Starting phenix.real_space_refine on Fri Mar 15 16:43:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a8l_3099/03_2024/5a8l_3099.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a8l_3099/03_2024/5a8l_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a8l_3099/03_2024/5a8l_3099.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a8l_3099/03_2024/5a8l_3099.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a8l_3099/03_2024/5a8l_3099.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a8l_3099/03_2024/5a8l_3099.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.95, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 5.76 Conformation dependent library (CDL) restraints added in 931.9 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: 4.76 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: 5.54 Time building geometry restraints manager: 6.15 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: 100.40 - 107.12: 2089 107.12 - 113.84: 7995 113.84 - 120.56: 4609 120.56 - 127.28: 4039 127.28 - 134.00: 684 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 2.440 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 2.440 ... (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 ========== 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: 9.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 14.950 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 38.650 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.450 ------------------------------------------------------------------------------- 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= 0.244 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 168 time to evaluate : 0.733 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: 0.2904 time to fit residues: 67.4313 Evaluate side-chains 87 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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: 6.9990 chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 84 optimal weight: 0.3980 overall best weight: 4.4788 ------------------------------------------------------------------------------- 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 129 ASN Q 162 GLN Q 200 ASN ** Q 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 266 GLN Q 296 GLN Q 334 HIS ** Q 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 366 HIS Q 381 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4593 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13188 Z= 0.235 Angle : 0.662 13.408 19416 Z= 0.332 Chirality : 0.034 0.219 2473 Planarity : 0.005 0.057 1204 Dihedral : 22.476 179.634 5954 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 1.63 % Allowed : 7.33 % Favored : 91.04 % Rotamer: Outliers : 4.17 % Allowed : 11.01 % Favored : 84.82 % 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: -1.74 (0.33), residues: 614 helix: -0.79 (0.30), residues: 225 sheet: -2.20 (0.61), residues: 60 loop : -1.13 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 377 HIS 0.004 0.001 HIS G 100 PHE 0.014 0.002 PHE Q 213 TYR 0.021 0.002 TYR D 130 ARG 0.012 0.001 ARG D 128 *********************** 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 124 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 162 GLN cc_start: 0.5111 (OUTLIER) cc_final: 0.4854 (tm-30) REVERT: Q 246 LEU cc_start: 0.3243 (OUTLIER) cc_final: 0.2683 (mp) outliers start: 22 outliers final: 10 residues processed: 113 average time/residue: 0.2415 time to fit residues: 38.7321 Evaluate side-chains 90 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 129 ASN Chi-restraints excluded: chain Q residue 162 GLN 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 317 VAL 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 46 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 57 optimal weight: 0.0000 chunk 23 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 91 optimal weight: 50.0000 chunk 75 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 overall best weight: 4.3992 ------------------------------------------------------------------------------- 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 265 ASN ** Q 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 325 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4788 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 13188 Z= 0.220 Angle : 0.618 12.470 19416 Z= 0.314 Chirality : 0.033 0.204 2473 Planarity : 0.005 0.036 1204 Dihedral : 22.547 177.752 5950 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 1.47 % Allowed : 7.33 % Favored : 91.21 % Rotamer: Outliers : 4.93 % Allowed : 12.71 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.76 (0.32), residues: 614 helix: -0.38 (0.32), residues: 238 sheet: -2.06 (0.58), residues: 65 loop : -1.56 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 377 HIS 0.004 0.001 HIS Q 199 PHE 0.049 0.003 PHE Q 357 TYR 0.025 0.002 TYR D 130 ARG 0.005 0.001 ARG Q 330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 34 MET cc_start: 0.4341 (mtp) cc_final: 0.4008 (tmm) REVERT: Q 245 ARG cc_start: 0.5303 (OUTLIER) cc_final: 0.3067 (ptp-170) outliers start: 26 outliers final: 12 residues processed: 95 average time/residue: 0.2682 time to fit residues: 35.8750 Evaluate side-chains 82 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 32 THR Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 229 SER Chi-restraints excluded: chain Q residue 245 ARG Chi-restraints excluded: chain Q residue 255 ASP 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 18 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.0870 chunk 63 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 56 optimal weight: 0.3980 chunk 84 optimal weight: 0.0070 chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 overall best weight: 1.2778 ------------------------------------------------------------------------------- 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 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4733 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13188 Z= 0.132 Angle : 0.537 10.280 19416 Z= 0.273 Chirality : 0.031 0.206 2473 Planarity : 0.003 0.029 1204 Dihedral : 22.427 179.454 5950 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 1.14 % Allowed : 6.68 % Favored : 92.18 % Rotamer: Outliers : 3.04 % Allowed : 15.18 % 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 (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: -1.51 (0.33), residues: 614 helix: 0.08 (0.34), residues: 242 sheet: -1.92 (0.56), residues: 65 loop : -1.67 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 53 HIS 0.003 0.001 HIS Q 356 PHE 0.018 0.002 PHE Q 280 TYR 0.019 0.002 TYR D 130 ARG 0.006 0.000 ARG Q 81 *********************** 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 94 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: Q 241 MET cc_start: 0.3828 (ptp) cc_final: 0.3561 (ptp) REVERT: Q 245 ARG cc_start: 0.5265 (OUTLIER) cc_final: 0.2993 (ptp-170) REVERT: Q 246 LEU cc_start: 0.3730 (OUTLIER) cc_final: 0.3361 (mp) outliers start: 16 outliers final: 9 residues processed: 88 average time/residue: 0.2677 time to fit residues: 33.1205 Evaluate side-chains 84 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 198 ARG Chi-restraints excluded: chain Q residue 245 ARG Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 317 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 0.0870 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 overall best weight: 5.6166 ------------------------------------------------------------------------------- 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 266 GLN ** Q 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5053 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13188 Z= 0.244 Angle : 0.677 6.910 19416 Z= 0.349 Chirality : 0.037 0.244 2473 Planarity : 0.005 0.056 1204 Dihedral : 22.960 178.623 5950 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 1.30 % Allowed : 7.49 % Favored : 91.21 % Rotamer: Outliers : 4.74 % Allowed : 15.75 % 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: -1.78 (0.32), residues: 614 helix: 0.01 (0.33), residues: 248 sheet: -1.76 (0.52), residues: 81 loop : -2.09 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 53 HIS 0.009 0.002 HIS Q 180 PHE 0.025 0.002 PHE Q 280 TYR 0.025 0.002 TYR D 130 ARG 0.007 0.001 ARG Q 166 *********************** 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 102 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 0.821 Fit side-chains REVERT: Q 198 ARG cc_start: 0.6450 (OUTLIER) cc_final: 0.5668 (mpp80) REVERT: Q 245 ARG cc_start: 0.5207 (OUTLIER) cc_final: 0.3448 (ptt180) outliers start: 25 outliers final: 16 residues processed: 93 average time/residue: 0.2919 time to fit residues: 37.5273 Evaluate side-chains 87 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 57 ARG Chi-restraints excluded: chain G residue 70 GLN 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 60 SER Chi-restraints excluded: chain Q residue 99 THR 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 198 ARG Chi-restraints excluded: chain Q residue 245 ARG 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 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 30 optimal weight: 20.0000 chunk 80 optimal weight: 50.0000 chunk 17 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 7 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 overall best weight: 11.9994 ------------------------------------------------------------------------------- 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 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5401 moved from start: 0.7769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 13188 Z= 0.445 Angle : 1.002 10.247 19416 Z= 0.504 Chirality : 0.050 0.291 2473 Planarity : 0.007 0.067 1204 Dihedral : 24.124 175.613 5946 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 23.50 Ramachandran Plot: Outliers : 1.30 % Allowed : 10.59 % Favored : 88.11 % Rotamer: Outliers : 6.83 % Allowed : 17.08 % Favored : 76.09 % 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: -2.72 (0.30), residues: 614 helix: -0.71 (0.32), residues: 236 sheet: -1.89 (0.53), residues: 79 loop : -2.73 (0.29), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP G 53 HIS 0.019 0.004 HIS Q 180 PHE 0.033 0.004 PHE Q 357 TYR 0.024 0.003 TYR D 130 ARG 0.011 0.002 ARG Q 203 *********************** 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 119 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 83 time to evaluate : 0.959 Fit side-chains REVERT: Q 65 ARG cc_start: 0.6874 (ttt-90) cc_final: 0.4422 (mmt180) REVERT: Q 196 GLU cc_start: 0.6151 (mm-30) cc_final: 0.5935 (mm-30) outliers start: 36 outliers final: 23 residues processed: 109 average time/residue: 0.2530 time to fit residues: 39.6484 Evaluate side-chains 94 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 129 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 58 THR Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain Q residue 160 THR Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 224 LEU Chi-restraints excluded: chain Q residue 234 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 329 MET Chi-restraints excluded: chain Z residue 7 SER 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 86 optimal weight: 0.0970 chunk 10 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.7584 ------------------------------------------------------------------------------- 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 Q 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5237 moved from start: 0.7671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13188 Z= 0.189 Angle : 0.677 8.660 19416 Z= 0.347 Chirality : 0.037 0.295 2473 Planarity : 0.005 0.067 1204 Dihedral : 23.469 178.902 5946 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 1.14 % Allowed : 8.63 % Favored : 90.23 % Rotamer: Outliers : 6.26 % Allowed : 17.08 % 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: -2.19 (0.33), residues: 614 helix: -0.12 (0.35), residues: 247 sheet: -1.90 (0.49), residues: 91 loop : -2.56 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 377 HIS 0.004 0.001 HIS G 100 PHE 0.022 0.002 PHE Q 280 TYR 0.020 0.002 TYR G 14 ARG 0.010 0.001 ARG D 128 *********************** 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 111 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 78 time to evaluate : 0.790 Fit side-chains REVERT: G 116 MET cc_start: 0.1524 (tpt) cc_final: 0.1286 (tpp) REVERT: Q 246 LEU cc_start: 0.5089 (OUTLIER) cc_final: 0.4771 (mp) REVERT: Q 414 ARG cc_start: 0.5572 (OUTLIER) cc_final: 0.4988 (mtp85) outliers start: 33 outliers final: 21 residues processed: 102 average time/residue: 0.3047 time to fit residues: 43.1015 Evaluate side-chains 90 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 67 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain G residue 97 ASN Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 85 HIS Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 101 VAL 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 162 GLN Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 255 ASP 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 414 ARG Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 17 CYS Chi-restraints excluded: chain Z residue 18 LYS Chi-restraints excluded: chain Z residue 19 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 56 optimal weight: 0.0170 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 0.2980 chunk 8 optimal weight: 30.0000 chunk 70 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 2.0624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5180 moved from start: 0.7680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13188 Z= 0.158 Angle : 0.622 10.498 19416 Z= 0.321 Chirality : 0.034 0.290 2473 Planarity : 0.004 0.063 1204 Dihedral : 23.215 178.802 5946 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.12 % Favored : 89.90 % Rotamer: Outliers : 4.17 % Allowed : 21.44 % Favored : 74.38 % 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: -2.05 (0.33), residues: 614 helix: 0.10 (0.34), residues: 249 sheet: -1.86 (0.50), residues: 86 loop : -2.60 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Q 377 HIS 0.006 0.001 HIS G 100 PHE 0.041 0.002 PHE Q 432 TYR 0.018 0.002 TYR D 130 ARG 0.006 0.000 ARG Q 414 *********************** 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 102 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.804 Fit side-chains REVERT: D 135 ARG cc_start: 0.6811 (mtm180) cc_final: 0.6504 (mtm180) REVERT: G 67 ARG cc_start: 0.2899 (mmt180) cc_final: 0.2641 (mmt180) REVERT: G 116 MET cc_start: 0.1370 (tpt) cc_final: 0.1133 (tpp) REVERT: Q 34 MET cc_start: 0.4070 (mpp) cc_final: 0.3799 (mtm) outliers start: 22 outliers final: 15 residues processed: 97 average time/residue: 0.2690 time to fit residues: 36.1741 Evaluate side-chains 87 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain H residue 79 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 160 THR Chi-restraints excluded: chain Q residue 274 VAL Chi-restraints excluded: chain Q residue 317 VAL Chi-restraints excluded: chain Q residue 322 VAL Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 17 CYS Chi-restraints excluded: chain Z residue 18 LYS Chi-restraints excluded: chain Z residue 19 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 88 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: G 70 GLN ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5283 moved from start: 0.8070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13188 Z= 0.228 Angle : 0.693 10.997 19416 Z= 0.352 Chirality : 0.037 0.337 2473 Planarity : 0.005 0.063 1204 Dihedral : 23.338 179.948 5946 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.59 % Favored : 88.60 % Rotamer: Outliers : 4.36 % Allowed : 21.25 % Favored : 74.38 % 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: -2.11 (0.32), residues: 614 helix: -0.13 (0.34), residues: 243 sheet: -1.54 (0.56), residues: 76 loop : -2.51 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 377 HIS 0.006 0.001 HIS Q 180 PHE 0.044 0.003 PHE Q 432 TYR 0.022 0.002 TYR D 130 ARG 0.006 0.001 ARG Q 81 *********************** 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 92 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 69 time to evaluate : 0.795 Fit side-chains REVERT: Q 34 MET cc_start: 0.4645 (mpp) cc_final: 0.4311 (mtm) REVERT: Q 65 ARG cc_start: 0.6841 (ttt-90) cc_final: 0.4375 (mmt180) outliers start: 23 outliers final: 20 residues processed: 86 average time/residue: 0.2666 time to fit residues: 32.3713 Evaluate side-chains 87 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 67 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 79 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 160 THR Chi-restraints excluded: chain Q residue 179 LYS Chi-restraints excluded: chain Q residue 255 ASP Chi-restraints excluded: chain Q residue 274 VAL Chi-restraints excluded: chain Q residue 281 ILE Chi-restraints excluded: chain Q residue 302 CYS 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 11 LEU Chi-restraints excluded: chain Z residue 17 CYS Chi-restraints excluded: chain Z residue 18 LYS Chi-restraints excluded: chain Z residue 19 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 6.9990 chunk 41 optimal weight: 0.0980 chunk 61 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 85 optimal weight: 40.0000 chunk 73 optimal weight: 9.9990 chunk 7 optimal weight: 30.0000 chunk 56 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 67 ASN ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5241 moved from start: 0.8212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13188 Z= 0.181 Angle : 0.639 10.760 19416 Z= 0.327 Chirality : 0.035 0.284 2473 Planarity : 0.005 0.063 1204 Dihedral : 23.286 179.862 5946 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.12 % Favored : 90.07 % Rotamer: Outliers : 4.74 % Allowed : 21.63 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.09 (0.33), residues: 614 helix: -0.05 (0.34), residues: 239 sheet: -1.67 (0.52), residues: 86 loop : -2.50 (0.34), residues: 289 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 0.044 0.003 PHE Q 431 TYR 0.017 0.002 TYR G 14 ARG 0.007 0.001 ARG Q 81 ********************** 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 97 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 72 time to evaluate : 0.715 Fit side-chains REVERT: Q 34 MET cc_start: 0.4986 (mpp) cc_final: 0.4695 (mtm) REVERT: Q 65 ARG cc_start: 0.6798 (ttt-90) cc_final: 0.4398 (mmt180) outliers start: 25 outliers final: 19 residues processed: 89 average time/residue: 0.2877 time to fit residues: 35.4006 Evaluate side-chains 84 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 79 VAL Chi-restraints excluded: chain H residue 85 HIS 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 160 THR Chi-restraints excluded: chain Q residue 179 LYS Chi-restraints excluded: chain Q residue 274 VAL Chi-restraints excluded: chain Q residue 302 CYS 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 11 LEU Chi-restraints excluded: chain Z residue 17 CYS Chi-restraints excluded: chain Z residue 18 LYS Chi-restraints excluded: chain Z residue 19 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 64 optimal weight: 0.3980 chunk 4 optimal weight: 40.0000 overall best weight: 8.6790 ------------------------------------------------------------------------------- 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 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 296 GLN ** Q 420 GLN ** 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 = 0.4318 r_free = 0.4318 target = 0.147598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.135976 restraints weight = 48592.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.137430 restraints weight = 23107.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.138301 restraints weight = 13580.948| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.8893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13188 Z= 0.297 Angle : 0.810 10.996 19416 Z= 0.409 Chirality : 0.042 0.274 2473 Planarity : 0.006 0.065 1204 Dihedral : 23.731 177.080 5946 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.89 % Favored : 87.30 % Rotamer: Outliers : 3.98 % Allowed : 23.53 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.35 (0.32), residues: 614 helix: -0.31 (0.34), residues: 229 sheet: -1.71 (0.57), residues: 75 loop : -2.56 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP Q 377 HIS 0.008 0.002 HIS Q 180 PHE 0.053 0.004 PHE Q 431 TYR 0.022 0.003 TYR G 14 ARG 0.006 0.001 ARG Q 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2146.20 seconds wall clock time: 39 minutes 57.43 seconds (2397.43 seconds total)