Starting phenix.real_space_refine on Tue Feb 11 04:24:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kjr_22898/02_2025/7kjr_22898.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kjr_22898/02_2025/7kjr_22898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kjr_22898/02_2025/7kjr_22898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kjr_22898/02_2025/7kjr_22898.map" model { file = "/net/cci-nas-00/data/ceres_data/7kjr_22898/02_2025/7kjr_22898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kjr_22898/02_2025/7kjr_22898.cif" } resolution = 2.08 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= 0.002 sd= 0.067 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 P 2 5.49 5 S 18 5.16 5 C 2446 2.51 5 N 580 2.21 5 O 794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3840 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1575 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1575 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "C" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 261 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "D" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 261 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Time building chain proxies: 3.26, per 1000 atoms: 0.85 Number of scatterers: 3840 At special positions: 0 Unit cell: (77.789, 67.611, 90.148, 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 18 16.00 P 2 15.00 O 794 8.00 N 580 7.00 C 2446 6.00 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: 0.98 Conformation dependent library (CDL) restraints added in 440.2 milliseconds 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 848 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 2 sheets defined 57.4% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 removed outlier: 3.596A pdb=" N ILE A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 100 Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 105 through 134 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'B' and resid 43 through 61 removed outlier: 3.716A pdb=" N ILE B 47 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 100 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 105 through 134 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'C' and resid 26 through 55 Proline residue: C 34 - end of helix removed outlier: 5.027A pdb=" N GLY C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 47 Proline residue: D 34 - end of helix Processing helix chain 'D' and resid 47 through 55 Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 160 removed outlier: 5.965A pdb=" N HIS A 150 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N CYS A 200 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU A 214 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASN A 234 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 155 through 160 removed outlier: 5.963A pdb=" N HIS B 150 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N CYS B 200 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU B 214 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASN B 234 " --> pdb=" O LEU B 214 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 741 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: 1.09 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 857 1.33 - 1.45: 906 1.45 - 1.57: 2029 1.57 - 1.69: 2 1.69 - 1.81: 24 Bond restraints: 3818 Sorted by residual: bond pdb=" O4P PEE B 301 " pdb=" P PEE B 301 " ideal model delta sigma weight residual 1.653 1.769 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" O4P PEE A 301 " pdb=" P PEE A 301 " ideal model delta sigma weight residual 1.653 1.769 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C4 PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 1.409 1.365 0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C4 PEE B 301 " pdb=" O4P PEE B 301 " ideal model delta sigma weight residual 1.409 1.366 0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" C ILE B 62 " pdb=" O ILE B 62 " ideal model delta sigma weight residual 1.236 1.218 0.018 1.19e-02 7.06e+03 2.25e+00 ... (remaining 3813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 5035 1.99 - 3.98: 113 3.98 - 5.97: 27 5.97 - 7.96: 5 7.96 - 9.95: 6 Bond angle restraints: 5186 Sorted by residual: angle pdb=" CB GLN C 37 " pdb=" CG GLN C 37 " pdb=" CD GLN C 37 " ideal model delta sigma weight residual 112.60 118.61 -6.01 1.70e+00 3.46e-01 1.25e+01 angle pdb=" CB GLU B 226 " pdb=" CG GLU B 226 " pdb=" CD GLU B 226 " ideal model delta sigma weight residual 112.60 118.44 -5.84 1.70e+00 3.46e-01 1.18e+01 angle pdb=" O1P PEE A 301 " pdb=" P PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 109.92 99.97 9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" O1P PEE B 301 " pdb=" P PEE B 301 " pdb=" O4P PEE B 301 " ideal model delta sigma weight residual 109.92 99.99 9.93 3.00e+00 1.11e-01 1.09e+01 angle pdb=" O1P PEE A 301 " pdb=" P PEE A 301 " pdb=" O2P PEE A 301 " ideal model delta sigma weight residual 119.43 129.00 -9.57 3.00e+00 1.11e-01 1.02e+01 ... (remaining 5181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.46: 2076 30.46 - 60.92: 93 60.92 - 91.39: 14 91.39 - 121.85: 1 121.85 - 152.31: 6 Dihedral angle restraints: 2190 sinusoidal: 868 harmonic: 1322 Sorted by residual: dihedral pdb=" C4 PEE A 301 " pdb=" O4P PEE A 301 " pdb=" P PEE A 301 " pdb=" O2P PEE A 301 " ideal model delta sinusoidal sigma weight residual 284.22 131.91 152.31 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C4 PEE B 301 " pdb=" O4P PEE B 301 " pdb=" P PEE B 301 " pdb=" O2P PEE B 301 " ideal model delta sinusoidal sigma weight residual 284.22 132.36 151.86 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C3 PEE B 301 " pdb=" C1 PEE B 301 " pdb=" C2 PEE B 301 " pdb=" O3P PEE B 301 " ideal model delta sinusoidal sigma weight residual 62.73 -63.97 126.70 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 2187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 352 0.036 - 0.071: 156 0.071 - 0.107: 47 0.107 - 0.142: 15 0.142 - 0.178: 6 Chirality restraints: 576 Sorted by residual: chirality pdb=" CG LEU A 147 " pdb=" CB LEU A 147 " pdb=" CD1 LEU A 147 " pdb=" CD2 LEU A 147 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CG LEU B 147 " pdb=" CB LEU B 147 " pdb=" CD1 LEU B 147 " pdb=" CD2 LEU B 147 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CG LEU A 101 " pdb=" CB LEU A 101 " pdb=" CD1 LEU A 101 " pdb=" CD2 LEU A 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 573 not shown) Planarity restraints: 626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 113 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C TYR B 113 " -0.040 2.00e-02 2.50e+03 pdb=" O TYR B 113 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE B 114 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 37 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" CD GLN D 37 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN D 37 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN D 37 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 114 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C PHE B 114 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE B 114 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU B 115 " 0.011 2.00e-02 2.50e+03 ... (remaining 623 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 914 2.78 - 3.31: 3567 3.31 - 3.84: 7367 3.84 - 4.37: 8430 4.37 - 4.90: 13680 Nonbonded interactions: 33958 Sorted by model distance: nonbonded pdb=" O HOH A 424 " pdb=" O HOH A 451 " model vdw 2.254 3.040 nonbonded pdb=" O HOH B 401 " pdb=" O HOH B 433 " model vdw 2.274 3.040 nonbonded pdb=" OG SER A 216 " pdb=" OE1 GLN A 218 " model vdw 2.274 3.040 nonbonded pdb=" OG SER B 216 " pdb=" OE1 GLN B 218 " model vdw 2.276 3.040 nonbonded pdb=" O HOH A 401 " pdb=" O HOH A 437 " model vdw 2.294 3.040 ... (remaining 33953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.120 Find NCS groups from input model: 0.100 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:15.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 0.116 3818 Z= 0.398 Angle : 0.843 9.946 5186 Z= 0.426 Chirality : 0.047 0.178 576 Planarity : 0.005 0.036 626 Dihedral : 19.500 152.312 1342 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.25 % Allowed : 13.05 % Favored : 86.70 % 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: 1.13 (0.37), residues: 436 helix: 1.81 (0.31), residues: 234 sheet: 0.02 (0.48), residues: 90 loop : -0.81 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 149 HIS 0.003 0.001 HIS B 204 PHE 0.015 0.003 PHE B 146 TYR 0.011 0.002 TYR B 109 ARG 0.011 0.001 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.445 Fit side-chains REVERT: A 43 PHE cc_start: 0.7754 (m-10) cc_final: 0.6681 (t80) REVERT: A 136 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7714 (mmtm) REVERT: B 136 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7686 (mmtm) REVERT: B 192 LYS cc_start: 0.8741 (tttm) cc_final: 0.8044 (tptt) outliers start: 1 outliers final: 1 residues processed: 69 average time/residue: 1.3670 time to fit residues: 97.1569 Evaluate side-chains 69 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN C 42 ASN D 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.098478 restraints weight = 3634.984| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.58 r_work: 0.3053 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3818 Z= 0.188 Angle : 0.535 6.555 5186 Z= 0.286 Chirality : 0.041 0.136 576 Planarity : 0.003 0.034 626 Dihedral : 17.658 171.119 525 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.22 % Allowed : 11.58 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.37), residues: 436 helix: 2.89 (0.31), residues: 224 sheet: 0.14 (0.45), residues: 86 loop : -0.56 (0.48), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 149 HIS 0.002 0.001 HIS A 204 PHE 0.011 0.002 PHE B 87 TYR 0.010 0.001 TYR B 109 ARG 0.004 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.408 Fit side-chains REVERT: A 43 PHE cc_start: 0.7939 (m-10) cc_final: 0.6465 (t80) REVERT: A 136 LYS cc_start: 0.8483 (mtpt) cc_final: 0.7680 (mmpt) REVERT: B 136 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7641 (mmpt) REVERT: B 152 ASN cc_start: 0.8269 (m-40) cc_final: 0.7131 (p0) REVERT: B 192 LYS cc_start: 0.8961 (tttm) cc_final: 0.8000 (tptt) outliers start: 9 outliers final: 5 residues processed: 75 average time/residue: 1.2174 time to fit residues: 94.6096 Evaluate side-chains 76 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.132990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.096919 restraints weight = 3591.011| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.57 r_work: 0.3025 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3818 Z= 0.252 Angle : 0.550 7.867 5186 Z= 0.294 Chirality : 0.042 0.138 576 Planarity : 0.003 0.035 626 Dihedral : 17.156 177.248 522 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.23 % Allowed : 12.07 % Favored : 86.70 % 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: 2.19 (0.38), residues: 436 helix: 3.08 (0.32), residues: 224 sheet: -0.18 (0.45), residues: 90 loop : -0.38 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 149 HIS 0.003 0.001 HIS A 150 PHE 0.014 0.002 PHE A 87 TYR 0.011 0.002 TYR B 109 ARG 0.004 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.427 Fit side-chains REVERT: A 43 PHE cc_start: 0.7941 (m-10) cc_final: 0.6411 (t80) REVERT: A 68 ARG cc_start: 0.8267 (ttt-90) cc_final: 0.7844 (ttt90) REVERT: A 136 LYS cc_start: 0.8521 (mtpt) cc_final: 0.7686 (mmpt) REVERT: B 136 LYS cc_start: 0.8493 (mtpt) cc_final: 0.7680 (mmpt) REVERT: B 152 ASN cc_start: 0.8292 (m-40) cc_final: 0.7136 (p0) REVERT: B 192 LYS cc_start: 0.8999 (tttm) cc_final: 0.8016 (tptt) outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 1.3638 time to fit residues: 100.0114 Evaluate side-chains 73 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.134390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.097998 restraints weight = 3620.954| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.61 r_work: 0.3023 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3818 Z= 0.160 Angle : 0.478 6.070 5186 Z= 0.259 Chirality : 0.040 0.132 576 Planarity : 0.003 0.035 626 Dihedral : 16.182 170.358 522 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.48 % Allowed : 12.07 % Favored : 86.45 % 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: 2.25 (0.38), residues: 436 helix: 3.26 (0.31), residues: 224 sheet: -0.37 (0.44), residues: 90 loop : -0.45 (0.52), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 149 HIS 0.002 0.001 HIS A 204 PHE 0.009 0.001 PHE B 87 TYR 0.008 0.001 TYR A 233 ARG 0.003 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.599 Fit side-chains REVERT: A 43 PHE cc_start: 0.7835 (m-10) cc_final: 0.6276 (t80) REVERT: A 68 ARG cc_start: 0.8151 (ttt-90) cc_final: 0.7712 (ttt90) REVERT: A 136 LYS cc_start: 0.8386 (mtpt) cc_final: 0.7477 (mmpt) REVERT: B 136 LYS cc_start: 0.8359 (mtpt) cc_final: 0.7485 (mmpt) REVERT: B 152 ASN cc_start: 0.8221 (m-40) cc_final: 0.7008 (p0) REVERT: B 192 LYS cc_start: 0.8870 (tttm) cc_final: 0.7908 (tptt) REVERT: C 36 THR cc_start: 0.7320 (m) cc_final: 0.7043 (p) REVERT: D 36 THR cc_start: 0.7211 (m) cc_final: 0.6986 (p) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 1.2909 time to fit residues: 90.6183 Evaluate side-chains 70 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.097022 restraints weight = 3668.527| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.61 r_work: 0.3006 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3818 Z= 0.180 Angle : 0.494 6.635 5186 Z= 0.264 Chirality : 0.040 0.133 576 Planarity : 0.003 0.035 626 Dihedral : 15.134 154.334 522 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.48 % Allowed : 12.32 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.38), residues: 436 helix: 3.27 (0.31), residues: 224 sheet: -0.43 (0.44), residues: 90 loop : -0.41 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 149 HIS 0.002 0.001 HIS A 204 PHE 0.011 0.002 PHE B 87 TYR 0.009 0.001 TYR A 109 ARG 0.004 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.359 Fit side-chains REVERT: A 43 PHE cc_start: 0.7870 (m-10) cc_final: 0.6289 (t80) REVERT: A 68 ARG cc_start: 0.8177 (ttt-90) cc_final: 0.7683 (ttt90) REVERT: A 136 LYS cc_start: 0.8402 (mtpt) cc_final: 0.7491 (mmpt) REVERT: B 136 LYS cc_start: 0.8387 (mtpt) cc_final: 0.7497 (mmpt) REVERT: B 152 ASN cc_start: 0.8251 (m-40) cc_final: 0.7030 (p0) REVERT: B 192 LYS cc_start: 0.8889 (tttm) cc_final: 0.7915 (tptt) REVERT: C 36 THR cc_start: 0.7273 (m) cc_final: 0.6991 (p) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 1.3496 time to fit residues: 94.6073 Evaluate side-chains 70 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.0060 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.133864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.097428 restraints weight = 3631.835| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.60 r_work: 0.3011 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3818 Z= 0.173 Angle : 0.488 6.398 5186 Z= 0.261 Chirality : 0.040 0.131 576 Planarity : 0.003 0.036 626 Dihedral : 14.194 133.604 522 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.99 % Allowed : 13.05 % Favored : 85.96 % 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: 2.27 (0.38), residues: 436 helix: 3.31 (0.31), residues: 224 sheet: -0.44 (0.44), residues: 90 loop : -0.45 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 149 HIS 0.002 0.001 HIS A 204 PHE 0.010 0.001 PHE A 87 TYR 0.008 0.001 TYR B 109 ARG 0.003 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.422 Fit side-chains REVERT: A 43 PHE cc_start: 0.7875 (m-10) cc_final: 0.6284 (t80) REVERT: A 68 ARG cc_start: 0.8181 (ttt-90) cc_final: 0.7688 (ttt90) REVERT: A 136 LYS cc_start: 0.8399 (mtpt) cc_final: 0.7483 (mmpt) REVERT: A 226 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7805 (mm-30) REVERT: B 136 LYS cc_start: 0.8369 (mtpt) cc_final: 0.7474 (mmpt) REVERT: B 152 ASN cc_start: 0.8260 (m-40) cc_final: 0.7034 (p0) REVERT: B 192 LYS cc_start: 0.8864 (tttm) cc_final: 0.7913 (tptt) REVERT: C 36 THR cc_start: 0.7320 (m) cc_final: 0.7051 (p) REVERT: D 36 THR cc_start: 0.7302 (m) cc_final: 0.7070 (p) outliers start: 4 outliers final: 4 residues processed: 70 average time/residue: 1.2550 time to fit residues: 90.7637 Evaluate side-chains 71 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.132861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.096327 restraints weight = 3596.111| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.60 r_work: 0.2999 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3818 Z= 0.204 Angle : 0.516 7.094 5186 Z= 0.274 Chirality : 0.041 0.132 576 Planarity : 0.003 0.036 626 Dihedral : 13.747 116.096 522 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.23 % Allowed : 12.81 % Favored : 85.96 % 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: 2.26 (0.38), residues: 436 helix: 3.28 (0.31), residues: 224 sheet: -0.42 (0.44), residues: 90 loop : -0.42 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 128 HIS 0.002 0.001 HIS B 204 PHE 0.012 0.002 PHE B 87 TYR 0.010 0.001 TYR A 109 ARG 0.004 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.449 Fit side-chains REVERT: A 43 PHE cc_start: 0.7873 (m-10) cc_final: 0.6260 (t80) REVERT: A 68 ARG cc_start: 0.8193 (ttt-90) cc_final: 0.7701 (ttt90) REVERT: A 136 LYS cc_start: 0.8420 (mtpt) cc_final: 0.7505 (mmpt) REVERT: B 136 LYS cc_start: 0.8396 (mtpt) cc_final: 0.7507 (mmpt) REVERT: B 152 ASN cc_start: 0.8241 (m-40) cc_final: 0.7031 (p0) REVERT: B 192 LYS cc_start: 0.8902 (tttm) cc_final: 0.7877 (tptt) outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 1.2937 time to fit residues: 94.8932 Evaluate side-chains 73 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS C 42 ASN D 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.132972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.096337 restraints weight = 3615.861| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.61 r_work: 0.2998 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3818 Z= 0.206 Angle : 0.520 7.072 5186 Z= 0.275 Chirality : 0.041 0.131 576 Planarity : 0.003 0.036 626 Dihedral : 13.152 124.946 522 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.48 % Allowed : 12.32 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.38), residues: 436 helix: 3.26 (0.31), residues: 224 sheet: -0.41 (0.44), residues: 90 loop : -0.45 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 128 HIS 0.002 0.001 HIS B 182 PHE 0.012 0.002 PHE B 87 TYR 0.010 0.001 TYR A 109 ARG 0.004 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.420 Fit side-chains REVERT: A 43 PHE cc_start: 0.7895 (m-10) cc_final: 0.6277 (t80) REVERT: A 68 ARG cc_start: 0.8220 (ttt-90) cc_final: 0.7732 (ttt90) REVERT: A 136 LYS cc_start: 0.8418 (mtpt) cc_final: 0.7496 (mmpt) REVERT: A 226 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7805 (mm-30) REVERT: B 64 THR cc_start: 0.8331 (m) cc_final: 0.7907 (p) REVERT: B 136 LYS cc_start: 0.8386 (mtpt) cc_final: 0.7496 (mmpt) REVERT: B 152 ASN cc_start: 0.8235 (m-40) cc_final: 0.7031 (p0) REVERT: B 192 LYS cc_start: 0.8892 (tttm) cc_final: 0.7872 (tptt) outliers start: 6 outliers final: 4 residues processed: 72 average time/residue: 1.2417 time to fit residues: 92.3046 Evaluate side-chains 74 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS C 42 ASN D 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.133551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.096947 restraints weight = 3603.358| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.60 r_work: 0.3007 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3818 Z= 0.183 Angle : 0.510 6.612 5186 Z= 0.270 Chirality : 0.041 0.131 576 Planarity : 0.003 0.036 626 Dihedral : 12.856 128.294 522 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.23 % Allowed : 13.55 % Favored : 85.22 % 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: 2.22 (0.38), residues: 436 helix: 3.28 (0.31), residues: 224 sheet: -0.44 (0.44), residues: 90 loop : -0.51 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 128 HIS 0.003 0.001 HIS B 204 PHE 0.010 0.002 PHE B 87 TYR 0.009 0.001 TYR B 109 ARG 0.003 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.427 Fit side-chains REVERT: A 43 PHE cc_start: 0.7866 (m-10) cc_final: 0.6262 (t80) REVERT: A 64 THR cc_start: 0.8308 (m) cc_final: 0.7963 (p) REVERT: A 68 ARG cc_start: 0.8208 (ttt-90) cc_final: 0.7745 (ttt90) REVERT: A 136 LYS cc_start: 0.8409 (mtpt) cc_final: 0.7486 (mmpt) REVERT: A 226 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7812 (mm-30) REVERT: B 64 THR cc_start: 0.8345 (m) cc_final: 0.7940 (p) REVERT: B 136 LYS cc_start: 0.8385 (mtpt) cc_final: 0.7491 (mmpt) REVERT: B 152 ASN cc_start: 0.8247 (m-40) cc_final: 0.7040 (p0) REVERT: B 192 LYS cc_start: 0.8863 (tttm) cc_final: 0.7898 (tptt) REVERT: C 36 THR cc_start: 0.7385 (m) cc_final: 0.7071 (p) REVERT: D 36 THR cc_start: 0.7333 (m) cc_final: 0.7039 (p) outliers start: 5 outliers final: 4 residues processed: 70 average time/residue: 1.2223 time to fit residues: 88.4818 Evaluate side-chains 71 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS C 42 ASN D 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.100550 restraints weight = 3639.513| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.62 r_work: 0.3097 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3818 Z= 0.162 Angle : 0.498 6.064 5186 Z= 0.265 Chirality : 0.040 0.133 576 Planarity : 0.003 0.036 626 Dihedral : 12.687 130.240 522 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.23 % Allowed : 13.55 % Favored : 85.22 % 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: 2.24 (0.38), residues: 436 helix: 3.31 (0.31), residues: 224 sheet: -0.44 (0.44), residues: 90 loop : -0.52 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 128 HIS 0.003 0.001 HIS B 204 PHE 0.009 0.001 PHE B 87 TYR 0.008 0.001 TYR B 109 ARG 0.004 0.001 ARG B 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.400 Fit side-chains REVERT: A 43 PHE cc_start: 0.7908 (m-10) cc_final: 0.6477 (t80) REVERT: A 64 THR cc_start: 0.8386 (m) cc_final: 0.8075 (p) REVERT: A 68 ARG cc_start: 0.8304 (ttt-90) cc_final: 0.7875 (ttt90) REVERT: A 136 LYS cc_start: 0.8523 (mtpt) cc_final: 0.7679 (mmpt) REVERT: A 226 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7972 (mm-30) REVERT: B 64 THR cc_start: 0.8433 (m) cc_final: 0.8070 (p) REVERT: B 136 LYS cc_start: 0.8501 (mtpt) cc_final: 0.7686 (mmpt) REVERT: B 152 ASN cc_start: 0.8347 (m-40) cc_final: 0.7214 (p0) REVERT: B 192 LYS cc_start: 0.8882 (tttm) cc_final: 0.8043 (tptt) REVERT: C 36 THR cc_start: 0.7545 (m) cc_final: 0.7251 (p) REVERT: D 36 THR cc_start: 0.7479 (m) cc_final: 0.7234 (p) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 1.2682 time to fit residues: 90.3502 Evaluate side-chains 70 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS C 42 ASN D 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.135859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.099792 restraints weight = 3572.869| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.58 r_work: 0.3084 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3818 Z= 0.187 Angle : 0.525 6.778 5186 Z= 0.277 Chirality : 0.041 0.132 576 Planarity : 0.003 0.036 626 Dihedral : 12.711 132.108 522 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.23 % Allowed : 13.79 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.38), residues: 436 helix: 3.29 (0.31), residues: 224 sheet: -0.43 (0.44), residues: 90 loop : -0.52 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 128 HIS 0.003 0.001 HIS B 182 PHE 0.011 0.002 PHE B 87 TYR 0.009 0.001 TYR A 109 ARG 0.004 0.001 ARG D 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4191.81 seconds wall clock time: 74 minutes 35.89 seconds (4475.89 seconds total)