Starting phenix.real_space_refine on Thu Feb 13 09:59:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5v6p_8637/02_2025/5v6p_8637.cif Found real_map, /net/cci-nas-00/data/ceres_data/5v6p_8637/02_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_8637/02_2025/5v6p_8637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5v6p_8637/02_2025/5v6p_8637.map" model { file = "/net/cci-nas-00/data/ceres_data/5v6p_8637/02_2025/5v6p_8637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5v6p_8637/02_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-5592/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: 7.66, per 1000 atoms: 0.83 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: 2.11 Conformation dependent library (CDL) restraints added in 705.3 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: 2.95 Time building geometry restraints manager: 2.59 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: 0.02 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: 0.320 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: 0.150 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.080 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: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.140 ------------------------------------------------------------------------------- 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 : 0.681 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: 0.3828 time to fit residues: 162.9609 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 : 0.731 ------------------------------------------------------------------------------- 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 = 0.132673 restraints weight = 34353.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.139313 restraints weight = 15309.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.143371 restraints weight = 8684.258| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 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 : 0.662 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: 0.8955 (mttt) cc_final: 0.8457 (mmmt) REVERT: A 76 LEU cc_start: 0.8320 (tt) cc_final: 0.7808 (tp) REVERT: A 149 ARG cc_start: 0.7495 (mmm160) cc_final: 0.7252 (tpt-90) REVERT: A 164 ILE cc_start: 0.8533 (mm) cc_final: 0.8218 (mm) REVERT: B 68 LYS cc_start: 0.9017 (mttt) cc_final: 0.8461 (mmmt) REVERT: B 76 LEU cc_start: 0.8268 (tt) cc_final: 0.7753 (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: 0.6631 (mtp) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3729 time to fit residues: 138.4613 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 : 0.718 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.152515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.130952 restraints weight = 35219.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.136688 restraints weight = 15691.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.140150 restraints weight = 9091.379| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.6341 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 : 0.679 11.440 6272 Z= 0.387 Chirality : 0.036 0.143 750 Planarity : 0.004 0.029 738 Dihedral : 4.587 25.900 578 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 1.88 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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 : -0.81 (0.73), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 305 HIS 0.005 0.002 HIS B 286 PHE 0.016 0.002 PHE A 150 TYR 0.014 0.002 TYR A 23 ARG 0.002 0.000 ARG A 149 *********************** 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 : 0.681 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 67 THR cc_start: 0.8865 (m) cc_final: 0.8632 (p) REVERT: A 68 LYS cc_start: 0.8978 (mttt) cc_final: 0.8355 (mmmt) REVERT: A 76 LEU cc_start: 0.8399 (tt) cc_final: 0.7622 (tp) REVERT: A 111 PHE cc_start: 0.7642 (m-80) cc_final: 0.7223 (m-80) REVERT: A 127 ASP cc_start: 0.8293 (m-30) cc_final: 0.8054 (m-30) REVERT: B 67 THR cc_start: 0.8820 (m) cc_final: 0.8603 (p) REVERT: B 68 LYS cc_start: 0.8994 (mttt) cc_final: 0.8377 (mmmt) REVERT: B 76 LEU cc_start: 0.8289 (tt) cc_final: 0.7644 (tp) REVERT: B 111 PHE cc_start: 0.7731 (m-80) cc_final: 0.7313 (m-80) REVERT: B 127 ASP cc_start: 0.8056 (m-30) cc_final: 0.7834 (m-30) REVERT: B 128 ARG cc_start: 0.8043 (mmt-90) cc_final: 0.7797 (mmt-90) REVERT: B 289 MET cc_start: 0.5572 (mtp) cc_final: 0.5296 (mtp) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.3625 time to fit residues: 128.7924 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 : 0.770 ------------------------------------------------------------------------------- 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: 0.8980 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 51 optimal weight: 0.0270 chunk 7 optimal weight: 3.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.151853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.130704 restraints weight = 34655.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.135988 restraints weight = 16133.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.139385 restraints weight = 9748.721| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.7037 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= 0.209 Angle : 0.615 7.357 6272 Z= 0.360 Chirality : 0.036 0.135 750 Planarity : 0.004 0.031 738 Dihedral : 4.619 26.777 578 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.26 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: 2.91 (0.34), residues: 532 helix: 2.24 (0.22), residues: 456 sheet: None (None), residues: 0 loop : 0.05 (0.81), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 305 HIS 0.004 0.002 HIS B 286 PHE 0.022 0.002 PHE B 214 TYR 0.012 0.001 TYR B 23 ARG 0.004 0.000 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 274 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.760 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: A 41 LYS cc_start: 0.8575 (mttt) cc_final: 0.8323 (tptp) REVERT: A 68 LYS cc_start: 0.8999 (mttt) cc_final: 0.8320 (mmmt) REVERT: A 111 PHE cc_start: 0.7400 (m-80) cc_final: 0.7182 (m-80) REVERT: A 127 ASP cc_start: 0.7885 (m-30) cc_final: 0.7677 (m-30) REVERT: A 128 ARG cc_start: 0.8002 (mmt-90) cc_final: 0.7716 (mmt-90) REVERT: B 41 LYS cc_start: 0.8629 (mttt) cc_final: 0.8358 (tptp) REVERT: B 68 LYS cc_start: 0.9006 (mttt) cc_final: 0.8345 (mmmt) REVERT: B 86 LEU cc_start: 0.9136 (tt) cc_final: 0.8818 (tp) REVERT: B 111 PHE cc_start: 0.7625 (m-80) cc_final: 0.7347 (m-80) REVERT: B 128 ARG cc_start: 0.7985 (mmt-90) cc_final: 0.7682 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.3578 time to fit residues: 124.0047 Evaluate side-chains 241 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.151372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.130295 restraints weight = 35059.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.135908 restraints weight = 15971.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.139314 restraints weight = 9391.589| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.7516 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= 0.207 Angle : 0.592 7.641 6272 Z= 0.348 Chirality : 0.034 0.149 750 Planarity : 0.003 0.026 738 Dihedral : 4.590 27.086 578 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.82 % Favored : 96.80 % 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: 2.89 (0.34), residues: 532 helix: 2.23 (0.22), residues: 468 sheet: None (None), residues: 0 loop : -0.48 (0.87), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 305 HIS 0.006 0.002 HIS A 286 PHE 0.019 0.002 PHE A 214 TYR 0.009 0.001 TYR B 23 ARG 0.003 0.001 ARG A 128 *********************** 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 278 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.803 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: 0.8626 (mttt) cc_final: 0.8232 (mmmt) REVERT: A 127 ASP cc_start: 0.7664 (m-30) cc_final: 0.7404 (m-30) REVERT: A 128 ARG cc_start: 0.7864 (mmt-90) cc_final: 0.7587 (mmt-90) REVERT: A 316 SER cc_start: 0.8896 (m) cc_final: 0.8571 (p) REVERT: B 68 LYS cc_start: 0.8738 (mttt) cc_final: 0.8283 (mmmt) REVERT: B 127 ASP cc_start: 0.7708 (m-30) cc_final: 0.7365 (m-30) REVERT: B 128 ARG cc_start: 0.7866 (mmt-90) cc_final: 0.7620 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.3480 time to fit residues: 121.6180 Evaluate side-chains 210 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 0.0670 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 49 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 HIS 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 = 0.151661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.130480 restraints weight = 34470.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.136182 restraints weight = 15572.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.139676 restraints weight = 9138.575| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.7936 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= 0.177 Angle : 0.573 7.540 6272 Z= 0.335 Chirality : 0.033 0.139 750 Planarity : 0.003 0.023 738 Dihedral : 4.583 27.570 578 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.63 % Favored : 96.99 % 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: 2.97 (0.34), residues: 532 helix: 2.23 (0.21), residues: 472 sheet: None (None), residues: 0 loop : -0.10 (0.96), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 305 HIS 0.006 0.002 HIS A 122 PHE 0.021 0.002 PHE B 214 TYR 0.009 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 269 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.813 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: 0.8716 (mttt) cc_final: 0.8243 (mmmt) REVERT: A 316 SER cc_start: 0.8831 (m) cc_final: 0.8512 (p) REVERT: B 68 LYS cc_start: 0.8672 (mttt) cc_final: 0.8257 (mmmt) REVERT: B 96 MET cc_start: 0.5475 (mmt) cc_final: 0.5253 (mmt) REVERT: B 316 SER cc_start: 0.8774 (m) cc_final: 0.8431 (p) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.3521 time to fit residues: 119.2168 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 : 0.741 ------------------------------------------------------------------------------- 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: 0.8980 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.150091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.130101 restraints weight = 34489.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.135536 restraints weight = 15382.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.138968 restraints weight = 8922.879| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.8259 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= 0.182 Angle : 0.558 7.325 6272 Z= 0.325 Chirality : 0.033 0.132 750 Planarity : 0.003 0.032 738 Dihedral : 4.537 27.833 578 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.26 % Favored : 97.37 % 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: 3.11 (0.34), residues: 532 helix: 2.31 (0.21), residues: 472 sheet: None (None), residues: 0 loop : -0.05 (0.99), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 305 HIS 0.006 0.002 HIS B 101 PHE 0.019 0.002 PHE A 54 TYR 0.008 0.001 TYR B 117 ARG 0.006 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 276 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.746 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: A 61 LEU cc_start: 0.8884 (mt) cc_final: 0.8656 (mt) REVERT: A 68 LYS cc_start: 0.8673 (mttt) cc_final: 0.8222 (mmmt) REVERT: A 316 SER cc_start: 0.8823 (m) cc_final: 0.8474 (p) REVERT: B 61 LEU cc_start: 0.8895 (mt) cc_final: 0.8656 (mt) REVERT: B 68 LYS cc_start: 0.8661 (mttt) cc_final: 0.8274 (mmmt) REVERT: B 316 SER cc_start: 0.8782 (m) cc_final: 0.8418 (p) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.3348 time to fit residues: 116.6078 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 : 0.676 ------------------------------------------------------------------------------- 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: 0.2980 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 38 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 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** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.151240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.130270 restraints weight = 33530.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.135989 restraints weight = 14738.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.139493 restraints weight = 8486.473| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.8401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4628 Z= 0.181 Angle : 0.572 7.450 6272 Z= 0.331 Chirality : 0.033 0.131 750 Planarity : 0.003 0.025 738 Dihedral : 4.562 29.890 578 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.63 % Favored : 96.99 % Rotamer: Outliers : 0.19 % Allowed : 1.17 % Favored : 98.64 % 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: 3.27 (0.35), residues: 532 helix: 2.41 (0.21), residues: 472 sheet: None (None), residues: 0 loop : 0.16 (1.04), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 305 HIS 0.011 0.003 HIS B 286 PHE 0.021 0.002 PHE B 214 TYR 0.008 0.001 TYR B 117 ARG 0.006 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 265 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 0.743 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: A 68 LYS cc_start: 0.8865 (mttt) cc_final: 0.8317 (mmmt) REVERT: A 128 ARG cc_start: 0.7642 (mmt-90) cc_final: 0.7441 (mmt-90) REVERT: A 130 GLU cc_start: 0.9002 (tp30) cc_final: 0.8708 (tp30) REVERT: A 316 SER cc_start: 0.8818 (m) cc_final: 0.8438 (p) REVERT: B 68 LYS cc_start: 0.8868 (mttt) cc_final: 0.8344 (mmmt) REVERT: B 316 SER cc_start: 0.8812 (m) cc_final: 0.8436 (p) outliers start: 1 outliers final: 0 residues processed: 265 average time/residue: 0.3551 time to fit residues: 119.7119 Evaluate side-chains 226 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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: 4.9990 chunk 52 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4218 r_free = 0.4218 target = 0.151105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.130350 restraints weight = 32755.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.135992 restraints weight = 14484.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.139625 restraints weight = 8247.553| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.8733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4628 Z= 0.182 Angle : 0.575 7.370 6272 Z= 0.337 Chirality : 0.034 0.134 750 Planarity : 0.003 0.026 738 Dihedral : 4.512 30.005 578 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.44 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 3.18 (0.34), residues: 532 helix: 2.30 (0.21), residues: 476 sheet: None (None), residues: 0 loop : 0.50 (1.10), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 305 HIS 0.010 0.003 HIS A 122 PHE 0.024 0.002 PHE A 54 TYR 0.006 0.001 TYR A 186 ARG 0.005 0.001 ARG A 85 *********************** 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 265 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.718 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: A 68 LYS cc_start: 0.8884 (mttt) cc_final: 0.8296 (mmmt) REVERT: A 128 ARG cc_start: 0.7591 (mmt-90) cc_final: 0.7349 (mmt-90) REVERT: A 130 GLU cc_start: 0.8944 (tp30) cc_final: 0.8636 (tp30) REVERT: A 152 PHE cc_start: 0.6631 (m-80) cc_final: 0.6415 (m-80) REVERT: A 316 SER cc_start: 0.8825 (m) cc_final: 0.8438 (p) REVERT: B 61 LEU cc_start: 0.9081 (mt) cc_final: 0.8874 (mt) REVERT: B 68 LYS cc_start: 0.8875 (mttt) cc_final: 0.8364 (mmmt) REVERT: B 316 SER cc_start: 0.8806 (m) cc_final: 0.8431 (p) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.3228 time to fit residues: 108.5711 Evaluate side-chains 203 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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: 2.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 ** 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 = 0.4201 r_free = 0.4201 target = 0.149635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.129306 restraints weight = 33508.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.134801 restraints weight = 14812.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.138225 restraints weight = 8504.702| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.8875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4628 Z= 0.196 Angle : 0.595 7.781 6272 Z= 0.341 Chirality : 0.033 0.129 750 Planarity : 0.003 0.019 738 Dihedral : 4.616 31.630 578 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.26 % Favored : 97.37 % 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 : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.34), residues: 532 helix: 2.34 (0.21), residues: 476 sheet: None (None), residues: 0 loop : 0.79 (1.12), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 305 HIS 0.008 0.003 HIS B 122 PHE 0.024 0.002 PHE A 54 TYR 0.007 0.001 TYR A 186 ARG 0.005 0.001 ARG B 85 ********************** 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 254 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.718 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: 0.8905 (mttt) cc_final: 0.8328 (mmmt) REVERT: A 86 LEU cc_start: 0.8747 (tt) cc_final: 0.8348 (tp) REVERT: A 119 LYS cc_start: 0.8535 (mttt) cc_final: 0.8328 (mtmt) REVERT: A 128 ARG cc_start: 0.7584 (mmt-90) cc_final: 0.7355 (mmt-90) REVERT: A 316 SER cc_start: 0.8808 (m) cc_final: 0.8437 (p) REVERT: B 68 LYS cc_start: 0.8877 (mttt) cc_final: 0.8407 (mmmt) REVERT: B 316 SER cc_start: 0.8795 (m) cc_final: 0.8415 (p) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.3517 time to fit residues: 112.5880 Evaluate side-chains 200 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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: 0.9990 chunk 53 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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 = 0.4203 r_free = 0.4203 target = 0.150065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.129421 restraints weight = 33551.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.134924 restraints weight = 14927.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.138408 restraints weight = 8674.707| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.9101 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= 0.179 Angle : 0.579 7.857 6272 Z= 0.330 Chirality : 0.033 0.131 750 Planarity : 0.003 0.026 738 Dihedral : 4.582 32.771 578 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.26 % Favored : 97.37 % 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 : 0.38 % 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: 3.36 (0.35), residues: 532 helix: 2.38 (0.21), residues: 476 sheet: None (None), residues: 0 loop : 0.89 (1.12), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 305 HIS 0.007 0.001 HIS B 101 PHE 0.020 0.002 PHE A 54 TYR 0.005 0.001 TYR A 186 ARG 0.005 0.001 ARG A 85 =============================================================================== Job complete usr+sys time: 3826.68 seconds wall clock time: 68 minutes 4.05 seconds (4084.05 seconds total)