Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 16:11:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a8l_3099/08_2023/5a8l_3099.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a8l_3099/08_2023/5a8l_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_3099/08_2023/5a8l_3099.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a8l_3099/08_2023/5a8l_3099.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a8l_3099/08_2023/5a8l_3099.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a8l_3099/08_2023/5a8l_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 6.54, per 1000 atoms: 0.53 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: 6.06 Conformation dependent library (CDL) restraints added in 798.6 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: 4.51 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: 5.14 Time building geometry restraints manager: 6.44 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: 6928 35.52 - 71.05: 141 71.05 - 106.57: 11 106.57 - 142.10: 0 142.10 - 177.62: 7 Dihedral angle restraints: 7087 sinusoidal: 5322 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 7084 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: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 17.030 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 37.250 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.200 ------------------------------------------------------------------------------- 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 : 12.361 177.623 5959 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 % 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 *********************** 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 : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 173 average time/residue: 0.2989 time to fit residues: 69.4737 Evaluate side-chains 86 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.695 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4022 time to fit residues: 1.8627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 84 optimal weight: 0.3980 overall best weight: 4.2788 ------------------------------------------------------------------------------- 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 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 366 HIS Q 381 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4578 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 13188 Z= 0.246 Angle : 0.667 14.002 19416 Z= 0.333 Chirality : 0.034 0.232 2473 Planarity : 0.005 0.058 1204 Dihedral : 13.212 179.906 4746 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 1.63 % Allowed : 7.33 % Favored : 91.04 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.33), residues: 614 helix: -0.78 (0.30), residues: 225 sheet: -2.24 (0.60), residues: 60 loop : -1.15 (0.36), residues: 329 *********************** 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 120 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 109 average time/residue: 0.2300 time to fit residues: 36.8555 Evaluate side-chains 86 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1226 time to fit residues: 3.2192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 91 optimal weight: 30.0000 chunk 75 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Q 325 ASN Q 334 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4987 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.096 13188 Z= 0.275 Angle : 0.725 10.720 19416 Z= 0.373 Chirality : 0.039 0.228 2473 Planarity : 0.006 0.050 1204 Dihedral : 14.776 177.513 4746 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 1.30 % Allowed : 7.82 % Favored : 90.88 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.32), residues: 614 helix: -0.52 (0.31), residues: 239 sheet: -2.01 (0.53), residues: 81 loop : -1.85 (0.35), residues: 294 *********************** 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 107 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 5 residues processed: 99 average time/residue: 0.2784 time to fit residues: 38.5047 Evaluate side-chains 75 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2144 time to fit residues: 2.4593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4973 moved from start: 0.5251 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= 0.183 Angle : 0.590 11.039 19416 Z= 0.305 Chirality : 0.034 0.232 2473 Planarity : 0.004 0.047 1204 Dihedral : 14.689 177.451 4746 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 1.14 % Allowed : 7.49 % Favored : 91.37 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.62 (0.33), residues: 614 helix: 0.07 (0.34), residues: 239 sheet: -2.15 (0.52), residues: 76 loop : -1.72 (0.36), residues: 299 *********************** 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 : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 87 average time/residue: 0.2769 time to fit residues: 34.0297 Evaluate side-chains 77 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1119 time to fit residues: 1.9845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 199 HIS ** 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: 0.5258 moved from start: 0.6847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 13188 Z= 0.299 Angle : 0.787 8.474 19416 Z= 0.401 Chirality : 0.041 0.270 2473 Planarity : 0.006 0.061 1204 Dihedral : 16.036 178.238 4746 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 1.30 % Allowed : 9.28 % Favored : 89.41 % Rotamer Outliers : 4.93 % 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: -2.21 (0.32), residues: 614 helix: -0.39 (0.32), residues: 243 sheet: -2.03 (0.51), residues: 76 loop : -2.26 (0.33), residues: 295 *********************** 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 115 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 106 average time/residue: 0.2385 time to fit residues: 36.7793 Evaluate side-chains 90 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1159 time to fit residues: 3.9039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 17 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 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 164 ASN ** Q 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5222 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 13188 Z= 0.226 Angle : 0.674 8.106 19416 Z= 0.347 Chirality : 0.037 0.284 2473 Planarity : 0.005 0.066 1204 Dihedral : 15.859 179.062 4746 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 1.30 % Allowed : 8.79 % Favored : 89.90 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.02 (0.32), residues: 614 helix: -0.19 (0.33), residues: 244 sheet: -1.83 (0.54), residues: 76 loop : -2.23 (0.34), residues: 294 *********************** 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 98 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.804 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 93 average time/residue: 0.2519 time to fit residues: 33.4390 Evaluate side-chains 81 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.724 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1153 time to fit residues: 3.2621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 50 optimal weight: 30.0000 chunk 75 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 164 ASN ** Q 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5304 moved from start: 0.7775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 13188 Z= 0.255 Angle : 0.730 9.210 19416 Z= 0.372 Chirality : 0.039 0.295 2473 Planarity : 0.005 0.064 1204 Dihedral : 16.194 177.865 4746 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 1.14 % Allowed : 9.45 % Favored : 89.41 % Rotamer Outliers : 2.47 % 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: -0.43 (0.33), residues: 246 sheet: -1.61 (0.56), residues: 76 loop : -2.39 (0.33), residues: 292 *********************** 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 96 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.837 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 85 average time/residue: 0.2778 time to fit residues: 33.0654 Evaluate side-chains 81 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1352 time to fit residues: 3.0879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.0870 chunk 53 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 56 optimal weight: 0.0470 chunk 61 optimal weight: 20.0000 chunk 44 optimal weight: 0.1980 chunk 8 optimal weight: 20.0000 chunk 70 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 overall best weight: 3.4660 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5221 moved from start: 0.7854 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= 0.169 Angle : 0.622 10.183 19416 Z= 0.318 Chirality : 0.034 0.290 2473 Planarity : 0.004 0.062 1204 Dihedral : 15.940 176.362 4746 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.12 % Favored : 89.90 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.92 (0.33), residues: 614 helix: -0.08 (0.34), residues: 246 sheet: -1.32 (0.57), residues: 76 loop : -2.34 (0.34), residues: 292 *********************** 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 83 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.782 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 82 average time/residue: 0.2618 time to fit residues: 30.7327 Evaluate side-chains 72 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 1.052 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1180 time to fit residues: 1.5129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 8.9990 chunk 83 optimal weight: 0.0030 chunk 85 optimal weight: 0.0270 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.9852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5155 moved from start: 0.7897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 13188 Z= 0.144 Angle : 0.588 10.804 19416 Z= 0.300 Chirality : 0.033 0.288 2473 Planarity : 0.004 0.062 1204 Dihedral : 15.686 173.853 4746 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.47 % Favored : 90.55 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.79 (0.33), residues: 614 helix: -0.12 (0.34), residues: 245 sheet: -1.04 (0.59), residues: 76 loop : -2.19 (0.35), residues: 293 *********************** 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 81 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.778 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 78 average time/residue: 0.3102 time to fit residues: 33.6161 Evaluate side-chains 71 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1157 time to fit residues: 1.7917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 61 optimal weight: 30.0000 chunk 92 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 7 optimal weight: 30.0000 chunk 56 optimal weight: 0.1980 chunk 45 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.5226 moved from start: 0.8172 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= 0.182 Angle : 0.627 11.104 19416 Z= 0.318 Chirality : 0.034 0.281 2473 Planarity : 0.005 0.063 1204 Dihedral : 15.820 175.490 4746 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.45 % Favored : 89.58 % Rotamer Outliers : 0.00 % 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: -1.79 (0.33), residues: 614 helix: -0.03 (0.34), residues: 245 sheet: -1.05 (0.58), residues: 78 loop : -2.29 (0.35), residues: 291 ********************** 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 69 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.807 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.2906 time to fit residues: 28.5458 Evaluate side-chains 68 residues out of total 533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 10 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 73 optimal weight: 0.2980 chunk 30 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 4 optimal weight: 40.0000 overall best weight: 8.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4332 r_free = 0.4332 target = 0.148699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.137004 restraints weight = 48773.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.138425 restraints weight = 23183.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.139281 restraints weight = 13639.977| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.8834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 13188 Z= 0.284 Angle : 0.775 11.361 19416 Z= 0.389 Chirality : 0.040 0.285 2473 Planarity : 0.006 0.064 1204 Dihedral : 16.585 179.721 4746 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 1.14 % Allowed : 10.75 % Favored : 88.11 % Rotamer Outliers : 1.33 % 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: -0.56 (0.33), residues: 231 sheet: -1.39 (0.57), residues: 78 loop : -2.44 (0.32), residues: 305 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1958.85 seconds wall clock time: 36 minutes 47.41 seconds (2207.41 seconds total)