.8032 (Cg_endo) REVERT: Q 126 LEU cc_start: 0.7715 (tp) cc_final: 0.7381 (mt) REVERT: Q 178 LYS cc_start: 0.6032 (pttt) cc_final: 0.5664 (pttp) REVERT: Q 199 HIS cc_start: 0.5586 (t70) cc_final: 0.5345 (t70) REVERT: Q 280 PHE cc_start: 0.7164 (m-10) cc_final: 0.6886 (m-80) REVERT: Q 324 GLU cc_start: 0.5455 (OUTLIER) cc_final: 0.5073 (pt0) outliers start: 32 outliers final: 19 residues processed: 102 average time/residue: 0.2452 time to fit residues: 35.8906 Evaluate side-chains 92 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 122 THR 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 229 SER Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 274 VAL Chi-restraints excluded: chain Q residue 305 VAL Chi-restraints excluded: chain Q residue 314 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 35 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 overall best weight: 14.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 129 ASN Q 132 HIS Q 266 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.146589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.135790 restraints weight = 48871.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.136147 restraints weight = 29266.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.137650 restraints weight = 20455.472| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.8221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 13188 Z= 0.417 Angle : 1.143 13.344 19416 Z= 0.571 Chirality : 0.055 0.283 2473 Planarity : 0.008 0.064 1204 Dihedral : 24.546 174.470 5950 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 1.63 % Allowed : 11.07 % Favored : 87.30 % Rotamer: Outliers : 7.78 % Allowed : 20.68 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.29), residues: 614 helix: -1.35 (0.29), residues: 233 sheet: -2.32 (0.51), residues: 80 loop : -2.82 (0.30), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP G 53 HIS 0.019 0.004 HIS Q 180 PHE 0.020 0.004 PHE Q 242 TYR 0.029 0.004 TYR D 130 ARG 0.012 0.002 ARG Q 203 Details of bonding type rmsd hydrogen bonds : bond 0.12007 ( 311) hydrogen bonds : angle 6.66473 ( 688) covalent geometry : bond 0.00818 (13188) covalent geometry : angle 1.14287 (19416) *********************** 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 126 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 85 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: G 95 GLN cc_start: 0.6894 (mm-40) cc_final: 0.6476 (tt0) REVERT: G 96 LYS cc_start: 0.5981 (mttt) cc_final: 0.5636 (pttt) REVERT: Q 34 MET cc_start: 0.4930 (mtt) cc_final: 0.4358 (mmm) REVERT: Q 179 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7652 (mptt) REVERT: Q 280 PHE cc_start: 0.6267 (m-10) cc_final: 0.5788 (m-80) REVERT: Q 287 ILE cc_start: 0.6358 (mt) cc_final: 0.6031 (tt) outliers start: 41 outliers final: 24 residues processed: 115 average time/residue: 0.2677 time to fit residues: 43.5512 Evaluate side-chains 95 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain G residue 71 ILE 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 39 ILE 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 129 ASN Chi-restraints excluded: chain Q residue 160 THR Chi-restraints excluded: chain Q residue 179 LYS Chi-restraints excluded: chain Q residue 234 THR Chi-restraints excluded: chain Q residue 246 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 79 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 78 optimal weight: 0.0030 chunk 85 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 76 optimal weight: 0.2980 chunk 7 optimal weight: 30.0000 overall best weight: 2.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 97 ASN Q 80 GLN Q 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.150762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.138534 restraints weight = 48559.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.140050 restraints weight = 21755.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.140985 restraints weight = 12357.493| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.7973 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= 0.150 Angle : 0.710 9.024 19416 Z= 0.367 Chirality : 0.039 0.409 2473 Planarity : 0.005 0.064 1204 Dihedral : 23.740 177.211 5946 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 1.14 % Allowed : 8.47 % Favored : 90.39 % Rotamer: Outliers : 4.93 % Allowed : 23.72 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.30), residues: 614 helix: -0.66 (0.31), residues: 234 sheet: -1.88 (0.52), residues: 80 loop : -2.52 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP Q 377 HIS 0.005 0.002 HIS D 133 PHE 0.020 0.002 PHE Q 131 TYR 0.016 0.002 TYR G 14 ARG 0.008 0.001 ARG Q 81 Details of bonding type rmsd hydrogen bonds : bond 0.07576 ( 311) hydrogen bonds : angle 5.81402 ( 688) covalent geometry : bond 0.00286 (13188) covalent geometry : angle 0.71027 (19416) *********************** 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 116 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: Q 107 GLU cc_start: 0.5499 (tm-30) cc_final: 0.4800 (mt-10) REVERT: Q 126 LEU cc_start: 0.6849 (tp) cc_final: 0.6430 (mt) REVERT: Q 179 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7324 (mptt) REVERT: Q 280 PHE cc_start: 0.6218 (m-10) cc_final: 0.5950 (m-80) REVERT: Z 18 LYS cc_start: 0.5206 (OUTLIER) cc_final: 0.4712 (pptt) outliers start: 26 outliers final: 16 residues processed: 109 average time/residue: 0.2671 time to fit residues: 41.5270 Evaluate side-chains 94 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 74 VAL 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 179 LYS 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 322 VAL Chi-restraints excluded: chain Z residue 10 LYS 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 59 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 30.0000 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 90 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.149813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.137696 restraints weight = 48451.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.139119 restraints weight = 22432.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.140047 restraints weight = 13048.826| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.8155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13188 Z= 0.186 Angle : 0.716 11.731 19416 Z= 0.368 Chirality : 0.039 0.301 2473 Planarity : 0.005 0.064 1204 Dihedral : 23.625 177.405 5946 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.61 % Favored : 89.41 % Rotamer: Outliers : 5.12 % Allowed : 24.86 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.32), residues: 614 helix: -0.50 (0.32), residues: 230 sheet: -1.73 (0.54), residues: 80 loop : -2.40 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Q 377 HIS 0.005 0.001 HIS Q 180 PHE 0.020 0.002 PHE Q 432 TYR 0.019 0.002 TYR D 130 ARG 0.015 0.001 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.07508 ( 311) hydrogen bonds : angle 5.70649 ( 688) covalent geometry : bond 0.00365 (13188) covalent geometry : angle 0.71639 (19416) *********************** 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 98 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: Q 126 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6912 (tp) REVERT: Q 179 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7474 (mptt) REVERT: Q 280 PHE cc_start: 0.6190 (m-10) cc_final: 0.5931 (m-80) REVERT: Z 18 LYS cc_start: 0.5313 (OUTLIER) cc_final: 0.4828 (pptt) outliers start: 27 outliers final: 21 residues processed: 89 average time/residue: 0.2575 time to fit residues: 33.0372 Evaluate side-chains 90 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 74 VAL 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 72 LEU Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 146 PHE Chi-restraints excluded: chain Q residue 179 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 56 optimal weight: 0.0570 chunk 64 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 18 optimal weight: 30.0000 chunk 87 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 GLN ** 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 = 0.4359 r_free = 0.4359 target = 0.150898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.138933 restraints weight = 48605.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.140382 restraints weight = 22028.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.141309 restraints weight = 12585.656| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.8281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13188 Z= 0.155 Angle : 0.660 13.262 19416 Z= 0.338 Chirality : 0.036 0.301 2473 Planarity : 0.005 0.062 1204 Dihedral : 23.446 178.748 5946 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.93 % Favored : 89.25 % Rotamer: Outliers : 5.12 % Allowed : 25.62 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.32), residues: 614 helix: -0.35 (0.33), residues: 230 sheet: -1.81 (0.53), residues: 80 loop : -2.32 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Q 377 HIS 0.004 0.001 HIS G 100 PHE 0.014 0.002 PHE Q 131 TYR 0.015 0.002 TYR G 14 ARG 0.011 0.001 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.06515 ( 311) hydrogen bonds : angle 5.43745 ( 688) covalent geometry : bond 0.00303 (13188) covalent geometry : angle 0.65970 (19416) *********************** 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 105 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: Q 34 MET cc_start: 0.6431 (mmp) cc_final: 0.5840 (mmp) REVERT: Q 126 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6275 (mt) REVERT: Q 179 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7365 (mptt) REVERT: Q 241 MET cc_start: 0.4758 (ptp) cc_final: 0.4312 (ptp) REVERT: Z 18 LYS cc_start: 0.5035 (OUTLIER) cc_final: 0.4166 (pptt) outliers start: 27 outliers final: 21 residues processed: 95 average time/residue: 0.2615 time to fit residues: 35.3192 Evaluate side-chains 98 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 74 VAL 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 126 LEU Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 146 PHE Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 179 LYS 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 35 optimal weight: 0.7980 chunk 3 optimal weight: 30.0000 chunk 75 optimal weight: 5.9990 chunk 82 optimal weight: 0.0020 chunk 26 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 53 optimal weight: 0.4980 chunk 54 optimal weight: 5.9990 overall best weight: 2.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.152182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.140304 restraints weight = 48121.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.141794 restraints weight = 21601.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.142716 restraints weight = 12261.045| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.8334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13188 Z= 0.129 Angle : 0.617 11.056 19416 Z= 0.319 Chirality : 0.034 0.290 2473 Planarity : 0.005 0.063 1204 Dihedral : 23.325 179.440 5946 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.61 % Favored : 89.58 % Rotamer: Outliers : 4.74 % Allowed : 26.94 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.33), residues: 614 helix: -0.28 (0.33), residues: 230 sheet: -1.77 (0.54), residues: 80 loop : -2.23 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Q 377 HIS 0.004 0.001 HIS D 133 PHE 0.026 0.002 PHE Q 432 TYR 0.019 0.002 TYR D 130 ARG 0.007 0.001 ARG Q 81 Details of bonding type rmsd hydrogen bonds : bond 0.06060 ( 311) hydrogen bonds : angle 5.27371 ( 688) covalent geometry : bond 0.00254 (13188) covalent geometry : angle 0.61701 (19416) *********************** 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 104 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: G 128 THR cc_start: -0.0349 (OUTLIER) cc_final: -0.0597 (m) REVERT: Q 34 MET cc_start: 0.6414 (mmp) cc_final: 0.5788 (mmp) REVERT: Q 126 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6881 (tp) REVERT: Q 179 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7282 (mptt) REVERT: Q 354 LYS cc_start: 0.1363 (mttt) cc_final: 0.0715 (mmtt) REVERT: Z 18 LYS cc_start: 0.4713 (OUTLIER) cc_final: 0.3649 (pptt) outliers start: 25 outliers final: 19 residues processed: 95 average time/residue: 0.4595 time to fit residues: 63.4779 Evaluate side-chains 98 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 74 VAL 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 66 VAL Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 160 THR Chi-restraints excluded: chain Q residue 179 LYS Chi-restraints excluded: chain Q residue 274 VAL Chi-restraints excluded: chain Q residue 275 LEU 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 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 22 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 50 optimal weight: 30.0000 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 20.0000 overall best weight: 6.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.149851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.138059 restraints weight = 48117.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.139491 restraints weight = 21857.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.140356 restraints weight = 12534.762| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.8710 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= 0.192 Angle : 0.701 9.661 19416 Z= 0.358 Chirality : 0.037 0.276 2473 Planarity : 0.005 0.064 1204 Dihedral : 23.539 178.979 5946 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.98 % Allowed : 10.10 % Favored : 88.93 % Rotamer: Outliers : 5.31 % Allowed : 26.57 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.32), residues: 614 helix: -0.44 (0.32), residues: 230 sheet: -1.47 (0.57), residues: 76 loop : -2.41 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP Q 377 HIS 0.006 0.001 HIS G 100 PHE 0.025 0.002 PHE Q 280 TYR 0.020 0.002 TYR D 130 ARG 0.006 0.001 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.07094 ( 311) hydrogen bonds : angle 5.41277 ( 688) covalent geometry : bond 0.00376 (13188) covalent geometry : angle 0.70104 (19416) ********************** 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 107 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: D 139 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.8074 (t80) REVERT: Q 126 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6660 (tp) REVERT: Q 179 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7473 (mptt) REVERT: Q 354 LYS cc_start: 0.1603 (mttt) cc_final: 0.0842 (mmtt) REVERT: Z 18 LYS cc_start: 0.5051 (OUTLIER) cc_final: 0.4401 (pptt) outliers start: 28 outliers final: 20 residues processed: 99 average time/residue: 0.3659 time to fit residues: 52.3267 Evaluate side-chains 96 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 74 VAL 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 126 LEU Chi-restraints excluded: chain Q residue 160 THR Chi-restraints excluded: chain Q residue 179 LYS Chi-restraints excluded: chain Q residue 274 VAL Chi-restraints excluded: chain Q residue 281 ILE Chi-restraints excluded: chain Q residue 312 LEU 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 45 optimal weight: 20.0000 chunk 4 optimal weight: 40.0000 chunk 78 optimal weight: 0.6980 chunk 89 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 53 optimal weight: 0.0670 chunk 71 optimal weight: 0.1980 chunk 52 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 296 GLN Q 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.152002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.140277 restraints weight = 48292.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.141717 restraints weight = 22109.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.142598 restraints weight = 12687.915| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.8729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13188 Z= 0.131 Angle : 0.631 9.134 19416 Z= 0.322 Chirality : 0.034 0.291 2473 Planarity : 0.005 0.063 1204 Dihedral : 23.340 178.743 5946 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.61 % Favored : 89.41 % Rotamer: Outliers : 4.55 % Allowed : 27.89 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.33), residues: 614 helix: -0.43 (0.33), residues: 226 sheet: -1.54 (0.56), residues: 77 loop : -2.27 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Q 377 HIS 0.012 0.002 HIS Q 199 PHE 0.028 0.002 PHE Q 432 TYR 0.023 0.002 TYR D 130 ARG 0.010 0.001 ARG Q 203 Details of bonding type rmsd hydrogen bonds : bond 0.05908 ( 311) hydrogen bonds : angle 5.27004 ( 688) covalent geometry : bond 0.00257 (13188) covalent geometry : angle 0.63066 (19416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4720.97 seconds wall clock time: 85 minutes 56.82 seconds (5156.82 seconds total)