Starting phenix.real_space_refine on Wed Mar 5 23:40:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kjr_22898/03_2025/7kjr_22898.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kjr_22898/03_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_22898/03_2025/7kjr_22898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kjr_22898/03_2025/7kjr_22898.map" model { file = "/net/cci-nas-00/data/ceres_data/7kjr_22898/03_2025/7kjr_22898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kjr_22898/03_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-5624/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: 3.64, per 1000 atoms: 0.95 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: 1.05 Conformation dependent library (CDL) restraints added in 459.6 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: 1.15 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: 2.130 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.970 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:14.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.000 ------------------------------------------------------------------------------- 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 : 0.463 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: 1.3831 time to fit residues: 98.3407 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 : 0.440 ------------------------------------------------------------------------------- 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 = 0.098483 restraints weight = 3634.990| |-----------------------------------------------------------------------------| 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: 0.8567 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 : 17.658 171.118 525 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 : 0.405 Fit side-chains REVERT: A 43 PHE cc_start: 0.7941 (m-10) cc_final: 0.6469 (t80) REVERT: A 136 LYS cc_start: 0.8484 (mtpt) cc_final: 0.7681 (mmpt) REVERT: B 136 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7642 (mmpt) REVERT: B 152 ASN cc_start: 0.8268 (m-40) cc_final: 0.7129 (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: 1.1633 time to fit residues: 90.4176 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 : 0.440 ------------------------------------------------------------------------------- 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: 2.9990 chunk 38 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.131993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.096857 restraints weight = 3604.953| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.54 r_work: 0.3018 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3818 Z= 0.287 Angle : 0.574 8.442 5186 Z= 0.305 Chirality : 0.043 0.164 576 Planarity : 0.003 0.033 626 Dihedral : 17.386 176.812 522 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: 2.15 (0.38), residues: 436 helix: 3.03 (0.32), residues: 224 sheet: -0.16 (0.45), residues: 90 loop : -0.39 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 149 HIS 0.003 0.001 HIS B 150 PHE 0.015 0.002 PHE B 87 TYR 0.012 0.002 TYR B 109 ARG 0.005 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 77 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.405 Fit side-chains REVERT: A 43 PHE cc_start: 0.7918 (m-10) cc_final: 0.6380 (t80) REVERT: A 68 ARG cc_start: 0.8280 (ttt-90) cc_final: 0.7860 (ttt90) REVERT: A 136 LYS cc_start: 0.8528 (mtpt) cc_final: 0.7683 (mmpt) REVERT: B 136 LYS cc_start: 0.8513 (mtpt) cc_final: 0.7693 (mmpt) REVERT: B 192 LYS cc_start: 0.9003 (tttm) cc_final: 0.8019 (tptt) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 1.2719 time to fit residues: 96.0295 Evaluate side-chains 75 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.133051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.096505 restraints weight = 3616.304| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.60 r_work: 0.2997 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.0985 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= 0.193 Angle : 0.504 6.977 5186 Z= 0.272 Chirality : 0.040 0.131 576 Planarity : 0.003 0.035 626 Dihedral : 16.534 173.820 522 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.23 % Allowed : 11.82 % Favored : 86.95 % 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: 3.22 (0.31), residues: 224 sheet: -0.33 (0.44), residues: 90 loop : -0.41 (0.52), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 149 HIS 0.002 0.001 HIS B 204 PHE 0.011 0.002 PHE A 87 TYR 0.009 0.001 TYR A 109 ARG 0.004 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 73 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.406 Fit side-chains REVERT: A 43 PHE cc_start: 0.7867 (m-10) cc_final: 0.6270 (t80) REVERT: A 68 ARG cc_start: 0.8162 (ttt-90) cc_final: 0.7728 (ttt90) REVERT: A 136 LYS cc_start: 0.8424 (mtpt) cc_final: 0.7509 (mmpt) REVERT: B 136 LYS cc_start: 0.8390 (mtpt) cc_final: 0.7508 (mmpt) REVERT: B 152 ASN cc_start: 0.8248 (m-40) cc_final: 0.7024 (p0) REVERT: B 192 LYS cc_start: 0.8919 (tttm) cc_final: 0.7879 (tptt) outliers start: 5 outliers final: 6 residues processed: 69 average time/residue: 1.2123 time to fit residues: 86.3869 Evaluate side-chains 74 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 101 LEU 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: 0.5980 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.135687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.099347 restraints weight = 3679.424| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.64 r_work: 0.3076 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1068 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= 0.191 Angle : 0.498 6.999 5186 Z= 0.268 Chirality : 0.040 0.134 576 Planarity : 0.003 0.036 626 Dihedral : 15.486 159.256 522 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.72 % Allowed : 12.07 % 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: 2.22 (0.38), residues: 436 helix: 3.23 (0.31), residues: 224 sheet: -0.39 (0.45), residues: 90 loop : -0.45 (0.52), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 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 74 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 1.147 Fit side-chains REVERT: A 43 PHE cc_start: 0.7903 (m-10) cc_final: 0.6442 (t80) REVERT: A 68 ARG cc_start: 0.8319 (ttt-90) cc_final: 0.7882 (ttt90) REVERT: A 136 LYS cc_start: 0.8554 (mtpt) cc_final: 0.7716 (mmpt) REVERT: B 136 LYS cc_start: 0.8528 (mtpt) cc_final: 0.7716 (mmpt) REVERT: B 152 ASN cc_start: 0.8329 (m-40) cc_final: 0.7202 (p0) REVERT: B 192 LYS cc_start: 0.8957 (tttm) cc_final: 0.8063 (tptt) REVERT: C 29 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.6482 (ttt180) outliers start: 7 outliers final: 5 residues processed: 70 average time/residue: 1.8407 time to fit residues: 133.5637 Evaluate side-chains 73 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU 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 C residue 29 ARG 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: 0.9980 chunk 38 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.135789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099567 restraints weight = 3649.847| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.62 r_work: 0.3080 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1101 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= 0.184 Angle : 0.497 6.780 5186 Z= 0.266 Chirality : 0.040 0.131 576 Planarity : 0.003 0.037 626 Dihedral : 14.295 134.932 522 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.48 % Allowed : 13.05 % Favored : 85.47 % 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: -0.40 (0.44), residues: 90 loop : -0.47 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 149 HIS 0.002 0.001 HIS B 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 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 75 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.854 Fit side-chains REVERT: A 43 PHE cc_start: 0.7900 (m-10) cc_final: 0.6451 (t80) REVERT: A 68 ARG cc_start: 0.8316 (ttt-90) cc_final: 0.7878 (ttt90) REVERT: A 136 LYS cc_start: 0.8561 (mtpt) cc_final: 0.7717 (mmpt) REVERT: A 226 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7968 (mm-30) REVERT: B 136 LYS cc_start: 0.8524 (mtpt) cc_final: 0.7713 (mmpt) REVERT: B 152 ASN cc_start: 0.8338 (m-40) cc_final: 0.7207 (p0) REVERT: B 192 LYS cc_start: 0.8936 (tttm) cc_final: 0.8056 (tptt) REVERT: C 29 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6483 (ttt180) REVERT: C 36 THR cc_start: 0.7551 (m) cc_final: 0.7235 (p) REVERT: D 36 THR cc_start: 0.7547 (m) cc_final: 0.7252 (p) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 1.6002 time to fit residues: 117.1814 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 : 0.446 ------------------------------------------------------------------------------- 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 C residue 29 ARG 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: 0.6980 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.135448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.099422 restraints weight = 3634.531| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.59 r_work: 0.3079 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1088 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= 0.194 Angle : 0.512 7.039 5186 Z= 0.272 Chirality : 0.041 0.131 576 Planarity : 0.003 0.036 626 Dihedral : 13.790 117.394 522 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.48 % Allowed : 12.56 % 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: 3.27 (0.31), residues: 224 sheet: -0.40 (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 0.011 0.002 PHE B 87 TYR 0.009 0.001 TYR B 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: 6 poor density : 68 time to evaluate : 0.481 Fit side-chains REVERT: A 43 PHE cc_start: 0.7913 (m-10) cc_final: 0.6413 (t80) REVERT: A 68 ARG cc_start: 0.8287 (ttt-90) cc_final: 0.7841 (ttt90) REVERT: A 136 LYS cc_start: 0.8523 (mtpt) cc_final: 0.7656 (mmpt) REVERT: A 226 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7918 (mm-30) REVERT: B 136 LYS cc_start: 0.8509 (mtpt) cc_final: 0.7669 (mmpt) REVERT: B 152 ASN cc_start: 0.8318 (m-40) cc_final: 0.7174 (p0) REVERT: B 192 LYS cc_start: 0.8929 (tttm) cc_final: 0.8017 (tptt) outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 1.9624 time to fit residues: 141.3733 Evaluate side-chains 72 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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: 0.7980 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.0770 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.135971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.099717 restraints weight = 3654.526| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.63 r_work: 0.3083 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1137 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= 0.177 Angle : 0.501 6.615 5186 Z= 0.267 Chirality : 0.040 0.131 576 Planarity : 0.003 0.036 626 Dihedral : 13.314 122.604 522 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.48 % Allowed : 12.81 % Favored : 85.71 % 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: -0.42 (0.44), residues: 90 loop : -0.46 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 128 HIS 0.002 0.001 HIS B 204 PHE 0.010 0.001 PHE B 87 TYR 0.009 0.001 TYR A 109 ARG 0.003 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 74 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.457 Fit side-chains REVERT: A 43 PHE cc_start: 0.7940 (m-10) cc_final: 0.6463 (t80) REVERT: A 68 ARG cc_start: 0.8304 (ttt-90) cc_final: 0.7868 (ttt90) REVERT: A 136 LYS cc_start: 0.8551 (mtpt) cc_final: 0.7707 (mmpt) REVERT: A 226 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7962 (mm-30) REVERT: B 64 THR cc_start: 0.8446 (m) cc_final: 0.8064 (p) REVERT: B 136 LYS cc_start: 0.8520 (mtpt) cc_final: 0.7697 (mmpt) REVERT: B 152 ASN cc_start: 0.8339 (m-40) cc_final: 0.7211 (p0) REVERT: B 192 LYS cc_start: 0.8926 (tttm) cc_final: 0.8059 (tptt) REVERT: C 36 THR cc_start: 0.7554 (m) cc_final: 0.7242 (p) REVERT: D 36 THR cc_start: 0.7513 (m) cc_final: 0.7227 (p) outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 1.1756 time to fit residues: 85.1884 Evaluate side-chains 72 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 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 = 0.3685 r_free = 0.3685 target = 0.135775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099524 restraints weight = 3651.033| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.62 r_work: 0.3081 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1139 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= 0.185 Angle : 0.512 6.785 5186 Z= 0.271 Chirality : 0.041 0.131 576 Planarity : 0.003 0.037 626 Dihedral : 13.057 126.981 522 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.23 % Allowed : 13.30 % Favored : 85.47 % 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: 3.28 (0.31), residues: 224 sheet: -0.42 (0.44), residues: 90 loop : -0.47 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 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 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 : 0.436 Fit side-chains REVERT: A 43 PHE cc_start: 0.7946 (m-10) cc_final: 0.6476 (t80) REVERT: A 68 ARG cc_start: 0.8318 (ttt-90) cc_final: 0.7882 (ttt90) REVERT: A 136 LYS cc_start: 0.8547 (mtpt) cc_final: 0.7704 (mmpt) REVERT: A 152 ASN cc_start: 0.8303 (m-40) cc_final: 0.7157 (p0) REVERT: A 226 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7965 (mm-30) REVERT: B 64 THR cc_start: 0.8451 (m) cc_final: 0.8083 (p) REVERT: B 136 LYS cc_start: 0.8523 (mtpt) cc_final: 0.7702 (mmpt) REVERT: B 152 ASN cc_start: 0.8341 (m-40) cc_final: 0.7214 (p0) REVERT: B 192 LYS cc_start: 0.8925 (tttm) cc_final: 0.8056 (tptt) REVERT: C 36 THR cc_start: 0.7550 (m) cc_final: 0.7238 (p) REVERT: D 36 THR cc_start: 0.7509 (m) cc_final: 0.7220 (p) outliers start: 5 outliers final: 4 residues processed: 70 average time/residue: 1.1703 time to fit residues: 84.8263 Evaluate side-chains 72 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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: 1.9990 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 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: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.136040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.099858 restraints weight = 3631.914| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.60 r_work: 0.3084 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1164 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= 0.181 Angle : 0.515 6.688 5186 Z= 0.273 Chirality : 0.041 0.131 576 Planarity : 0.003 0.036 626 Dihedral : 12.828 129.166 522 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.60 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: 3.29 (0.31), residues: 224 sheet: -0.43 (0.44), residues: 90 loop : -0.51 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 128 HIS 0.003 0.001 HIS B 182 PHE 0.010 0.001 PHE B 87 TYR 0.009 0.001 TYR B 109 ARG 0.004 0.001 ARG D 29 ********************** 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 74 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.445 Fit side-chains REVERT: A 43 PHE cc_start: 0.7917 (m-10) cc_final: 0.6425 (t80) REVERT: A 64 THR cc_start: 0.8400 (m) cc_final: 0.8072 (p) REVERT: A 68 ARG cc_start: 0.8274 (ttt-90) cc_final: 0.7829 (ttt90) REVERT: A 136 LYS cc_start: 0.8505 (mtpt) cc_final: 0.7637 (mmpt) REVERT: A 152 ASN cc_start: 0.8280 (m-40) cc_final: 0.7109 (p0) REVERT: A 226 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7919 (mm-30) REVERT: B 64 THR cc_start: 0.8422 (m) cc_final: 0.8041 (p) REVERT: B 136 LYS cc_start: 0.8482 (mtpt) cc_final: 0.7639 (mmpt) REVERT: B 152 ASN cc_start: 0.8314 (m-40) cc_final: 0.7165 (p0) REVERT: B 192 LYS cc_start: 0.8901 (tttm) cc_final: 0.8008 (tptt) REVERT: C 36 THR cc_start: 0.7486 (m) cc_final: 0.7184 (p) REVERT: D 36 THR cc_start: 0.7472 (m) cc_final: 0.7171 (p) outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 1.1556 time to fit residues: 84.9455 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 : 0.406 ------------------------------------------------------------------------------- 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: 1.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 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: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.135291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099121 restraints weight = 3555.034| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.58 r_work: 0.3077 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1134 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= 0.201 Angle : 0.533 7.151 5186 Z= 0.281 Chirality : 0.041 0.130 576 Planarity : 0.003 0.037 626 Dihedral : 12.769 131.458 522 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.87 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: 2.21 (0.38), residues: 436 helix: 3.24 (0.31), residues: 224 sheet: -0.40 (0.45), residues: 90 loop : -0.50 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 128 HIS 0.003 0.001 HIS B 182 PHE 0.011 0.002 PHE B 87 TYR 0.010 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: 4461.11 seconds wall clock time: 79 minutes 20.85 seconds (4760.85 seconds total)