Starting phenix.real_space_refine on Tue Mar 11 20:26:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8il3_35526/03_2025/8il3_35526.cif Found real_map, /net/cci-nas-00/data/ceres_data/8il3_35526/03_2025/8il3_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/cci-nas-00/data/ceres_data/8il3_35526/03_2025/8il3_35526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8il3_35526/03_2025/8il3_35526.map" model { file = "/net/cci-nas-00/data/ceres_data/8il3_35526/03_2025/8il3_35526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8il3_35526/03_2025/8il3_35526.cif" } 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. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.17, per 1000 atoms: 0.81 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 670.2 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: 0.71 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: 1.44 Time building geometry restraints manager: 1.43 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: 0.00 - 2.15: 6474 2.15 - 4.30: 604 4.30 - 6.45: 100 6.45 - 8.60: 16 8.60 - 10.75: 6 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 3.040 nonbonded pdb=" O ARG C 35 " pdb=" OG1 THR C 39 " model vdw 2.366 3.040 nonbonded pdb=" O THR A 87 " pdb=" OG1 THR A 87 " model vdw 2.370 3.040 nonbonded pdb=" O GLU A 127 " pdb=" OG SER A 131 " model vdw 2.374 3.040 nonbonded pdb=" OG SER C 227 " pdb=" OD1 ASP C 233 " model vdw 2.388 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.540 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.200 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 51 poor density : 55 time to evaluate : 0.595 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: 0.2057 time to fit residues: 26.1155 Evaluate side-chains 49 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 29 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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: 1.9990 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN C 25 GLN C 92 GLN C 116 GLN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.100152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.085594 restraints weight = 18437.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.087388 restraints weight = 12258.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.088762 restraints weight = 9189.323| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5297 Z= 0.222 Angle : 0.684 7.554 7200 Z= 0.355 Chirality : 0.043 0.129 800 Planarity : 0.006 0.060 928 Dihedral : 9.064 82.513 743 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 6.69 % Allowed : 18.01 % Favored : 75.30 % 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 (0.28), residues: 659 helix: -2.06 (0.39), residues: 119 sheet: -3.33 (0.32), residues: 180 loop : -2.63 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 136 HIS 0.002 0.001 HIS B 59 PHE 0.011 0.001 PHE C 66 TYR 0.026 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 75 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 36 time to evaluate : 0.594 Fit side-chains REVERT: A 11 LEU cc_start: 0.8577 (mt) cc_final: 0.8357 (mp) REVERT: A 112 ARG cc_start: 0.5854 (OUTLIER) cc_final: 0.4333 (ppt170) REVERT: A 174 ASP cc_start: 0.6300 (p0) cc_final: 0.5717 (p0) REVERT: A 179 LEU cc_start: 0.9284 (tp) cc_final: 0.8434 (mp) REVERT: B 31 ASP cc_start: 0.8096 (t0) cc_final: 0.7740 (t70) REVERT: B 180 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.8004 (mp) REVERT: C 25 GLN cc_start: 0.6248 (OUTLIER) cc_final: 0.5738 (tm-30) REVERT: C 97 ASN cc_start: 0.7659 (m-40) cc_final: 0.7217 (m-40) outliers start: 39 outliers final: 22 residues processed: 73 average time/residue: 0.1451 time to fit residues: 14.3673 Evaluate side-chains 55 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 30 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 112 ARG 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 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 180 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 194 LEU 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 103 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 157 CYS 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: 10.0000 chunk 21 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 chunk 8 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.099075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.084808 restraints weight = 18690.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.086578 restraints weight = 12578.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.087878 restraints weight = 9461.577| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5297 Z= 0.194 Angle : 0.625 6.517 7200 Z= 0.322 Chirality : 0.042 0.123 800 Planarity : 0.005 0.051 928 Dihedral : 7.015 56.730 727 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.80 % Allowed : 21.78 % Favored : 73.41 % 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: -1.27 (0.43), residues: 119 sheet: -3.10 (0.33), residues: 181 loop : -2.37 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 108 HIS 0.004 0.001 HIS C 74 PHE 0.013 0.001 PHE A 75 TYR 0.018 0.002 TYR A 144 ARG 0.003 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 60 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 32 time to evaluate : 0.595 Fit side-chains REVERT: A 11 LEU cc_start: 0.8575 (mt) cc_final: 0.8345 (mp) REVERT: A 112 ARG cc_start: 0.5972 (OUTLIER) cc_final: 0.4395 (ppt170) REVERT: A 174 ASP cc_start: 0.6255 (p0) cc_final: 0.5722 (p0) REVERT: A 179 LEU cc_start: 0.9194 (tp) cc_final: 0.8448 (mp) REVERT: B 31 ASP cc_start: 0.8045 (t0) cc_final: 0.7722 (t70) outliers start: 28 outliers final: 17 residues processed: 58 average time/residue: 0.1806 time to fit residues: 13.7942 Evaluate side-chains 46 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 28 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 182 THR 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 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 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 1.9990 chunk 7 optimal weight: 0.0670 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 11 optimal weight: 0.0270 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.0040 chunk 10 optimal weight: 0.0770 chunk 35 optimal weight: 4.9990 overall best weight: 0.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 ASN B 176 GLN ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.101456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.086682 restraints weight = 18686.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.088719 restraints weight = 12239.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.090163 restraints weight = 9012.821| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5297 Z= 0.134 Angle : 0.570 6.685 7200 Z= 0.289 Chirality : 0.041 0.126 800 Planarity : 0.004 0.041 928 Dihedral : 5.928 58.443 722 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.29 % Allowed : 22.30 % Favored : 73.41 % 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: -3.10 (0.30), residues: 659 helix: -0.30 (0.48), residues: 111 sheet: -2.79 (0.33), residues: 174 loop : -2.27 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 108 HIS 0.002 0.001 HIS A 38 PHE 0.010 0.001 PHE A 75 TYR 0.011 0.001 TYR A 144 ARG 0.003 0.000 ARG A 24 *********************** 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 58 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 33 time to evaluate : 0.540 Fit side-chains REVERT: A 11 LEU cc_start: 0.8596 (mt) cc_final: 0.8326 (mp) REVERT: A 112 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.4388 (ppt170) REVERT: A 174 ASP cc_start: 0.6136 (p0) cc_final: 0.5589 (p0) REVERT: B 31 ASP cc_start: 0.8094 (t0) cc_final: 0.7695 (t70) outliers start: 25 outliers final: 17 residues processed: 53 average time/residue: 0.1983 time to fit residues: 13.6009 Evaluate side-chains 46 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 28 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 73 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 150 TYR 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 198 THR 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 162 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 22 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.0000 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- 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 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.099905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.085477 restraints weight = 18533.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.087341 restraints weight = 12217.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.088734 restraints weight = 9095.687| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5297 Z= 0.164 Angle : 0.571 6.727 7200 Z= 0.289 Chirality : 0.041 0.125 800 Planarity : 0.004 0.035 928 Dihedral : 5.777 57.740 722 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.63 % Allowed : 22.47 % Favored : 72.90 % 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: -2.89 (0.31), residues: 659 helix: -0.24 (0.48), residues: 118 sheet: -2.63 (0.34), residues: 180 loop : -2.10 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 108 HIS 0.005 0.001 HIS C 51 PHE 0.010 0.001 PHE C 66 TYR 0.015 0.001 TYR A 53 ARG 0.003 0.000 ARG A 146 *********************** 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 56 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 29 time to evaluate : 0.587 Fit side-chains REVERT: A 11 LEU cc_start: 0.8607 (mt) cc_final: 0.8318 (mp) REVERT: B 31 ASP cc_start: 0.8079 (t0) cc_final: 0.7732 (t70) outliers start: 27 outliers final: 26 residues processed: 52 average time/residue: 0.1624 time to fit residues: 12.1612 Evaluate side-chains 53 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 27 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 73 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 140 LEU 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 76 VAL 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 169 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 62 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 103 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 60 optimal weight: 0.0060 chunk 25 optimal weight: 0.0020 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 48 optimal weight: 0.1980 chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.2804 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.102182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.087630 restraints weight = 18319.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.089542 restraints weight = 12092.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.090942 restraints weight = 8935.830| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.3404 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= 0.128 Angle : 0.552 7.097 7200 Z= 0.275 Chirality : 0.041 0.122 800 Planarity : 0.004 0.031 928 Dihedral : 4.872 41.650 718 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.80 % Allowed : 22.64 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.31), residues: 659 helix: -0.08 (0.49), residues: 119 sheet: -2.43 (0.37), residues: 162 loop : -1.85 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 27 HIS 0.006 0.001 HIS C 51 PHE 0.011 0.001 PHE A 75 TYR 0.007 0.001 TYR B 107 ARG 0.002 0.000 ARG A 24 *********************** 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 59 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 31 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8570 (mt) cc_final: 0.8295 (mp) REVERT: A 112 ARG cc_start: 0.6177 (OUTLIER) cc_final: 0.4335 (ppt170) REVERT: A 174 ASP cc_start: 0.6180 (p0) cc_final: 0.5678 (p0) REVERT: B 31 ASP cc_start: 0.8118 (t0) cc_final: 0.7771 (t70) outliers start: 28 outliers final: 21 residues processed: 55 average time/residue: 0.1740 time to fit residues: 12.7769 Evaluate side-chains 45 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 23 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 73 THR 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 B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 150 TYR 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 184 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS 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 103 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 1 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** C 25 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 = 0.3889 r_free = 0.3889 target = 0.100320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.085739 restraints weight = 18362.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.087555 restraints weight = 12229.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.088916 restraints weight = 9099.962| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3473 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= 0.171 Angle : 0.578 7.951 7200 Z= 0.285 Chirality : 0.041 0.122 800 Planarity : 0.004 0.033 928 Dihedral : 4.942 39.735 718 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.29 % Allowed : 23.67 % Favored : 72.04 % 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: -2.38 (0.32), residues: 659 helix: -0.10 (0.48), residues: 119 sheet: -2.35 (0.38), residues: 163 loop : -1.70 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 108 HIS 0.003 0.001 HIS B 35 PHE 0.010 0.001 PHE C 66 TYR 0.016 0.001 TYR A 53 ARG 0.003 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 51 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 26 time to evaluate : 0.557 Fit side-chains REVERT: A 11 LEU cc_start: 0.8595 (mt) cc_final: 0.8316 (mp) REVERT: A 53 TYR cc_start: 0.7500 (p90) cc_final: 0.7236 (p90) REVERT: A 112 ARG cc_start: 0.6249 (OUTLIER) cc_final: 0.4374 (ppt170) REVERT: A 174 ASP cc_start: 0.6255 (p0) cc_final: 0.5784 (p0) REVERT: B 31 ASP cc_start: 0.8046 (t0) cc_final: 0.7669 (t70) outliers start: 25 outliers final: 20 residues processed: 48 average time/residue: 0.1790 time to fit residues: 11.4383 Evaluate side-chains 44 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 23 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 112 ARG Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 140 LEU 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 76 VAL Chi-restraints excluded: chain B residue 150 TYR 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 198 THR Chi-restraints excluded: chain B residue 206 LYS 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 162 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.099847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.085179 restraints weight = 18745.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.086974 restraints weight = 12640.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.088316 restraints weight = 9447.948| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3584 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= 0.159 Angle : 0.575 7.370 7200 Z= 0.283 Chirality : 0.041 0.121 800 Planarity : 0.004 0.034 928 Dihedral : 4.915 37.836 718 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.46 % Allowed : 25.04 % Favored : 70.50 % 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: -2.31 (0.32), residues: 659 helix: -0.02 (0.48), residues: 119 sheet: -2.28 (0.38), residues: 163 loop : -1.67 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 102 HIS 0.006 0.001 HIS A 38 PHE 0.009 0.001 PHE C 66 TYR 0.016 0.001 TYR A 53 ARG 0.002 0.000 ARG A 24 *********************** 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 53 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 27 time to evaluate : 0.610 Fit side-chains REVERT: A 11 LEU cc_start: 0.8588 (mt) cc_final: 0.8305 (mp) REVERT: A 24 ARG cc_start: 0.5381 (ttp80) cc_final: 0.5050 (tmt170) REVERT: A 112 ARG cc_start: 0.6364 (OUTLIER) cc_final: 0.4392 (ppt170) REVERT: A 174 ASP cc_start: 0.6343 (p0) cc_final: 0.5875 (p0) REVERT: B 31 ASP cc_start: 0.8013 (t0) cc_final: 0.7677 (t70) outliers start: 26 outliers final: 24 residues processed: 50 average time/residue: 0.1913 time to fit residues: 12.8070 Evaluate side-chains 49 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 24 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 112 ARG Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 140 LEU 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 76 VAL 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 169 HIS 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 B residue 212 VAL Chi-restraints excluded: chain C residue 62 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 162 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS C 92 GLN C 146 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.094775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.080753 restraints weight = 18980.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.082484 restraints weight = 12741.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.083719 restraints weight = 9536.443| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5297 Z= 0.328 Angle : 0.689 7.334 7200 Z= 0.349 Chirality : 0.044 0.148 800 Planarity : 0.005 0.042 928 Dihedral : 5.777 36.742 718 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.46 % Allowed : 25.90 % Favored : 69.64 % 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: -2.64 (0.31), residues: 659 helix: -0.58 (0.45), residues: 119 sheet: -2.57 (0.36), residues: 179 loop : -1.67 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 39 HIS 0.005 0.001 HIS B 59 PHE 0.020 0.002 PHE C 66 TYR 0.015 0.002 TYR A 144 ARG 0.003 0.000 ARG C 154 *********************** 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 56 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 30 time to evaluate : 0.611 Fit side-chains REVERT: A 11 LEU cc_start: 0.8641 (mt) cc_final: 0.8367 (mp) REVERT: A 112 ARG cc_start: 0.6418 (OUTLIER) cc_final: 0.4630 (ppt170) REVERT: A 174 ASP cc_start: 0.6375 (p0) cc_final: 0.5907 (p0) REVERT: B 31 ASP cc_start: 0.7975 (t0) cc_final: 0.7648 (t70) outliers start: 26 outliers final: 20 residues processed: 52 average time/residue: 0.1808 time to fit residues: 12.6154 Evaluate side-chains 48 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 27 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 140 LEU 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 76 VAL 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 B residue 212 VAL 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 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 15 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.096008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.081885 restraints weight = 18684.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.083661 restraints weight = 12264.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.084993 restraints weight = 9092.345| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5297 Z= 0.218 Angle : 0.629 8.253 7200 Z= 0.314 Chirality : 0.042 0.133 800 Planarity : 0.004 0.053 928 Dihedral : 5.332 36.055 716 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.95 % Allowed : 25.21 % Favored : 70.84 % 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: -2.44 (0.32), residues: 659 helix: -0.26 (0.46), residues: 117 sheet: -2.43 (0.38), residues: 167 loop : -1.66 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 102 HIS 0.004 0.001 HIS C 51 PHE 0.014 0.001 PHE B 95 TYR 0.009 0.001 TYR A 144 ARG 0.009 0.000 ARG A 72 ********************** 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 52 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 29 time to evaluate : 0.602 Fit side-chains REVERT: A 11 LEU cc_start: 0.8615 (mt) cc_final: 0.8344 (mp) REVERT: A 24 ARG cc_start: 0.5181 (ttp80) cc_final: 0.4966 (tmt170) REVERT: A 112 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.4604 (ppt170) REVERT: A 174 ASP cc_start: 0.6217 (p0) cc_final: 0.5705 (p0) REVERT: B 31 ASP cc_start: 0.7969 (t0) cc_final: 0.7658 (t70) outliers start: 23 outliers final: 21 residues processed: 50 average time/residue: 0.1672 time to fit residues: 11.6479 Evaluate side-chains 49 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 27 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 140 LEU 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 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 B residue 212 VAL 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 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.096373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.082224 restraints weight = 18579.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.084084 restraints weight = 12170.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.085390 restraints weight = 8925.421| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3906 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= 0.199 Angle : 0.613 8.306 7200 Z= 0.306 Chirality : 0.042 0.130 800 Planarity : 0.004 0.049 928 Dihedral : 5.195 35.505 716 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.29 % Allowed : 25.04 % Favored : 70.67 % 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: -2.34 (0.32), residues: 659 helix: -0.09 (0.47), residues: 117 sheet: -2.33 (0.38), residues: 167 loop : -1.65 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 102 HIS 0.006 0.001 HIS C 51 PHE 0.011 0.001 PHE B 95 TYR 0.021 0.002 TYR B 181 ARG 0.010 0.000 ARG A 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1870.60 seconds wall clock time: 33 minutes 23.98 seconds (2003.98 seconds total)