Starting phenix.real_space_refine on Tue Mar 11 21:35:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d1b_27121/03_2025/8d1b_27121.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1b_27121/03_2025/8d1b_27121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d1b_27121/03_2025/8d1b_27121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1b_27121/03_2025/8d1b_27121.map" model { file = "/net/cci-nas-00/data/ceres_data/8d1b_27121/03_2025/8d1b_27121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1b_27121/03_2025/8d1b_27121.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.041 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: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 4196 2.51 5 N 1204 2.21 5 O 1286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6724 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1379 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "A" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1983 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 17, 'TRANS': 241} Chain breaks: 1 Restraints were copied for chains: D, B Time building chain proxies: 6.00, per 1000 atoms: 0.89 Number of scatterers: 6724 At special positions: 0 Unit cell: (86.355, 88.065, 112.005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1286 8.00 N 1204 7.00 C 4196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 987 " - pdb=" SG CYS D1014 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 985.0 milliseconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 6 sheets defined 10.3% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'D' and resid 852 through 857 removed outlier: 4.190A pdb=" N VAL D 857 " --> pdb=" O ILE D 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 996 removed outlier: 3.983A pdb=" N THR D 995 " --> pdb=" O THR D 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 857 removed outlier: 4.190A pdb=" N VAL C 857 " --> pdb=" O ILE C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 996 removed outlier: 3.983A pdb=" N THR C 995 " --> pdb=" O THR C 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 removed outlier: 3.788A pdb=" N ALA B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 96 removed outlier: 3.660A pdb=" N GLN B 96 " --> pdb=" O PRO B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.720A pdb=" N ALA B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'A' and resid 56 through 64 removed outlier: 3.787A pdb=" N ALA A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 removed outlier: 3.659A pdb=" N GLN A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 105 removed outlier: 3.720A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 136 through 140 Processing sheet with id=AA1, first strand: chain 'D' and resid 894 through 897 removed outlier: 3.562A pdb=" N GLY D 895 " --> pdb=" O VAL D 902 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 894 through 897 removed outlier: 3.562A pdb=" N GLY C 895 " --> pdb=" O VAL C 902 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 246 through 249 removed outlier: 3.590A pdb=" N ASP B 271 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG B 146 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 149 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N THR B 173 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 219 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 216 through 221 removed outlier: 3.671A pdb=" N GLY B 219 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 173 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 149 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG A 146 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP A 271 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 236 through 237 removed outlier: 3.718A pdb=" N GLN B 237 " --> pdb=" O ARG B 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 236 through 237 removed outlier: 3.717A pdb=" N GLN A 237 " --> pdb=" O ARG A 240 " (cutoff:3.500A) 76 hydrogen bonds defined for protein. 162 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.36 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2301 1.34 - 1.46: 1523 1.46 - 1.58: 2976 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6858 Sorted by residual: bond pdb=" C GLN A 114 " pdb=" N ALA A 115 " ideal model delta sigma weight residual 1.331 1.306 0.025 1.73e-02 3.34e+03 2.10e+00 bond pdb=" C GLN B 114 " pdb=" N ALA B 115 " ideal model delta sigma weight residual 1.331 1.306 0.025 1.73e-02 3.34e+03 2.02e+00 bond pdb=" C ALA B 106 " pdb=" N ASN B 107 " ideal model delta sigma weight residual 1.331 1.311 0.019 1.38e-02 5.25e+03 1.97e+00 bond pdb=" C ALA A 106 " pdb=" N ASN A 107 " ideal model delta sigma weight residual 1.331 1.313 0.018 1.38e-02 5.25e+03 1.68e+00 bond pdb=" CB VAL A 134 " pdb=" CG1 VAL A 134 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.63e+00 ... (remaining 6853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 8475 1.85 - 3.69: 703 3.69 - 5.54: 96 5.54 - 7.39: 16 7.39 - 9.24: 4 Bond angle restraints: 9294 Sorted by residual: angle pdb=" N GLY B 86 " pdb=" CA GLY B 86 " pdb=" C GLY B 86 " ideal model delta sigma weight residual 113.99 108.54 5.45 1.28e+00 6.10e-01 1.81e+01 angle pdb=" N GLY A 86 " pdb=" CA GLY A 86 " pdb=" C GLY A 86 " ideal model delta sigma weight residual 113.99 108.55 5.44 1.28e+00 6.10e-01 1.81e+01 angle pdb=" N LYS B 257 " pdb=" CA LYS B 257 " pdb=" C LYS B 257 " ideal model delta sigma weight residual 109.83 104.83 5.00 1.27e+00 6.20e-01 1.55e+01 angle pdb=" N LYS A 257 " pdb=" CA LYS A 257 " pdb=" C LYS A 257 " ideal model delta sigma weight residual 109.83 104.88 4.95 1.27e+00 6.20e-01 1.52e+01 angle pdb=" CA LEU B 71 " pdb=" C LEU B 71 " pdb=" N SER B 72 " ideal model delta sigma weight residual 114.17 119.36 -5.19 1.45e+00 4.76e-01 1.28e+01 ... (remaining 9289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 3660 17.78 - 35.56: 381 35.56 - 53.34: 56 53.34 - 71.13: 6 71.13 - 88.91: 4 Dihedral angle restraints: 4107 sinusoidal: 1635 harmonic: 2472 Sorted by residual: dihedral pdb=" CA ARG C 886 " pdb=" C ARG C 886 " pdb=" N PRO C 887 " pdb=" CA PRO C 887 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ARG D 886 " pdb=" C ARG D 886 " pdb=" N PRO D 887 " pdb=" CA PRO D 887 " ideal model delta harmonic sigma weight residual 180.00 -152.27 -27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA GLU A 263 " pdb=" C GLU A 263 " pdb=" N VAL A 264 " pdb=" CA VAL A 264 " ideal model delta harmonic sigma weight residual 180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 4104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 550 0.037 - 0.073: 308 0.073 - 0.109: 119 0.109 - 0.146: 23 0.146 - 0.182: 10 Chirality restraints: 1010 Sorted by residual: chirality pdb=" CA PRO D 887 " pdb=" N PRO D 887 " pdb=" C PRO D 887 " pdb=" CB PRO D 887 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" CA PRO C 887 " pdb=" N PRO C 887 " pdb=" C PRO C 887 " pdb=" CB PRO C 887 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CB THR B 173 " pdb=" CA THR B 173 " pdb=" OG1 THR B 173 " pdb=" CG2 THR B 173 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.44e-01 ... (remaining 1007 not shown) Planarity restraints: 1232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 92 " -0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO A 93 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 92 " 0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO B 93 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 257 " -0.046 5.00e-02 4.00e+02 6.96e-02 7.75e+00 pdb=" N PRO B 258 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " -0.039 5.00e-02 4.00e+02 ... (remaining 1229 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 106 2.60 - 3.18: 6070 3.18 - 3.75: 9159 3.75 - 4.33: 13116 4.33 - 4.90: 21669 Nonbonded interactions: 50120 Sorted by model distance: nonbonded pdb=" SG CYS A 76 " pdb=" SG CYS A 236 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS B 76 " pdb=" SG CYS B 236 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS A 295 " pdb=" SG CYS A 317 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 295 " pdb=" SG CYS B 317 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS A 282 " pdb=" SG CYS A 302 " model vdw 2.031 3.760 ... (remaining 50115 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 'C' selection = chain 'D' } 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: 6.220 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.130 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 : 0.006 0.042 6858 Z= 0.405 Angle : 1.086 9.237 9294 Z= 0.620 Chirality : 0.052 0.182 1010 Planarity : 0.008 0.084 1232 Dihedral : 14.425 88.908 2532 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.13 % Favored : 75.87 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.45 % 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: -6.32 (0.22), residues: 862 helix: -5.21 (0.17), residues: 100 sheet: -3.30 (0.35), residues: 164 loop : -4.63 (0.20), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 182 HIS 0.003 0.001 HIS D 926 PHE 0.013 0.002 PHE D 868 TYR 0.023 0.002 TYR A 62 ARG 0.005 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.775 Fit side-chains REVERT: D 965 TYR cc_start: 0.8098 (m-80) cc_final: 0.7772 (m-80) REVERT: D 998 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.6789 (m90) REVERT: D 1010 ASN cc_start: 0.8319 (t0) cc_final: 0.8105 (t0) REVERT: C 965 TYR cc_start: 0.8096 (m-80) cc_final: 0.7685 (m-80) REVERT: C 998 HIS cc_start: 0.7115 (OUTLIER) cc_final: 0.6721 (m90) outliers start: 2 outliers final: 0 residues processed: 127 average time/residue: 0.1412 time to fit residues: 26.0340 Evaluate side-chains 102 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 998 HIS Chi-restraints excluded: chain C residue 998 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.0070 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 990 HIS C 990 HIS B 161 GLN B 165 GLN B 237 GLN A 161 GLN A 165 GLN A 237 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.152271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122258 restraints weight = 10385.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.125922 restraints weight = 6265.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128377 restraints weight = 4567.746| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6858 Z= 0.239 Angle : 0.833 8.534 9294 Z= 0.420 Chirality : 0.048 0.204 1010 Planarity : 0.007 0.072 1232 Dihedral : 7.067 26.301 962 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.77 % Favored : 79.23 % Rotamer: Outliers : 1.25 % Allowed : 9.70 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.82 (0.23), residues: 862 helix: -4.73 (0.27), residues: 90 sheet: -2.83 (0.37), residues: 168 loop : -4.39 (0.21), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 288 HIS 0.006 0.001 HIS D 990 PHE 0.008 0.001 PHE C 865 TYR 0.021 0.002 TYR A 62 ARG 0.005 0.001 ARG D 861 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.705 Fit side-chains REVERT: D 905 TYR cc_start: 0.8806 (p90) cc_final: 0.8536 (p90) REVERT: D 955 MET cc_start: 0.6348 (ptt) cc_final: 0.6068 (ptt) REVERT: D 965 TYR cc_start: 0.7800 (m-80) cc_final: 0.7510 (m-80) REVERT: D 1010 ASN cc_start: 0.8476 (t0) cc_final: 0.8026 (t0) REVERT: C 965 TYR cc_start: 0.7844 (m-80) cc_final: 0.7622 (m-80) REVERT: C 975 HIS cc_start: 0.6932 (m-70) cc_final: 0.6729 (m170) REVERT: C 1010 ASN cc_start: 0.8746 (t0) cc_final: 0.8348 (t0) outliers start: 9 outliers final: 3 residues processed: 127 average time/residue: 0.1440 time to fit residues: 26.1834 Evaluate side-chains 105 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 990 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 76 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 990 HIS C 990 HIS B 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.154375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.125330 restraints weight = 10836.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.128573 restraints weight = 6917.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.130656 restraints weight = 5244.668| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6858 Z= 0.268 Angle : 0.810 8.261 9294 Z= 0.406 Chirality : 0.047 0.206 1010 Planarity : 0.006 0.070 1232 Dihedral : 6.674 27.152 958 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.79 % Favored : 81.21 % Rotamer: Outliers : 1.52 % Allowed : 15.37 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.66 (0.23), residues: 862 helix: -4.42 (0.31), residues: 90 sheet: -2.79 (0.36), residues: 168 loop : -4.28 (0.21), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 288 HIS 0.003 0.001 HIS D 990 PHE 0.008 0.001 PHE D 868 TYR 0.013 0.002 TYR B 80 ARG 0.004 0.000 ARG C 880 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.722 Fit side-chains REVERT: D 905 TYR cc_start: 0.8874 (p90) cc_final: 0.8578 (p90) REVERT: D 911 VAL cc_start: 0.9228 (t) cc_final: 0.8989 (p) REVERT: D 965 TYR cc_start: 0.7908 (m-80) cc_final: 0.7611 (m-80) REVERT: D 1010 ASN cc_start: 0.8228 (t0) cc_final: 0.7733 (t0) REVERT: C 1010 ASN cc_start: 0.8521 (t0) cc_final: 0.7958 (t0) REVERT: A 81 GLU cc_start: 0.8179 (mp0) cc_final: 0.7959 (mp0) outliers start: 11 outliers final: 6 residues processed: 117 average time/residue: 0.1441 time to fit residues: 24.3822 Evaluate side-chains 108 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain C residue 990 HIS Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 57 optimal weight: 0.6980 chunk 63 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 37 optimal weight: 0.0770 chunk 70 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 0.0970 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 990 HIS C 975 HIS C 990 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.157481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.128388 restraints weight = 10765.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131748 restraints weight = 6798.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.133951 restraints weight = 5085.695| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6858 Z= 0.223 Angle : 0.779 8.055 9294 Z= 0.385 Chirality : 0.045 0.206 1010 Planarity : 0.006 0.067 1232 Dihedral : 6.295 27.362 958 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.87 % Favored : 82.13 % Rotamer: Outliers : 2.63 % Allowed : 18.14 % Favored : 79.22 % 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: -5.53 (0.24), residues: 862 helix: -4.33 (0.30), residues: 98 sheet: -2.75 (0.35), residues: 184 loop : -4.16 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 288 HIS 0.005 0.001 HIS D 990 PHE 0.007 0.001 PHE C 991 TYR 0.014 0.001 TYR B 80 ARG 0.005 0.000 ARG D 867 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.686 Fit side-chains REVERT: D 905 TYR cc_start: 0.8864 (p90) cc_final: 0.8587 (p90) REVERT: D 911 VAL cc_start: 0.9138 (t) cc_final: 0.8872 (p) REVERT: D 1010 ASN cc_start: 0.8189 (t0) cc_final: 0.7550 (t0) REVERT: C 902 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8353 (m) REVERT: C 1010 ASN cc_start: 0.8473 (t0) cc_final: 0.7858 (t0) REVERT: B 88 MET cc_start: 0.6042 (mmp) cc_final: 0.5744 (mmm) REVERT: A 88 MET cc_start: 0.6081 (mmp) cc_final: 0.5791 (mmm) outliers start: 19 outliers final: 8 residues processed: 128 average time/residue: 0.1380 time to fit residues: 25.5022 Evaluate side-chains 115 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 989 SER Chi-restraints excluded: chain C residue 990 HIS Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 311 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 81 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 990 HIS C 990 HIS B 237 GLN A 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.154922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.126258 restraints weight = 10645.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.129534 restraints weight = 6712.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.131672 restraints weight = 5023.202| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6858 Z= 0.269 Angle : 0.800 9.032 9294 Z= 0.391 Chirality : 0.046 0.213 1010 Planarity : 0.006 0.065 1232 Dihedral : 6.106 27.077 958 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.26 % Favored : 80.74 % Rotamer: Outliers : 2.63 % Allowed : 18.84 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.50 (0.24), residues: 862 helix: -4.23 (0.30), residues: 98 sheet: -2.93 (0.33), residues: 202 loop : -4.08 (0.22), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 245 HIS 0.007 0.001 HIS D 990 PHE 0.007 0.001 PHE A 253 TYR 0.008 0.001 TYR B 254 ARG 0.003 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.714 Fit side-chains REVERT: D 905 TYR cc_start: 0.8889 (p90) cc_final: 0.8621 (p90) REVERT: D 1010 ASN cc_start: 0.8223 (t0) cc_final: 0.7414 (t0) REVERT: C 902 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8415 (m) REVERT: C 1010 ASN cc_start: 0.8426 (t0) cc_final: 0.7770 (t0) outliers start: 19 outliers final: 7 residues processed: 124 average time/residue: 0.1321 time to fit residues: 24.1275 Evaluate side-chains 111 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 990 HIS Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 311 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 64 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.0000 chunk 28 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 990 HIS C 990 HIS B 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.153415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.123395 restraints weight = 10463.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127149 restraints weight = 6178.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129557 restraints weight = 4467.705| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6858 Z= 0.260 Angle : 0.785 9.650 9294 Z= 0.387 Chirality : 0.045 0.216 1010 Planarity : 0.006 0.065 1232 Dihedral : 6.039 26.464 958 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.45 % Favored : 81.55 % Rotamer: Outliers : 3.19 % Allowed : 19.11 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.33 (0.24), residues: 862 helix: -4.12 (0.33), residues: 96 sheet: -2.83 (0.34), residues: 202 loop : -3.96 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 245 HIS 0.002 0.001 HIS D 975 PHE 0.008 0.001 PHE B 253 TYR 0.011 0.001 TYR A 80 ARG 0.003 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.698 Fit side-chains REVERT: D 905 TYR cc_start: 0.8854 (p90) cc_final: 0.8569 (p90) REVERT: D 950 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7334 (tttt) REVERT: D 1010 ASN cc_start: 0.8452 (t0) cc_final: 0.7960 (t0) REVERT: C 902 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8285 (m) REVERT: C 1010 ASN cc_start: 0.8512 (t0) cc_final: 0.7881 (t0) outliers start: 23 outliers final: 11 residues processed: 125 average time/residue: 0.1524 time to fit residues: 26.8082 Evaluate side-chains 121 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 950 LYS Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 990 HIS Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 0.0020 chunk 74 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 990 HIS C 990 HIS B 237 GLN A 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.152761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.122720 restraints weight = 10466.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.126424 restraints weight = 6185.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128877 restraints weight = 4484.867| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6858 Z= 0.273 Angle : 0.777 10.232 9294 Z= 0.385 Chirality : 0.045 0.207 1010 Planarity : 0.006 0.064 1232 Dihedral : 5.981 25.801 958 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.07 % Favored : 79.93 % Rotamer: Outliers : 4.43 % Allowed : 18.84 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.27 (0.25), residues: 862 helix: -4.05 (0.34), residues: 96 sheet: -2.76 (0.34), residues: 202 loop : -3.94 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 245 HIS 0.003 0.001 HIS C 990 PHE 0.016 0.002 PHE A 253 TYR 0.012 0.001 TYR B 80 ARG 0.005 0.000 ARG D 978 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.742 Fit side-chains REVERT: D 905 TYR cc_start: 0.8858 (p90) cc_final: 0.8561 (p90) REVERT: D 975 HIS cc_start: 0.6341 (m-70) cc_final: 0.6132 (m170) REVERT: D 1010 ASN cc_start: 0.8425 (t0) cc_final: 0.7884 (t0) REVERT: C 902 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8308 (m) REVERT: C 955 MET cc_start: 0.6213 (ptt) cc_final: 0.5836 (ptt) REVERT: C 979 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.7139 (pm20) REVERT: C 1010 ASN cc_start: 0.8537 (t0) cc_final: 0.7904 (t0) REVERT: B 76 CYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7168 (t) REVERT: B 297 LEU cc_start: 0.4536 (OUTLIER) cc_final: 0.4268 (pp) REVERT: A 76 CYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7159 (t) REVERT: A 297 LEU cc_start: 0.4430 (OUTLIER) cc_final: 0.4161 (pp) outliers start: 32 outliers final: 16 residues processed: 128 average time/residue: 0.1458 time to fit residues: 26.6145 Evaluate side-chains 121 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 950 LYS Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 979 GLN Chi-restraints excluded: chain C residue 989 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 76 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 0.0370 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 990 HIS A 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.153366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.123808 restraints weight = 10522.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.127386 restraints weight = 6165.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129861 restraints weight = 4448.927| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6858 Z= 0.237 Angle : 0.771 10.846 9294 Z= 0.379 Chirality : 0.045 0.208 1010 Planarity : 0.005 0.063 1232 Dihedral : 5.855 25.704 958 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.29 % Favored : 82.71 % Rotamer: Outliers : 4.02 % Allowed : 18.84 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.15 (0.25), residues: 862 helix: -3.88 (0.36), residues: 96 sheet: -2.63 (0.35), residues: 202 loop : -3.89 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 288 HIS 0.005 0.001 HIS D 990 PHE 0.009 0.001 PHE D 991 TYR 0.009 0.001 TYR B 80 ARG 0.002 0.000 ARG D 861 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.791 Fit side-chains REVERT: D 905 TYR cc_start: 0.8839 (p90) cc_final: 0.8618 (p90) REVERT: D 954 MET cc_start: 0.6071 (tmm) cc_final: 0.5853 (tmm) REVERT: D 975 HIS cc_start: 0.6322 (m-70) cc_final: 0.6103 (m170) REVERT: D 1010 ASN cc_start: 0.8394 (t0) cc_final: 0.7829 (t0) REVERT: C 902 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8278 (m) REVERT: C 979 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.7088 (pm20) REVERT: C 1010 ASN cc_start: 0.8521 (t0) cc_final: 0.7907 (t0) REVERT: B 76 CYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7292 (t) REVERT: B 297 LEU cc_start: 0.4517 (OUTLIER) cc_final: 0.4254 (pp) REVERT: A 76 CYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7287 (t) REVERT: A 297 LEU cc_start: 0.4410 (OUTLIER) cc_final: 0.4148 (pp) outliers start: 29 outliers final: 17 residues processed: 124 average time/residue: 0.1489 time to fit residues: 26.0541 Evaluate side-chains 121 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 892 ILE Chi-restraints excluded: chain D residue 950 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 979 GLN Chi-restraints excluded: chain C residue 989 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 80 optimal weight: 0.0060 chunk 54 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 11 optimal weight: 0.0170 chunk 40 optimal weight: 1.9990 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.156296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.125931 restraints weight = 10489.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.129907 restraints weight = 6055.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.132482 restraints weight = 4315.573| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6858 Z= 0.213 Angle : 0.765 11.539 9294 Z= 0.372 Chirality : 0.044 0.203 1010 Planarity : 0.005 0.062 1232 Dihedral : 5.691 25.636 958 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.94 % Favored : 83.06 % Rotamer: Outliers : 3.32 % Allowed : 19.53 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.25), residues: 862 helix: -3.69 (0.39), residues: 96 sheet: -2.03 (0.38), residues: 168 loop : -3.85 (0.22), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 288 HIS 0.001 0.001 HIS D 975 PHE 0.009 0.001 PHE D 840 TYR 0.007 0.001 TYR B 254 ARG 0.003 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.761 Fit side-chains REVERT: D 880 ARG cc_start: 0.8226 (ttt90) cc_final: 0.7687 (tmt-80) REVERT: D 975 HIS cc_start: 0.6341 (m-70) cc_final: 0.6141 (m170) REVERT: D 1010 ASN cc_start: 0.8402 (t0) cc_final: 0.7828 (t0) REVERT: C 902 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8262 (m) REVERT: C 905 TYR cc_start: 0.8848 (p90) cc_final: 0.8535 (p90) REVERT: C 979 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.7076 (pm20) REVERT: C 1010 ASN cc_start: 0.8556 (t0) cc_final: 0.7971 (t0) REVERT: B 297 LEU cc_start: 0.4549 (OUTLIER) cc_final: 0.4291 (pp) REVERT: A 224 THR cc_start: 0.8576 (t) cc_final: 0.8273 (m) REVERT: A 297 LEU cc_start: 0.4466 (OUTLIER) cc_final: 0.4213 (pp) outliers start: 24 outliers final: 15 residues processed: 123 average time/residue: 0.1731 time to fit residues: 30.0823 Evaluate side-chains 120 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 950 LYS Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 979 GLN Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 83 optimal weight: 0.0030 chunk 15 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 54 optimal weight: 0.0470 chunk 59 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 68 optimal weight: 0.0170 chunk 40 optimal weight: 0.5980 overall best weight: 0.2526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.158730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.128248 restraints weight = 10511.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.132275 restraints weight = 6053.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.134904 restraints weight = 4304.620| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6858 Z= 0.204 Angle : 0.770 12.111 9294 Z= 0.373 Chirality : 0.044 0.203 1010 Planarity : 0.005 0.063 1232 Dihedral : 5.553 25.503 958 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.59 % Favored : 83.41 % Rotamer: Outliers : 1.94 % Allowed : 21.75 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.74 (0.25), residues: 862 helix: -3.59 (0.40), residues: 96 sheet: -1.96 (0.38), residues: 168 loop : -3.72 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 288 HIS 0.001 0.000 HIS D 990 PHE 0.007 0.001 PHE C 840 TYR 0.008 0.001 TYR B 254 ARG 0.002 0.000 ARG C 861 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.690 Fit side-chains REVERT: D 866 MET cc_start: 0.7288 (mtp) cc_final: 0.6947 (mtt) REVERT: D 880 ARG cc_start: 0.8239 (ttt90) cc_final: 0.7800 (tmt-80) REVERT: D 1010 ASN cc_start: 0.8425 (t0) cc_final: 0.7880 (t0) REVERT: C 902 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8222 (m) REVERT: C 905 TYR cc_start: 0.8821 (p90) cc_final: 0.8495 (p90) REVERT: C 979 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6949 (pm20) REVERT: C 1010 ASN cc_start: 0.8509 (t0) cc_final: 0.7899 (t0) REVERT: B 297 LEU cc_start: 0.4646 (OUTLIER) cc_final: 0.4409 (pp) REVERT: A 224 THR cc_start: 0.8577 (t) cc_final: 0.8274 (m) REVERT: A 297 LEU cc_start: 0.4499 (OUTLIER) cc_final: 0.4262 (pp) outliers start: 14 outliers final: 7 residues processed: 119 average time/residue: 0.1610 time to fit residues: 26.7119 Evaluate side-chains 111 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 892 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 979 GLN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 32 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 14 optimal weight: 0.0870 chunk 57 optimal weight: 0.0040 chunk 6 optimal weight: 1.9990 overall best weight: 0.3570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 975 HIS B 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.159041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.127872 restraints weight = 10256.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.131871 restraints weight = 6033.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.134543 restraints weight = 4358.912| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6858 Z= 0.212 Angle : 0.751 11.896 9294 Z= 0.367 Chirality : 0.044 0.202 1010 Planarity : 0.005 0.063 1232 Dihedral : 5.451 24.786 958 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.94 % Favored : 83.06 % Rotamer: Outliers : 2.08 % Allowed : 22.71 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.68 (0.26), residues: 862 helix: -3.45 (0.41), residues: 96 sheet: -2.17 (0.35), residues: 192 loop : -3.63 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 879 HIS 0.002 0.001 HIS D 975 PHE 0.009 0.001 PHE D 840 TYR 0.008 0.001 TYR B 254 ARG 0.002 0.000 ARG C 861 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2529.13 seconds wall clock time: 44 minutes 38.73 seconds (2678.73 seconds total)