Starting phenix.real_space_refine on Wed Jan 17 23:55:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8il3_35526/01_2024/8il3_35526.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8il3_35526/01_2024/8il3_35526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8il3_35526/01_2024/8il3_35526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8il3_35526/01_2024/8il3_35526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8il3_35526/01_2024/8il3_35526.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8il3_35526/01_2024/8il3_35526.pdb" } resolution = 3.86 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1762 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3255 2.51 5 N 888 2.21 5 O 1005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 109": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C GLU 238": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 5172 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1682 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 204} Chain: "B" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1609 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 13, 'TRANS': 201} Chain: "C" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1881 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Time building chain proxies: 3.39, per 1000 atoms: 0.66 Number of scatterers: 5172 At special positions: 0 Unit cell: (68, 73.95, 128.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1005 8.00 N 888 7.00 C 3255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 59 " distance=2.97 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: 1.84 Conformation dependent library (CDL) restraints added in 986.2 milliseconds 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1246 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 18 sheets defined 17.9% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.134A pdb=" N THR B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 removed outlier: 3.518A pdb=" N GLY B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 51 Processing helix chain 'C' and resid 58 through 71 removed outlier: 3.679A pdb=" N PHE C 70 " --> pdb=" O PHE C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.957A pdb=" N ILE C 78 " --> pdb=" O PRO C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 89 Processing helix chain 'C' and resid 106 through 116 Processing helix chain 'C' and resid 125 through 131 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 233 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 5.905A pdb=" N LEU A 11 " --> pdb=" O GLU A 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.611A pdb=" N PHE A 75 " --> pdb=" O CYS A 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AA5, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA6, first strand: chain 'A' and resid 134 through 135 removed outlier: 3.619A pdb=" N ALA A 134 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 185 " --> pdb=" O ALA A 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 152 through 154 removed outlier: 3.543A pdb=" N LYS A 211 " --> pdb=" O CYS A 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 166 through 167 Processing sheet with id=AA9, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AB3, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AB4, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AB5, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.672A pdb=" N LEU B 143 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 185 " --> pdb=" O CYS B 145 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR B 181 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.672A pdb=" N LEU B 143 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 185 " --> pdb=" O CYS B 145 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR B 181 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 201 through 202 Processing sheet with id=AB8, first strand: chain 'C' and resid 179 through 181 removed outlier: 8.203A pdb=" N ASP C 179 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU C 215 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 181 " --> pdb=" O LEU C 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 184 through 185 removed outlier: 6.862A pdb=" N VAL C 219 " --> pdb=" O ILE C 255 " (cutoff:3.500A) 145 hydrogen bonds defined for protein. 357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.36 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1301 1.33 - 1.45: 1179 1.45 - 1.58: 2788 1.58 - 1.70: 0 1.70 - 1.82: 29 Bond restraints: 5297 Sorted by residual: bond pdb=" N VAL B 189 " pdb=" CA VAL B 189 " ideal model delta sigma weight residual 1.461 1.493 -0.033 8.70e-03 1.32e+04 1.40e+01 bond pdb=" N ILE C 105 " pdb=" CA ILE C 105 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.22e-02 6.72e+03 1.08e+01 bond pdb=" N CYS C 157 " pdb=" CA CYS C 157 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" N CYS C 231 " pdb=" CA CYS C 231 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" N ASP C 152 " pdb=" CA ASP C 152 " ideal model delta sigma weight residual 1.453 1.495 -0.042 1.31e-02 5.83e+03 1.01e+01 ... (remaining 5292 not shown) Histogram of bond angle deviations from ideal: 98.69 - 106.10: 168 106.10 - 113.51: 2838 113.51 - 120.93: 2512 120.93 - 128.34: 1620 128.34 - 135.75: 62 Bond angle restraints: 7200 Sorted by residual: angle pdb=" N PRO A 145 " pdb=" CA PRO A 145 " pdb=" C PRO A 145 " ideal model delta sigma weight residual 112.26 101.75 10.51 1.44e+00 4.82e-01 5.33e+01 angle pdb=" N VAL C 45 " pdb=" CA VAL C 45 " pdb=" C VAL C 45 " ideal model delta sigma weight residual 110.72 104.26 6.46 1.01e+00 9.80e-01 4.09e+01 angle pdb=" N PHE A 143 " pdb=" CA PHE A 143 " pdb=" C PHE A 143 " ideal model delta sigma weight residual 113.97 120.31 -6.34 1.28e+00 6.10e-01 2.45e+01 angle pdb=" N ASP C 229 " pdb=" CA ASP C 229 " pdb=" C ASP C 229 " ideal model delta sigma weight residual 111.56 104.50 7.06 1.43e+00 4.89e-01 2.44e+01 angle pdb=" N GLN C 84 " pdb=" CA GLN C 84 " pdb=" C GLN C 84 " ideal model delta sigma weight residual 109.81 120.33 -10.52 2.21e+00 2.05e-01 2.27e+01 ... (remaining 7195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 2701 17.97 - 35.95: 336 35.95 - 53.92: 96 53.92 - 71.89: 27 71.89 - 89.87: 8 Dihedral angle restraints: 3168 sinusoidal: 1236 harmonic: 1932 Sorted by residual: dihedral pdb=" CB CYS C 44 " pdb=" SG CYS C 44 " pdb=" SG CYS C 59 " pdb=" CB CYS C 59 " ideal model delta sinusoidal sigma weight residual 93.00 -179.04 -87.96 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CA THR B 101 " pdb=" C THR B 101 " pdb=" N PRO B 102 " pdb=" CA PRO B 102 " ideal model delta harmonic sigma weight residual 180.00 153.19 26.81 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA MET C 54 " pdb=" C MET C 54 " pdb=" N ARG C 55 " pdb=" CA ARG C 55 " ideal model delta harmonic sigma weight residual 180.00 153.47 26.53 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 3165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 505 0.061 - 0.121: 177 0.121 - 0.182: 78 0.182 - 0.242: 31 0.242 - 0.303: 9 Chirality restraints: 800 Sorted by residual: chirality pdb=" CA GLN C 84 " pdb=" N GLN C 84 " pdb=" C GLN C 84 " pdb=" CB GLN C 84 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA CYS C 44 " pdb=" N CYS C 44 " pdb=" C CYS C 44 " pdb=" CB CYS C 44 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB VAL C 202 " pdb=" CA VAL C 202 " pdb=" CG1 VAL C 202 " pdb=" CG2 VAL C 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 797 not shown) Planarity restraints: 928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 105 " -0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO B 106 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 106 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 106 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 101 " -0.052 5.00e-02 4.00e+02 7.80e-02 9.73e+00 pdb=" N PRO B 102 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 199 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C PHE C 199 " -0.053 2.00e-02 2.50e+03 pdb=" O PHE C 199 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY C 200 " 0.018 2.00e-02 2.50e+03 ... (remaining 925 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1859 2.87 - 3.38: 4397 3.38 - 3.88: 8911 3.88 - 4.39: 9170 4.39 - 4.90: 15848 Nonbonded interactions: 40185 Sorted by model distance: nonbonded pdb=" O GLU C 238 " pdb=" OG SER C 241 " model vdw 2.362 2.440 nonbonded pdb=" O ARG C 35 " pdb=" OG1 THR C 39 " model vdw 2.366 2.440 nonbonded pdb=" O THR A 87 " pdb=" OG1 THR A 87 " model vdw 2.370 2.440 nonbonded pdb=" O GLU A 127 " pdb=" OG SER A 131 " model vdw 2.374 2.440 nonbonded pdb=" OG SER C 227 " pdb=" OD1 ASP C 233 " model vdw 2.388 2.440 ... (remaining 40180 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 6.980 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 18.520 Find NCS groups from input model: 0.180 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 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 : 0.009 0.072 5297 Z= 0.620 Angle : 1.386 10.750 7200 Z= 0.876 Chirality : 0.084 0.303 800 Planarity : 0.010 0.080 928 Dihedral : 18.377 89.866 1919 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 8.75 % Allowed : 16.47 % Favored : 74.79 % 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: -5.16 (0.25), residues: 659 helix: -3.96 (0.24), residues: 116 sheet: -3.82 (0.32), residues: 167 loop : -3.10 (0.25), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 108 HIS 0.011 0.002 HIS B 35 PHE 0.038 0.004 PHE C 112 TYR 0.020 0.003 TYR B 107 ARG 0.008 0.001 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 55 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8660 (mt) cc_final: 0.8376 (mp) REVERT: A 112 ARG cc_start: 0.5701 (OUTLIER) cc_final: 0.4337 (ppt170) REVERT: A 174 ASP cc_start: 0.6356 (p0) cc_final: 0.5614 (p0) REVERT: B 31 ASP cc_start: 0.8401 (t0) cc_final: 0.8018 (t70) REVERT: B 187 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7254 (m) REVERT: B 197 GLN cc_start: 0.2839 (OUTLIER) cc_final: 0.2553 (tm-30) outliers start: 51 outliers final: 17 residues processed: 102 average time/residue: 0.2073 time to fit residues: 26.2158 Evaluate side-chains 49 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 29 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 41 GLN A 214 ASN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN C 92 GLN C 111 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5297 Z= 0.220 Angle : 0.676 7.853 7200 Z= 0.351 Chirality : 0.043 0.136 800 Planarity : 0.006 0.058 928 Dihedral : 9.213 87.125 743 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 7.03 % Allowed : 19.73 % Favored : 73.24 % 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: -4.11 (0.27), residues: 659 helix: -2.09 (0.39), residues: 118 sheet: -3.39 (0.32), residues: 179 loop : -2.59 (0.28), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 136 HIS 0.003 0.001 HIS B 59 PHE 0.012 0.001 PHE C 66 TYR 0.021 0.002 TYR A 144 ARG 0.004 0.001 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 35 time to evaluate : 0.639 Fit side-chains REVERT: A 11 LEU cc_start: 0.8635 (mt) cc_final: 0.8382 (mp) REVERT: A 112 ARG cc_start: 0.5924 (OUTLIER) cc_final: 0.4421 (ppt170) REVERT: A 174 ASP cc_start: 0.6543 (p0) cc_final: 0.5981 (p0) REVERT: A 179 LEU cc_start: 0.9353 (tp) cc_final: 0.8478 (mp) REVERT: B 31 ASP cc_start: 0.8126 (t0) cc_final: 0.7825 (t70) REVERT: C 25 GLN cc_start: 0.5665 (OUTLIER) cc_final: 0.5243 (tm-30) REVERT: C 97 ASN cc_start: 0.6816 (OUTLIER) cc_final: 0.6460 (m-40) outliers start: 41 outliers final: 26 residues processed: 71 average time/residue: 0.1733 time to fit residues: 16.7684 Evaluate side-chains 58 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 29 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 20 optimal weight: 0.0470 chunk 47 optimal weight: 3.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5297 Z= 0.257 Angle : 0.662 6.870 7200 Z= 0.340 Chirality : 0.043 0.127 800 Planarity : 0.005 0.052 928 Dihedral : 8.052 87.611 729 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 6.69 % Allowed : 21.96 % Favored : 71.36 % 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: -3.59 (0.29), residues: 659 helix: -1.34 (0.43), residues: 118 sheet: -3.18 (0.33), residues: 180 loop : -2.29 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 108 HIS 0.003 0.001 HIS B 59 PHE 0.016 0.002 PHE C 66 TYR 0.022 0.002 TYR A 144 ARG 0.004 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 34 time to evaluate : 0.635 Fit side-chains REVERT: A 11 LEU cc_start: 0.8676 (mt) cc_final: 0.8389 (mp) REVERT: A 112 ARG cc_start: 0.6255 (OUTLIER) cc_final: 0.4655 (pmt-80) REVERT: A 174 ASP cc_start: 0.6755 (p0) cc_final: 0.6268 (p0) REVERT: A 179 LEU cc_start: 0.9291 (tp) cc_final: 0.8508 (mp) REVERT: B 31 ASP cc_start: 0.8093 (t0) cc_final: 0.7766 (t70) outliers start: 39 outliers final: 28 residues processed: 69 average time/residue: 0.1569 time to fit residues: 14.6668 Evaluate side-chains 58 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 29 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN B 35 HIS B 59 HIS ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN C 51 HIS C 92 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 ASN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 5297 Z= 0.495 Angle : 0.839 7.363 7200 Z= 0.440 Chirality : 0.048 0.160 800 Planarity : 0.006 0.058 928 Dihedral : 7.732 43.657 724 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 7.38 % Allowed : 23.67 % Favored : 68.95 % 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: -3.76 (0.29), residues: 659 helix: -1.63 (0.42), residues: 112 sheet: -3.40 (0.30), residues: 198 loop : -2.15 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 39 HIS 0.008 0.002 HIS C 56 PHE 0.031 0.003 PHE C 66 TYR 0.036 0.003 TYR A 144 ARG 0.006 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 31 time to evaluate : 0.645 Fit side-chains REVERT: A 11 LEU cc_start: 0.8861 (mt) cc_final: 0.8459 (mp) REVERT: A 112 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.4983 (pmt-80) REVERT: A 174 ASP cc_start: 0.6942 (p0) cc_final: 0.6426 (p0) REVERT: B 110 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8064 (pt0) REVERT: B 165 THR cc_start: 0.7082 (OUTLIER) cc_final: 0.6758 (m) REVERT: C 25 GLN cc_start: 0.5913 (OUTLIER) cc_final: 0.5706 (tm-30) outliers start: 43 outliers final: 28 residues processed: 69 average time/residue: 0.1605 time to fit residues: 14.9756 Evaluate side-chains 58 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 26 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS C 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5297 Z= 0.205 Angle : 0.649 7.943 7200 Z= 0.329 Chirality : 0.043 0.129 800 Planarity : 0.005 0.052 928 Dihedral : 6.628 46.799 721 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.97 % Allowed : 25.21 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.30), residues: 659 helix: -0.91 (0.46), residues: 112 sheet: -3.25 (0.32), residues: 168 loop : -2.06 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 39 HIS 0.004 0.001 HIS B 35 PHE 0.014 0.002 PHE B 95 TYR 0.020 0.002 TYR A 144 ARG 0.003 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 28 time to evaluate : 0.606 Fit side-chains REVERT: A 11 LEU cc_start: 0.8770 (mt) cc_final: 0.8359 (mp) REVERT: A 112 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.4811 (pmt-80) REVERT: A 174 ASP cc_start: 0.6741 (OUTLIER) cc_final: 0.6313 (p0) REVERT: B 31 ASP cc_start: 0.8009 (t0) cc_final: 0.7736 (t70) REVERT: C 110 HIS cc_start: 0.6280 (OUTLIER) cc_final: 0.5989 (m-70) outliers start: 29 outliers final: 24 residues processed: 53 average time/residue: 0.1781 time to fit residues: 12.7052 Evaluate side-chains 55 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 28 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 62 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN C 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5297 Z= 0.160 Angle : 0.584 6.629 7200 Z= 0.294 Chirality : 0.041 0.124 800 Planarity : 0.004 0.042 928 Dihedral : 5.849 50.299 721 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.66 % Allowed : 26.07 % Favored : 68.27 % 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: -2.67 (0.31), residues: 659 helix: -0.39 (0.47), residues: 116 sheet: -2.99 (0.38), residues: 142 loop : -1.74 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 108 HIS 0.004 0.001 HIS B 35 PHE 0.009 0.001 PHE B 95 TYR 0.013 0.001 TYR A 144 ARG 0.002 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 34 time to evaluate : 0.577 Fit side-chains REVERT: A 11 LEU cc_start: 0.8718 (mt) cc_final: 0.8329 (mp) REVERT: B 31 ASP cc_start: 0.8000 (t0) cc_final: 0.7731 (t70) REVERT: B 110 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8130 (pt0) REVERT: C 25 GLN cc_start: 0.5585 (OUTLIER) cc_final: 0.5285 (tm-30) REVERT: C 110 HIS cc_start: 0.6249 (OUTLIER) cc_final: 0.5962 (m-70) outliers start: 33 outliers final: 22 residues processed: 63 average time/residue: 0.1483 time to fit residues: 12.7917 Evaluate side-chains 54 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 29 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 0.0470 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5297 Z= 0.175 Angle : 0.589 6.880 7200 Z= 0.296 Chirality : 0.041 0.123 800 Planarity : 0.004 0.042 928 Dihedral : 5.295 35.294 716 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 5.66 % Allowed : 27.44 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.32), residues: 659 helix: -0.28 (0.47), residues: 116 sheet: -2.78 (0.38), residues: 147 loop : -1.71 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 108 HIS 0.003 0.001 HIS B 35 PHE 0.017 0.001 PHE C 70 TYR 0.016 0.001 TYR A 53 ARG 0.002 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 30 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8735 (mt) cc_final: 0.8333 (mp) REVERT: B 31 ASP cc_start: 0.7974 (t0) cc_final: 0.7697 (t70) REVERT: C 110 HIS cc_start: 0.6263 (OUTLIER) cc_final: 0.5962 (m-70) REVERT: C 135 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7525 (p) outliers start: 33 outliers final: 27 residues processed: 60 average time/residue: 0.1554 time to fit residues: 12.7961 Evaluate side-chains 56 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 27 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 240 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5297 Z= 0.185 Angle : 0.590 7.321 7200 Z= 0.297 Chirality : 0.041 0.122 800 Planarity : 0.004 0.045 928 Dihedral : 5.274 34.319 716 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 6.17 % Allowed : 27.62 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.48 (0.31), residues: 659 helix: 0.02 (0.49), residues: 111 sheet: -2.68 (0.38), residues: 147 loop : -1.74 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 102 HIS 0.006 0.001 HIS C 51 PHE 0.016 0.001 PHE C 70 TYR 0.014 0.001 TYR A 144 ARG 0.002 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 31 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8748 (mt) cc_final: 0.8363 (mp) REVERT: B 31 ASP cc_start: 0.7964 (t0) cc_final: 0.7687 (t70) REVERT: C 100 LEU cc_start: 0.7545 (tt) cc_final: 0.7326 (tt) REVERT: C 110 HIS cc_start: 0.6261 (OUTLIER) cc_final: 0.5966 (m-70) outliers start: 36 outliers final: 32 residues processed: 64 average time/residue: 0.1533 time to fit residues: 13.4389 Evaluate side-chains 62 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 29 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain C residue 27 TRP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 240 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5297 Z= 0.394 Angle : 0.717 7.043 7200 Z= 0.369 Chirality : 0.045 0.146 800 Planarity : 0.005 0.056 928 Dihedral : 6.075 38.217 716 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 6.17 % Allowed : 27.79 % Favored : 66.04 % 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: -2.89 (0.30), residues: 659 helix: -0.58 (0.47), residues: 112 sheet: -2.80 (0.34), residues: 172 loop : -1.89 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 102 HIS 0.005 0.001 HIS B 35 PHE 0.023 0.002 PHE B 95 TYR 0.024 0.002 TYR A 144 ARG 0.003 0.001 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 31 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8880 (mt) cc_final: 0.8443 (mp) REVERT: B 31 ASP cc_start: 0.7891 (t0) cc_final: 0.7636 (t70) REVERT: C 110 HIS cc_start: 0.6370 (OUTLIER) cc_final: 0.6081 (m-70) outliers start: 36 outliers final: 34 residues processed: 64 average time/residue: 0.1500 time to fit residues: 13.2077 Evaluate side-chains 64 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 29 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 27 TRP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 240 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 5 optimal weight: 0.0170 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5297 Z= 0.159 Angle : 0.624 10.250 7200 Z= 0.307 Chirality : 0.041 0.127 800 Planarity : 0.004 0.050 928 Dihedral : 5.376 35.577 716 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 5.32 % Allowed : 29.50 % Favored : 65.18 % 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: -2.47 (0.31), residues: 659 helix: -0.16 (0.48), residues: 113 sheet: -2.39 (0.36), residues: 169 loop : -1.73 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 102 HIS 0.004 0.001 HIS C 51 PHE 0.015 0.001 PHE C 70 TYR 0.011 0.001 TYR A 144 ARG 0.001 0.000 ARG C 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 33 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8725 (mt) cc_final: 0.8318 (mp) REVERT: B 31 ASP cc_start: 0.7914 (t0) cc_final: 0.7682 (t70) REVERT: B 181 TYR cc_start: 0.7340 (m-80) cc_final: 0.6996 (m-10) REVERT: C 110 HIS cc_start: 0.6283 (OUTLIER) cc_final: 0.5975 (m-70) outliers start: 31 outliers final: 29 residues processed: 62 average time/residue: 0.1513 time to fit residues: 13.0375 Evaluate side-chains 60 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 30 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 240 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.0010 chunk 51 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 9.9990 chunk 34 optimal weight: 0.0870 overall best weight: 0.4566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.097165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.083497 restraints weight = 18720.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.085329 restraints weight = 12546.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.086577 restraints weight = 9354.185| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5297 Z= 0.144 Angle : 0.595 9.079 7200 Z= 0.291 Chirality : 0.041 0.127 800 Planarity : 0.004 0.047 928 Dihedral : 4.928 33.246 716 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.29 % Allowed : 30.87 % Favored : 64.84 % 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: 659 helix: -0.00 (0.49), residues: 117 sheet: -2.34 (0.40), residues: 148 loop : -1.60 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 102 HIS 0.005 0.001 HIS C 51 PHE 0.015 0.001 PHE C 70 TYR 0.011 0.001 TYR A 144 ARG 0.001 0.000 ARG C 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1350.05 seconds wall clock time: 25 minutes 22.71 seconds (1522.71 seconds total)