Starting phenix.real_space_refine on Thu Mar 13 12:16:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5v6p_8637/03_2025/5v6p_8637.cif Found real_map, /net/cci-nas-00/data/ceres_data/5v6p_8637/03_2025/5v6p_8637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5v6p_8637/03_2025/5v6p_8637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5v6p_8637/03_2025/5v6p_8637.map" model { file = "/net/cci-nas-00/data/ceres_data/5v6p_8637/03_2025/5v6p_8637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5v6p_8637/03_2025/5v6p_8637.cif" } resolution = 4.1 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 ------------------------------------------------------------------------------- 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 3030 2.51 5 N 698 2.21 5 O 764 1.98 5 H 4676 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9194 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 4597 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 3, 'TRANS': 266} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 8.23, per 1000 atoms: 0.90 Number of scatterers: 9194 At special positions: 0 Unit cell: (87.75, 90.45, 76.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 764 8.00 N 698 7.00 C 3030 6.00 H 4676 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 690.0 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1060 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 94.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 10 through 31 Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 45 through 69 removed outlier: 3.702A pdb=" N MET A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 Proline residue: A 87 - end of helix removed outlier: 3.623A pdb=" N LEU A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 135 removed outlier: 8.314A pdb=" N PHE A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 147 through 176 removed outlier: 3.638A pdb=" N SER A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 220 removed outlier: 3.642A pdb=" N LEU A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 289 Processing helix chain 'A' and resid 295 through 324 removed outlier: 4.106A pdb=" N LYS A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASP A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 31 Processing helix chain 'B' and resid 34 through 45 Processing helix chain 'B' and resid 45 through 69 removed outlier: 3.702A pdb=" N MET B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 99 Proline residue: B 87 - end of helix removed outlier: 3.624A pdb=" N LEU B 99 " --> pdb=" O PHE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 135 removed outlier: 8.314A pdb=" N PHE B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 147 through 176 removed outlier: 3.638A pdb=" N SER B 151 " --> pdb=" O PHE B 147 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 220 removed outlier: 3.641A pdb=" N LEU B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 289 Processing helix chain 'B' and resid 295 through 324 removed outlier: 4.106A pdb=" N LYS B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASP B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 1185 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: 3.11 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 4670 1.13 - 1.30: 681 1.30 - 1.48: 1955 1.48 - 1.65: 1952 1.65 - 1.83: 46 Bond restraints: 9304 Sorted by residual: bond pdb=" NE2 HIS A 79 " pdb=" HE2 HIS A 79 " ideal model delta sigma weight residual 0.860 1.052 -0.192 2.00e-02 2.50e+03 9.24e+01 bond pdb=" NE2 HIS B 79 " pdb=" HE2 HIS B 79 " ideal model delta sigma weight residual 0.860 1.052 -0.192 2.00e-02 2.50e+03 9.20e+01 bond pdb=" NH1 ARG A 128 " pdb="HH12 ARG A 128 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.42e+01 bond pdb=" NH1 ARG B 128 " pdb="HH12 ARG B 128 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" NE2 HIS B 122 " pdb=" HE2 HIS B 122 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.36e+01 ... (remaining 9299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 15244 2.91 - 5.81: 1086 5.81 - 8.72: 442 8.72 - 11.62: 34 11.62 - 14.53: 6 Bond angle restraints: 16812 Sorted by residual: angle pdb=" CA ASP B 161 " pdb=" CB ASP B 161 " pdb=" CG ASP B 161 " ideal model delta sigma weight residual 112.60 118.59 -5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" CA ASP A 161 " pdb=" CB ASP A 161 " pdb=" CG ASP A 161 " ideal model delta sigma weight residual 112.60 118.57 -5.97 1.00e+00 1.00e+00 3.57e+01 angle pdb=" C ILE A 291 " pdb=" N PRO A 292 " pdb=" CA PRO A 292 " ideal model delta sigma weight residual 119.78 125.76 -5.98 1.03e+00 9.43e-01 3.37e+01 angle pdb=" C ILE B 291 " pdb=" N PRO B 292 " pdb=" CA PRO B 292 " ideal model delta sigma weight residual 119.78 125.73 -5.95 1.03e+00 9.43e-01 3.33e+01 angle pdb=" C ILE A 53 " pdb=" CA ILE A 53 " pdb=" CB ILE A 53 " ideal model delta sigma weight residual 111.97 105.84 6.13 1.28e+00 6.10e-01 2.30e+01 ... (remaining 16807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.41: 3978 11.41 - 22.81: 276 22.81 - 34.22: 58 34.22 - 45.62: 18 45.62 - 57.03: 14 Dihedral angle restraints: 4344 sinusoidal: 2276 harmonic: 2068 Sorted by residual: dihedral pdb=" CD2 HIS A 286 " pdb=" CG HIS A 286 " pdb=" ND1 HIS A 286 " pdb=" HD1 HIS A 286 " ideal model delta harmonic sigma weight residual -180.00 -139.78 -40.22 0 5.00e+00 4.00e-02 6.47e+01 dihedral pdb=" CD2 HIS B 286 " pdb=" CG HIS B 286 " pdb=" ND1 HIS B 286 " pdb=" HD1 HIS B 286 " ideal model delta harmonic sigma weight residual -180.00 -139.82 -40.18 0 5.00e+00 4.00e-02 6.46e+01 dihedral pdb=" CD2 HIS B 101 " pdb=" CG HIS B 101 " pdb=" ND1 HIS B 101 " pdb=" HD1 HIS B 101 " ideal model delta harmonic sigma weight residual 180.00 142.02 37.98 0 5.00e+00 4.00e-02 5.77e+01 ... (remaining 4341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 416 0.061 - 0.121: 227 0.121 - 0.182: 80 0.182 - 0.243: 19 0.243 - 0.304: 8 Chirality restraints: 750 Sorted by residual: chirality pdb=" CG LEU A 129 " pdb=" CB LEU A 129 " pdb=" CD1 LEU A 129 " pdb=" CD2 LEU A 129 " both_signs ideal model delta sigma weight residual False -2.59 -2.89 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CG LEU B 129 " pdb=" CB LEU B 129 " pdb=" CD1 LEU B 129 " pdb=" CD2 LEU B 129 " both_signs ideal model delta sigma weight residual False -2.59 -2.89 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CG LEU A 197 " pdb=" CB LEU A 197 " pdb=" CD1 LEU A 197 " pdb=" CD2 LEU A 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.87 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 747 not shown) Planarity restraints: 1268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 286 " 0.157 2.00e-02 2.50e+03 1.59e-01 5.69e+02 pdb=" CG HIS A 286 " 0.091 2.00e-02 2.50e+03 pdb=" ND1 HIS A 286 " 0.141 2.00e-02 2.50e+03 pdb=" CD2 HIS A 286 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS A 286 " 0.075 2.00e-02 2.50e+03 pdb=" NE2 HIS A 286 " -0.028 2.00e-02 2.50e+03 pdb=" HD1 HIS A 286 " -0.371 2.00e-02 2.50e+03 pdb=" HD2 HIS A 286 " -0.134 2.00e-02 2.50e+03 pdb=" HE1 HIS A 286 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 286 " -0.156 2.00e-02 2.50e+03 1.59e-01 5.68e+02 pdb=" CG HIS B 286 " -0.091 2.00e-02 2.50e+03 pdb=" ND1 HIS B 286 " -0.141 2.00e-02 2.50e+03 pdb=" CD2 HIS B 286 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS B 286 " -0.075 2.00e-02 2.50e+03 pdb=" NE2 HIS B 286 " 0.027 2.00e-02 2.50e+03 pdb=" HD1 HIS B 286 " 0.371 2.00e-02 2.50e+03 pdb=" HD2 HIS B 286 " 0.134 2.00e-02 2.50e+03 pdb=" HE1 HIS B 286 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 101 " -0.140 2.00e-02 2.50e+03 1.43e-01 4.60e+02 pdb=" CG HIS A 101 " -0.074 2.00e-02 2.50e+03 pdb=" ND1 HIS A 101 " -0.125 2.00e-02 2.50e+03 pdb=" CD2 HIS A 101 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS A 101 " -0.074 2.00e-02 2.50e+03 pdb=" NE2 HIS A 101 " 0.029 2.00e-02 2.50e+03 pdb=" HD1 HIS A 101 " 0.334 2.00e-02 2.50e+03 pdb=" HD2 HIS A 101 " 0.115 2.00e-02 2.50e+03 pdb=" HE1 HIS A 101 " -0.104 2.00e-02 2.50e+03 ... (remaining 1265 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 732 2.24 - 2.83: 20114 2.83 - 3.42: 26087 3.42 - 4.01: 33152 4.01 - 4.60: 50653 Nonbonded interactions: 130738 Sorted by model distance: nonbonded pdb=" O VAL A 190 " pdb=" HG1 THR A 194 " model vdw 1.653 2.450 nonbonded pdb=" O VAL B 190 " pdb=" HG1 THR B 194 " model vdw 1.653 2.450 nonbonded pdb=" O LEU A 203 " pdb=" HG1 THR A 207 " model vdw 1.665 2.450 nonbonded pdb=" O LEU B 203 " pdb=" HG1 THR B 207 " model vdw 1.665 2.450 nonbonded pdb=" OD1 ASP B 199 " pdb=" HZ1 LYS B 282 " model vdw 1.668 2.450 ... (remaining 130733 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.630 Find NCS groups from input model: 0.120 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 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 : 0.015 0.076 4628 Z= 0.921 Angle : 1.365 7.304 6272 Z= 0.975 Chirality : 0.083 0.304 750 Planarity : 0.010 0.069 738 Dihedral : 9.648 55.820 1640 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.63 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.33), residues: 532 helix: 0.44 (0.22), residues: 456 sheet: None (None), residues: 0 loop : -1.20 (0.74), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.008 TRP A 212 HIS 0.009 0.004 HIS B 286 PHE 0.025 0.005 PHE A 95 TYR 0.030 0.005 TYR B 270 ARG 0.004 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.8858 (mt0) cc_final: 0.8480 (mp10) REVERT: A 68 LYS cc_start: 0.8880 (mttt) cc_final: 0.8422 (mmmt) REVERT: A 116 LEU cc_start: 0.8482 (tt) cc_final: 0.8222 (mt) REVERT: A 206 GLN cc_start: 0.8574 (mt0) cc_final: 0.8371 (tm-30) REVERT: B 58 ASN cc_start: 0.7585 (m-40) cc_final: 0.7370 (m-40) REVERT: B 64 GLN cc_start: 0.8874 (mt0) cc_final: 0.8507 (mp10) REVERT: B 68 LYS cc_start: 0.8898 (mttt) cc_final: 0.8464 (mmmt) REVERT: B 116 LEU cc_start: 0.8442 (tt) cc_final: 0.8192 (mt) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.3720 time to fit residues: 158.7430 Evaluate side-chains 262 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.155112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.132677 restraints weight = 34353.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.139313 restraints weight = 15306.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.143351 restraints weight = 8682.856| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4628 Z= 0.255 Angle : 0.738 11.502 6272 Z= 0.426 Chirality : 0.038 0.150 750 Planarity : 0.005 0.036 738 Dihedral : 4.618 25.124 578 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.38 % Allowed : 1.88 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.32), residues: 532 helix: 1.74 (0.21), residues: 462 sheet: None (None), residues: 0 loop : -1.10 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 305 HIS 0.008 0.003 HIS A 286 PHE 0.024 0.002 PHE B 100 TYR 0.020 0.002 TYR A 23 ARG 0.006 0.001 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8957 (mttt) cc_final: 0.8457 (mmmt) REVERT: A 76 LEU cc_start: 0.8321 (tt) cc_final: 0.7808 (tp) REVERT: A 149 ARG cc_start: 0.7497 (mmm160) cc_final: 0.7253 (tpt-90) REVERT: A 164 ILE cc_start: 0.8533 (mm) cc_final: 0.8219 (mm) REVERT: B 68 LYS cc_start: 0.9018 (mttt) cc_final: 0.8461 (mmmt) REVERT: B 76 LEU cc_start: 0.8269 (tt) cc_final: 0.7756 (tp) REVERT: B 164 ILE cc_start: 0.8344 (mm) cc_final: 0.8125 (tp) REVERT: B 297 MET cc_start: 0.7233 (ptp) cc_final: 0.6633 (mtp) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3572 time to fit residues: 133.7711 Evaluate side-chains 240 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN B 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.152562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.131011 restraints weight = 35264.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.136733 restraints weight = 15718.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.140183 restraints weight = 9132.669| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4628 Z= 0.239 Angle : 0.685 11.454 6272 Z= 0.390 Chirality : 0.036 0.170 750 Planarity : 0.004 0.032 738 Dihedral : 4.582 25.892 578 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.07 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: 2.61 (0.33), residues: 532 helix: 2.10 (0.21), residues: 462 sheet: None (None), residues: 0 loop : -0.80 (0.73), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 305 HIS 0.006 0.002 HIS B 286 PHE 0.018 0.002 PHE A 54 TYR 0.014 0.002 TYR A 23 ARG 0.003 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8547 (mttt) cc_final: 0.8279 (tptp) REVERT: A 68 LYS cc_start: 0.8883 (mttt) cc_final: 0.8319 (mmmt) REVERT: A 76 LEU cc_start: 0.8340 (tt) cc_final: 0.7568 (tp) REVERT: A 111 PHE cc_start: 0.7690 (m-80) cc_final: 0.7381 (m-80) REVERT: A 127 ASP cc_start: 0.8207 (m-30) cc_final: 0.8007 (m-30) REVERT: B 68 LYS cc_start: 0.8904 (mttt) cc_final: 0.8366 (mmmt) REVERT: B 76 LEU cc_start: 0.8240 (tt) cc_final: 0.7589 (tp) REVERT: B 111 PHE cc_start: 0.7564 (m-80) cc_final: 0.7164 (m-80) REVERT: B 128 ARG cc_start: 0.7956 (mmt-90) cc_final: 0.7709 (mmt-90) REVERT: B 289 MET cc_start: 0.5442 (mtp) cc_final: 0.5214 (mtp) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.3496 time to fit residues: 124.6415 Evaluate side-chains 208 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN B 189 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** 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 = 0.4209 r_free = 0.4209 target = 0.150012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.129066 restraints weight = 34861.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.134437 restraints weight = 16113.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.137853 restraints weight = 9632.771| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.7195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4628 Z= 0.244 Angle : 0.648 7.033 6272 Z= 0.385 Chirality : 0.037 0.124 750 Planarity : 0.004 0.030 738 Dihedral : 4.696 26.232 578 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.82 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: 2.81 (0.34), residues: 532 helix: 2.19 (0.21), residues: 464 sheet: None (None), residues: 0 loop : -0.45 (0.85), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 305 HIS 0.004 0.002 HIS B 286 PHE 0.022 0.002 PHE B 214 TYR 0.010 0.002 TYR B 23 ARG 0.004 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8739 (mttt) cc_final: 0.8286 (mmmt) REVERT: A 200 LEU cc_start: 0.8734 (tp) cc_final: 0.8531 (tp) REVERT: B 68 LYS cc_start: 0.8833 (mttt) cc_final: 0.8324 (mmmt) REVERT: B 200 LEU cc_start: 0.8762 (tp) cc_final: 0.8534 (tp) REVERT: B 201 LEU cc_start: 0.9026 (tp) cc_final: 0.8812 (tt) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.3853 time to fit residues: 129.8626 Evaluate side-chains 237 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** 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 = 0.4215 r_free = 0.4215 target = 0.150101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.129807 restraints weight = 34058.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.135148 restraints weight = 15516.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.138518 restraints weight = 9126.311| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.7739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4628 Z= 0.194 Angle : 0.583 7.116 6272 Z= 0.337 Chirality : 0.034 0.151 750 Planarity : 0.004 0.034 738 Dihedral : 4.592 27.029 578 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.01 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: 2.94 (0.34), residues: 532 helix: 2.25 (0.21), residues: 470 sheet: None (None), residues: 0 loop : -0.46 (0.88), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.005 0.002 HIS A 122 PHE 0.018 0.002 PHE A 214 TYR 0.009 0.001 TYR B 23 ARG 0.004 0.001 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8728 (mttt) cc_final: 0.8309 (mmmt) REVERT: A 127 ASP cc_start: 0.7698 (m-30) cc_final: 0.7293 (m-30) REVERT: A 128 ARG cc_start: 0.7957 (mmt-90) cc_final: 0.7717 (mmt-90) REVERT: A 316 SER cc_start: 0.8900 (m) cc_final: 0.8575 (p) REVERT: B 68 LYS cc_start: 0.8800 (mttt) cc_final: 0.8360 (mmmt) REVERT: B 86 LEU cc_start: 0.8985 (tp) cc_final: 0.8610 (tp) REVERT: B 128 ARG cc_start: 0.7949 (mmt-90) cc_final: 0.7715 (mmt-90) REVERT: B 203 LEU cc_start: 0.8626 (mt) cc_final: 0.8418 (mt) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.3246 time to fit residues: 112.0029 Evaluate side-chains 205 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** 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 = 0.4217 r_free = 0.4217 target = 0.149774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.129086 restraints weight = 35042.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.134792 restraints weight = 15701.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.138258 restraints weight = 9114.986| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.8198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4628 Z= 0.221 Angle : 0.616 7.012 6272 Z= 0.364 Chirality : 0.035 0.144 750 Planarity : 0.003 0.024 738 Dihedral : 4.741 27.106 578 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.44 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 3.02 (0.34), residues: 532 helix: 2.24 (0.21), residues: 472 sheet: None (None), residues: 0 loop : 0.08 (0.99), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 305 HIS 0.009 0.002 HIS A 286 PHE 0.021 0.002 PHE B 214 TYR 0.010 0.001 TYR B 117 ARG 0.005 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8752 (mttt) cc_final: 0.8305 (mmmt) REVERT: A 127 ASP cc_start: 0.7753 (m-30) cc_final: 0.7434 (m-30) REVERT: A 128 ARG cc_start: 0.7898 (mmt-90) cc_final: 0.7642 (mmt-90) REVERT: A 316 SER cc_start: 0.8793 (m) cc_final: 0.8436 (p) REVERT: B 64 GLN cc_start: 0.8822 (mp10) cc_final: 0.8522 (mp10) REVERT: B 68 LYS cc_start: 0.8764 (mttt) cc_final: 0.8342 (mmmt) REVERT: B 128 ARG cc_start: 0.7925 (mmt-90) cc_final: 0.7703 (mmt-90) REVERT: B 316 SER cc_start: 0.8779 (m) cc_final: 0.8413 (p) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.3477 time to fit residues: 114.3185 Evaluate side-chains 222 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 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 = 0.4193 r_free = 0.4193 target = 0.147784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.127601 restraints weight = 35168.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.133125 restraints weight = 15543.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.136620 restraints weight = 8940.618| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.8485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4628 Z= 0.204 Angle : 0.587 7.059 6272 Z= 0.343 Chirality : 0.034 0.144 750 Planarity : 0.004 0.037 738 Dihedral : 4.659 27.564 578 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.44 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 3.14 (0.34), residues: 532 helix: 2.33 (0.21), residues: 472 sheet: None (None), residues: 0 loop : 0.00 (1.00), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.008 0.003 HIS A 122 PHE 0.024 0.002 PHE B 100 TYR 0.011 0.001 TYR B 117 ARG 0.005 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8751 (mttt) cc_final: 0.8360 (mmmt) REVERT: A 86 LEU cc_start: 0.9013 (tp) cc_final: 0.8741 (tp) REVERT: A 128 ARG cc_start: 0.7935 (mmt-90) cc_final: 0.7718 (mmt-90) REVERT: A 300 LEU cc_start: 0.8089 (tp) cc_final: 0.7667 (tt) REVERT: A 316 SER cc_start: 0.8806 (m) cc_final: 0.8430 (p) REVERT: B 36 LEU cc_start: 0.7946 (mt) cc_final: 0.7741 (mt) REVERT: B 61 LEU cc_start: 0.8903 (mt) cc_final: 0.8609 (mm) REVERT: B 68 LYS cc_start: 0.8766 (mttt) cc_final: 0.8396 (mmmt) REVERT: B 103 ARG cc_start: 0.7342 (mtt90) cc_final: 0.5936 (tpp-160) REVERT: B 128 ARG cc_start: 0.7950 (mmt-90) cc_final: 0.7709 (mmt-90) REVERT: B 200 LEU cc_start: 0.8929 (tp) cc_final: 0.8707 (tp) REVERT: B 316 SER cc_start: 0.8800 (m) cc_final: 0.8430 (p) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.3408 time to fit residues: 111.2689 Evaluate side-chains 207 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** 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 = 0.4200 r_free = 0.4200 target = 0.148022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.127837 restraints weight = 35499.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.133290 restraints weight = 15786.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.136594 restraints weight = 9292.738| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.8861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4628 Z= 0.208 Angle : 0.599 7.301 6272 Z= 0.348 Chirality : 0.035 0.162 750 Planarity : 0.003 0.022 738 Dihedral : 4.648 28.408 578 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.01 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 3.07 (0.34), residues: 532 helix: 2.24 (0.21), residues: 474 sheet: None (None), residues: 0 loop : 0.29 (0.99), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.008 0.003 HIS A 122 PHE 0.018 0.002 PHE B 214 TYR 0.008 0.001 TYR B 117 ARG 0.005 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8901 (mttt) cc_final: 0.8473 (mmmt) REVERT: A 128 ARG cc_start: 0.7960 (mmt-90) cc_final: 0.7582 (mmt-90) REVERT: A 316 SER cc_start: 0.8807 (m) cc_final: 0.8433 (p) REVERT: B 61 LEU cc_start: 0.8913 (mt) cc_final: 0.8603 (mm) REVERT: B 68 LYS cc_start: 0.8897 (mttt) cc_final: 0.8452 (mmmt) REVERT: B 84 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7861 (tm-30) REVERT: B 128 ARG cc_start: 0.7968 (mmt-90) cc_final: 0.7594 (mmt-90) REVERT: B 316 SER cc_start: 0.8808 (m) cc_final: 0.8424 (p) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.3469 time to fit residues: 105.3438 Evaluate side-chains 208 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 210 ASN B 206 GLN B 210 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.144862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.125299 restraints weight = 35057.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.130430 restraints weight = 15572.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.133549 restraints weight = 9192.901| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.9250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4628 Z= 0.241 Angle : 0.627 7.137 6272 Z= 0.365 Chirality : 0.034 0.121 750 Planarity : 0.004 0.027 738 Dihedral : 4.716 25.209 578 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.82 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 2.90 (0.34), residues: 532 helix: 2.10 (0.21), residues: 476 sheet: None (None), residues: 0 loop : 0.46 (1.04), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 305 HIS 0.016 0.003 HIS A 286 PHE 0.018 0.002 PHE A 54 TYR 0.011 0.002 TYR A 117 ARG 0.008 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8812 (mttt) cc_final: 0.8516 (mmmt) REVERT: A 283 THR cc_start: 0.7874 (m) cc_final: 0.7574 (m) REVERT: A 316 SER cc_start: 0.8758 (m) cc_final: 0.8399 (p) REVERT: B 36 LEU cc_start: 0.8000 (mt) cc_final: 0.7788 (mt) REVERT: B 68 LYS cc_start: 0.8813 (mttt) cc_final: 0.8507 (mmmt) REVERT: B 84 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7734 (tm-30) REVERT: B 283 THR cc_start: 0.8019 (m) cc_final: 0.7796 (m) REVERT: B 316 SER cc_start: 0.8785 (m) cc_final: 0.8401 (p) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.3636 time to fit residues: 105.9472 Evaluate side-chains 206 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.148800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.128759 restraints weight = 33651.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.134128 restraints weight = 14646.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.137379 restraints weight = 8497.950| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.9565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4628 Z= 0.176 Angle : 0.569 7.568 6272 Z= 0.321 Chirality : 0.034 0.143 750 Planarity : 0.004 0.047 738 Dihedral : 4.548 22.755 578 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.63 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 3.30 (0.34), residues: 532 helix: 2.36 (0.21), residues: 478 sheet: None (None), residues: 0 loop : 0.64 (1.07), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 305 HIS 0.007 0.002 HIS B 101 PHE 0.019 0.002 PHE A 54 TYR 0.009 0.001 TYR B 117 ARG 0.005 0.001 ARG A 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8915 (mttt) cc_final: 0.8504 (mmmt) REVERT: A 130 GLU cc_start: 0.8949 (tp30) cc_final: 0.8696 (tp30) REVERT: A 316 SER cc_start: 0.8765 (m) cc_final: 0.8396 (p) REVERT: B 68 LYS cc_start: 0.8891 (mttt) cc_final: 0.8456 (mmmt) REVERT: B 128 ARG cc_start: 0.7910 (mmt-90) cc_final: 0.7607 (mmt-90) REVERT: B 130 GLU cc_start: 0.8921 (tp30) cc_final: 0.8704 (tp30) REVERT: B 316 SER cc_start: 0.8765 (m) cc_final: 0.8382 (p) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.3348 time to fit residues: 99.3896 Evaluate side-chains 206 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.151228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.130598 restraints weight = 31985.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.136416 restraints weight = 14200.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.139957 restraints weight = 8188.741| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.9785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 4628 Z= 0.219 Angle : 0.591 6.964 6272 Z= 0.344 Chirality : 0.037 0.377 750 Planarity : 0.004 0.034 738 Dihedral : 4.433 20.883 578 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.63 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.35), residues: 532 helix: 2.22 (0.22), residues: 476 sheet: None (None), residues: 0 loop : 0.71 (1.04), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 305 HIS 0.011 0.002 HIS A 122 PHE 0.023 0.002 PHE B 35 TYR 0.009 0.001 TYR A 117 ARG 0.007 0.001 ARG B 128 =============================================================================== Job complete usr+sys time: 3814.34 seconds wall clock time: 66 minutes 11.19 seconds (3971.19 seconds total)