Starting phenix.real_space_refine on Fri Aug 22 17:58:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v8s_43044/08_2025/8v8s_43044.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v8s_43044/08_2025/8v8s_43044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v8s_43044/08_2025/8v8s_43044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v8s_43044/08_2025/8v8s_43044.map" model { file = "/net/cci-nas-00/data/ceres_data/8v8s_43044/08_2025/8v8s_43044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v8s_43044/08_2025/8v8s_43044.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 4368 2.51 5 N 1060 2.21 5 O 1237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6717 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1654 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Restraints were copied for chains: B, C, D Time building chain proxies: 1.54, per 1000 atoms: 0.23 Number of scatterers: 6717 At special positions: 0 Unit cell: (77.562, 77.562, 67.554, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1237 8.00 N 1060 7.00 C 4368 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: 0.61 Conformation dependent library (CDL) restraints added in 447.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 73.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 32 through 56 removed outlier: 3.644A pdb=" N THR A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 93 removed outlier: 5.659A pdb=" N HIS A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 107 Processing helix chain 'A' and resid 111 through 137 removed outlier: 3.567A pdb=" N PHE A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 178 Processing helix chain 'A' and resid 188 through 205 Processing helix chain 'A' and resid 213 through 225 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 231 through 251 Proline residue: A 237 - end of helix Processing helix chain 'B' and resid 33 through 56 removed outlier: 3.644A pdb=" N THR B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 93 removed outlier: 5.659A pdb=" N HIS B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 107 Processing helix chain 'B' and resid 111 through 137 removed outlier: 3.567A pdb=" N PHE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 178 Processing helix chain 'B' and resid 188 through 205 Processing helix chain 'B' and resid 213 through 225 Proline residue: B 220 - end of helix Processing helix chain 'B' and resid 231 through 251 Proline residue: B 237 - end of helix Processing helix chain 'C' and resid 33 through 56 removed outlier: 3.644A pdb=" N THR C 56 " --> pdb=" O SER C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 93 removed outlier: 5.659A pdb=" N HIS C 90 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE C 91 " --> pdb=" O CYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 107 Processing helix chain 'C' and resid 111 through 137 removed outlier: 3.567A pdb=" N PHE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 178 Processing helix chain 'C' and resid 188 through 205 Processing helix chain 'C' and resid 213 through 225 Proline residue: C 220 - end of helix Processing helix chain 'C' and resid 231 through 251 Proline residue: C 237 - end of helix Processing helix chain 'D' and resid 33 through 56 removed outlier: 3.644A pdb=" N THR D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 93 removed outlier: 5.659A pdb=" N HIS D 90 " --> pdb=" O GLN D 86 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE D 91 " --> pdb=" O CYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 107 Processing helix chain 'D' and resid 111 through 137 removed outlier: 3.568A pdb=" N PHE D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 178 Processing helix chain 'D' and resid 188 through 205 Processing helix chain 'D' and resid 213 through 225 Proline residue: D 220 - end of helix Processing helix chain 'D' and resid 231 through 251 Proline residue: D 237 - end of helix 485 hydrogen bonds defined for protein. 1455 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: 1.01 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2016 1.34 - 1.46: 1641 1.46 - 1.58: 3051 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 6788 Sorted by residual: bond pdb=" N MET C 212 " pdb=" CA MET C 212 " ideal model delta sigma weight residual 1.462 1.475 -0.013 1.48e-02 4.57e+03 7.57e-01 bond pdb=" N MET D 212 " pdb=" CA MET D 212 " ideal model delta sigma weight residual 1.462 1.475 -0.013 1.48e-02 4.57e+03 7.55e-01 bond pdb=" N MET A 212 " pdb=" CA MET A 212 " ideal model delta sigma weight residual 1.462 1.474 -0.013 1.48e-02 4.57e+03 7.37e-01 bond pdb=" N MET B 212 " pdb=" CA MET B 212 " ideal model delta sigma weight residual 1.462 1.474 -0.013 1.48e-02 4.57e+03 7.37e-01 bond pdb=" CB ASN C 226 " pdb=" CG ASN C 226 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.35e-01 ... (remaining 6783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 9017 1.16 - 2.32: 187 2.32 - 3.48: 44 3.48 - 4.64: 8 4.64 - 5.80: 12 Bond angle restraints: 9268 Sorted by residual: angle pdb=" C SER C 211 " pdb=" N MET C 212 " pdb=" CA MET C 212 " ideal model delta sigma weight residual 122.61 125.79 -3.18 1.56e+00 4.11e-01 4.17e+00 angle pdb=" C SER D 211 " pdb=" N MET D 212 " pdb=" CA MET D 212 " ideal model delta sigma weight residual 122.61 125.78 -3.17 1.56e+00 4.11e-01 4.13e+00 angle pdb=" C TYR B 250 " pdb=" N VAL B 251 " pdb=" CA VAL B 251 " ideal model delta sigma weight residual 123.16 121.01 2.15 1.06e+00 8.90e-01 4.12e+00 angle pdb=" C SER A 211 " pdb=" N MET A 212 " pdb=" CA MET A 212 " ideal model delta sigma weight residual 122.61 125.77 -3.16 1.56e+00 4.11e-01 4.11e+00 angle pdb=" C TYR A 250 " pdb=" N VAL A 251 " pdb=" CA VAL A 251 " ideal model delta sigma weight residual 123.16 121.01 2.15 1.06e+00 8.90e-01 4.10e+00 ... (remaining 9263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.10: 3215 11.10 - 22.19: 369 22.19 - 33.29: 124 33.29 - 44.39: 76 44.39 - 55.48: 48 Dihedral angle restraints: 3832 sinusoidal: 1344 harmonic: 2488 Sorted by residual: dihedral pdb=" CA PHE D 203 " pdb=" C PHE D 203 " pdb=" N ALA D 204 " pdb=" CA ALA D 204 " ideal model delta harmonic sigma weight residual -180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA PHE A 203 " pdb=" C PHE A 203 " pdb=" N ALA A 204 " pdb=" CA ALA A 204 " ideal model delta harmonic sigma weight residual 180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA PHE B 203 " pdb=" C PHE B 203 " pdb=" N ALA B 204 " pdb=" CA ALA B 204 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 3829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 598 0.023 - 0.046: 266 0.046 - 0.069: 173 0.069 - 0.092: 42 0.092 - 0.114: 33 Chirality restraints: 1112 Sorted by residual: chirality pdb=" CA PRO D 237 " pdb=" N PRO D 237 " pdb=" C PRO D 237 " pdb=" CB PRO D 237 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.27e-01 chirality pdb=" CA PRO A 237 " pdb=" N PRO A 237 " pdb=" C PRO A 237 " pdb=" CB PRO A 237 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.01e-01 chirality pdb=" CA MET C 212 " pdb=" N MET C 212 " pdb=" C MET C 212 " pdb=" CB MET C 212 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.00e-01 ... (remaining 1109 not shown) Planarity restraints: 1132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 236 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO B 237 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 237 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 237 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 236 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 237 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 236 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO D 237 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 237 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 237 " -0.018 5.00e-02 4.00e+02 ... (remaining 1129 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 557 2.74 - 3.28: 7142 3.28 - 3.82: 12239 3.82 - 4.36: 14558 4.36 - 4.90: 24304 Nonbonded interactions: 58800 Sorted by model distance: nonbonded pdb=" O HOH A 407 " pdb=" O HOH A 419 " model vdw 2.203 3.040 nonbonded pdb=" O HOH B 407 " pdb=" O HOH B 419 " model vdw 2.203 3.040 nonbonded pdb=" O HOH C 407 " pdb=" O HOH C 419 " model vdw 2.203 3.040 nonbonded pdb=" O HOH D 407 " pdb=" O HOH D 419 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG C 108 " pdb=" OH TYR C 250 " model vdw 2.308 3.120 ... (remaining 58795 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = 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: 2.480 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: 0.020 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.980 Find NCS groups from input model: 0.060 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:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 0.002 0.018 6788 Z= 0.087 Angle : 0.472 5.805 9268 Z= 0.246 Chirality : 0.037 0.114 1112 Planarity : 0.004 0.033 1132 Dihedral : 14.020 55.483 2256 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.27), residues: 884 helix: 0.29 (0.21), residues: 584 sheet: None (None), residues: 0 loop : 0.40 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 108 TYR 0.004 0.001 TYR B 233 PHE 0.007 0.001 PHE C 168 TRP 0.008 0.001 TRP A 59 HIS 0.002 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00174 ( 6788) covalent geometry : angle 0.47195 ( 9268) hydrogen bonds : bond 0.22866 ( 485) hydrogen bonds : angle 8.11788 ( 1455) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7492 (mtm-85) cc_final: 0.6827 (mtm-85) REVERT: B 250 TYR cc_start: 0.8740 (m-10) cc_final: 0.8355 (m-80) REVERT: C 108 ARG cc_start: 0.7490 (mtm-85) cc_final: 0.6821 (mtm-85) REVERT: C 250 TYR cc_start: 0.8738 (m-10) cc_final: 0.8357 (m-80) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.4357 time to fit residues: 65.1248 Evaluate side-chains 116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0050 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.0030 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN B 206 ASN C 86 GLN C 206 ASN D 86 GLN D 206 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5505 r_free = 0.5505 target = 0.265376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5434 r_free = 0.5434 target = 0.249955 restraints weight = 6376.165| |-----------------------------------------------------------------------------| r_work (start): 0.5425 rms_B_bonded: 1.64 r_work: 0.5415 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.5309 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.5309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6788 Z= 0.127 Angle : 0.552 7.045 9268 Z= 0.291 Chirality : 0.040 0.137 1112 Planarity : 0.004 0.032 1132 Dihedral : 3.901 19.021 924 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.30 % Allowed : 11.93 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.27), residues: 884 helix: 1.64 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.22 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 108 TYR 0.006 0.001 TYR C 250 PHE 0.007 0.001 PHE A 203 TRP 0.011 0.001 TRP A 35 HIS 0.002 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6788) covalent geometry : angle 0.55161 ( 9268) hydrogen bonds : bond 0.04698 ( 485) hydrogen bonds : angle 4.94822 ( 1455) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.207 Fit side-chains REVERT: A 108 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7275 (mpt180) REVERT: B 108 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7263 (mpt180) REVERT: C 108 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7278 (mpt180) REVERT: D 108 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7279 (mpt180) outliers start: 16 outliers final: 12 residues processed: 140 average time/residue: 0.4957 time to fit residues: 73.3140 Evaluate side-chains 116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 72 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN C 86 GLN D 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5515 r_free = 0.5515 target = 0.271560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5477 r_free = 0.5477 target = 0.250360 restraints weight = 6622.744| |-----------------------------------------------------------------------------| r_work (start): 0.5402 rms_B_bonded: 1.56 r_work: 0.5399 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.5296 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.5296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6788 Z= 0.128 Angle : 0.544 6.826 9268 Z= 0.284 Chirality : 0.040 0.112 1112 Planarity : 0.004 0.032 1132 Dihedral : 3.975 20.395 924 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.16 % Allowed : 11.93 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.28), residues: 884 helix: 1.95 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.19 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 108 TYR 0.007 0.001 TYR C 233 PHE 0.006 0.001 PHE B 218 TRP 0.011 0.001 TRP A 35 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6788) covalent geometry : angle 0.54424 ( 9268) hydrogen bonds : bond 0.04714 ( 485) hydrogen bonds : angle 4.71759 ( 1455) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.248 Fit side-chains REVERT: A 108 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7476 (mtm-85) REVERT: B 108 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7481 (mtm-85) REVERT: C 108 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7501 (mtm-85) REVERT: D 108 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7498 (mtm-85) outliers start: 22 outliers final: 16 residues processed: 119 average time/residue: 0.5473 time to fit residues: 68.7267 Evaluate side-chains 124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN C 86 GLN D 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5510 r_free = 0.5510 target = 0.270919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5469 r_free = 0.5469 target = 0.249607 restraints weight = 6629.968| |-----------------------------------------------------------------------------| r_work (start): 0.5393 rms_B_bonded: 1.56 r_work: 0.5388 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.5284 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.5284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6788 Z= 0.133 Angle : 0.548 6.874 9268 Z= 0.284 Chirality : 0.040 0.109 1112 Planarity : 0.004 0.034 1132 Dihedral : 4.020 20.674 924 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.59 % Allowed : 10.92 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.28), residues: 884 helix: 2.01 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.13 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 108 TYR 0.008 0.001 TYR B 233 PHE 0.006 0.001 PHE B 218 TRP 0.011 0.001 TRP A 35 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6788) covalent geometry : angle 0.54835 ( 9268) hydrogen bonds : bond 0.04661 ( 485) hydrogen bonds : angle 4.66673 ( 1455) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.324 Fit side-chains REVERT: A 108 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7489 (mtm-85) REVERT: B 108 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7478 (mtm-85) REVERT: C 108 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7491 (mtm-85) REVERT: D 108 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7488 (mtm-85) outliers start: 25 outliers final: 16 residues processed: 124 average time/residue: 0.5373 time to fit residues: 70.1002 Evaluate side-chains 124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN C 86 GLN D 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5515 r_free = 0.5515 target = 0.271273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5474 r_free = 0.5474 target = 0.249876 restraints weight = 6621.243| |-----------------------------------------------------------------------------| r_work (start): 0.5402 rms_B_bonded: 1.57 r_work: 0.5401 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.5298 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.5298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6788 Z= 0.133 Angle : 0.550 6.619 9268 Z= 0.285 Chirality : 0.040 0.109 1112 Planarity : 0.004 0.035 1132 Dihedral : 4.030 21.073 924 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.59 % Allowed : 10.78 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.28), residues: 884 helix: 2.03 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.09 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 108 TYR 0.007 0.001 TYR A 233 PHE 0.006 0.001 PHE A 218 TRP 0.010 0.001 TRP A 35 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6788) covalent geometry : angle 0.54953 ( 9268) hydrogen bonds : bond 0.04598 ( 485) hydrogen bonds : angle 4.63680 ( 1455) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.262 Fit side-chains REVERT: A 108 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7477 (mtm-85) REVERT: B 108 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7453 (mtm-85) REVERT: C 108 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7484 (mtm-85) REVERT: D 108 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7471 (mtm-85) outliers start: 25 outliers final: 16 residues processed: 119 average time/residue: 0.5422 time to fit residues: 68.0869 Evaluate side-chains 124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 84 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 54 optimal weight: 0.0070 chunk 21 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 206 ASN B 86 GLN B 206 ASN C 86 GLN C 206 ASN D 86 GLN D 206 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5501 r_free = 0.5501 target = 0.264820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5423 r_free = 0.5423 target = 0.248618 restraints weight = 6381.119| |-----------------------------------------------------------------------------| r_work (start): 0.5412 rms_B_bonded: 1.65 r_work: 0.5403 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.5290 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.5290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6788 Z= 0.120 Angle : 0.537 6.474 9268 Z= 0.276 Chirality : 0.040 0.113 1112 Planarity : 0.004 0.035 1132 Dihedral : 3.946 20.532 924 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.16 % Allowed : 12.93 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.28), residues: 884 helix: 2.09 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.02 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 108 TYR 0.007 0.001 TYR C 233 PHE 0.007 0.001 PHE B 168 TRP 0.011 0.001 TRP A 35 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6788) covalent geometry : angle 0.53727 ( 9268) hydrogen bonds : bond 0.04231 ( 485) hydrogen bonds : angle 4.56331 ( 1455) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.267 Fit side-chains REVERT: A 108 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7487 (mtm-85) REVERT: B 108 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7475 (mtm-85) REVERT: C 108 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7490 (mtm-85) REVERT: D 108 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7489 (mtm-85) outliers start: 22 outliers final: 16 residues processed: 125 average time/residue: 0.5209 time to fit residues: 68.6554 Evaluate side-chains 124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 59 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 chunk 55 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 206 ASN B 86 GLN B 206 ASN C 86 GLN C 206 ASN D 86 GLN D 206 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5500 r_free = 0.5500 target = 0.264687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.5423 r_free = 0.5423 target = 0.248504 restraints weight = 6338.407| |-----------------------------------------------------------------------------| r_work (start): 0.5412 rms_B_bonded: 1.65 r_work: 0.5403 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.5294 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.5294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6788 Z= 0.124 Angle : 0.545 6.464 9268 Z= 0.280 Chirality : 0.040 0.107 1112 Planarity : 0.004 0.035 1132 Dihedral : 3.968 21.128 924 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.16 % Allowed : 13.51 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.28), residues: 884 helix: 2.10 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.05 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 108 TYR 0.007 0.001 TYR D 233 PHE 0.006 0.001 PHE C 168 TRP 0.011 0.001 TRP A 35 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6788) covalent geometry : angle 0.54541 ( 9268) hydrogen bonds : bond 0.04323 ( 485) hydrogen bonds : angle 4.55762 ( 1455) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.262 Fit side-chains REVERT: A 108 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7482 (mtm-85) REVERT: B 108 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7466 (mtm-85) REVERT: C 108 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7480 (mtm-85) REVERT: D 108 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7487 (mtm-85) outliers start: 22 outliers final: 12 residues processed: 118 average time/residue: 0.5040 time to fit residues: 62.7156 Evaluate side-chains 120 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 55 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 33 optimal weight: 0.0370 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 206 ASN B 86 GLN C 86 GLN D 86 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5542 r_free = 0.5542 target = 0.273639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5503 r_free = 0.5503 target = 0.252833 restraints weight = 6642.308| |-----------------------------------------------------------------------------| r_work (start): 0.5430 rms_B_bonded: 1.57 r_work: 0.5425 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.5319 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.5319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6788 Z= 0.119 Angle : 0.545 6.484 9268 Z= 0.278 Chirality : 0.040 0.109 1112 Planarity : 0.004 0.035 1132 Dihedral : 3.935 20.950 924 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.87 % Allowed : 14.22 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.28), residues: 884 helix: 2.11 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.09 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 108 TYR 0.007 0.001 TYR D 233 PHE 0.007 0.001 PHE B 168 TRP 0.011 0.001 TRP A 35 HIS 0.002 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 6788) covalent geometry : angle 0.54519 ( 9268) hydrogen bonds : bond 0.04132 ( 485) hydrogen bonds : angle 4.52852 ( 1455) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.170 Fit side-chains REVERT: A 108 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7445 (mtm-85) REVERT: B 108 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7457 (mtm-85) REVERT: C 108 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7462 (mtm-85) REVERT: D 108 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7468 (mtm-85) outliers start: 20 outliers final: 16 residues processed: 122 average time/residue: 0.4997 time to fit residues: 64.3915 Evaluate side-chains 129 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN C 86 GLN D 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5484 r_free = 0.5484 target = 0.268218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5443 r_free = 0.5443 target = 0.245496 restraints weight = 6669.678| |-----------------------------------------------------------------------------| r_work (start): 0.5358 rms_B_bonded: 1.56 r_work: 0.5349 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.5244 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.5244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6788 Z= 0.178 Angle : 0.624 6.953 9268 Z= 0.324 Chirality : 0.043 0.111 1112 Planarity : 0.004 0.036 1132 Dihedral : 4.243 23.083 924 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.73 % Allowed : 14.08 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.28), residues: 884 helix: 1.90 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.06 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 108 TYR 0.011 0.002 TYR B 207 PHE 0.013 0.002 PHE D 48 TRP 0.008 0.001 TRP B 59 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 6788) covalent geometry : angle 0.62387 ( 9268) hydrogen bonds : bond 0.05402 ( 485) hydrogen bonds : angle 4.72247 ( 1455) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.267 Fit side-chains REVERT: A 108 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7465 (mtm-85) REVERT: B 108 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7432 (mtm-85) REVERT: C 108 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7463 (mtm-85) REVERT: D 108 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7464 (mtm-85) outliers start: 19 outliers final: 12 residues processed: 118 average time/residue: 0.5102 time to fit residues: 63.4883 Evaluate side-chains 122 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 0.0030 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 206 ASN B 86 GLN B 206 ASN C 86 GLN C 206 ASN D 86 GLN D 206 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5533 r_free = 0.5533 target = 0.272592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5491 r_free = 0.5491 target = 0.251823 restraints weight = 6583.206| |-----------------------------------------------------------------------------| r_work (start): 0.5418 rms_B_bonded: 1.57 r_work: 0.5412 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.5305 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.5305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6788 Z= 0.124 Angle : 0.573 6.475 9268 Z= 0.291 Chirality : 0.040 0.112 1112 Planarity : 0.004 0.036 1132 Dihedral : 4.048 20.951 924 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.73 % Allowed : 13.79 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.28), residues: 884 helix: 2.03 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.22 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 108 TYR 0.007 0.001 TYR D 233 PHE 0.007 0.001 PHE B 48 TRP 0.026 0.001 TRP A 35 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6788) covalent geometry : angle 0.57255 ( 9268) hydrogen bonds : bond 0.04235 ( 485) hydrogen bonds : angle 4.56908 ( 1455) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.225 Fit side-chains REVERT: A 108 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7431 (mtm-85) REVERT: B 108 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7435 (mtm-85) REVERT: C 108 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7453 (mtm-85) REVERT: D 108 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7419 (mtm-85) outliers start: 19 outliers final: 14 residues processed: 112 average time/residue: 0.5654 time to fit residues: 66.6753 Evaluate side-chains 119 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 72 optimal weight: 0.0570 chunk 69 optimal weight: 0.0570 chunk 80 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN C 86 GLN D 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5524 r_free = 0.5524 target = 0.267190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5452 r_free = 0.5452 target = 0.251387 restraints weight = 6344.002| |-----------------------------------------------------------------------------| r_work (start): 0.5436 rms_B_bonded: 1.64 r_work: 0.5427 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.5318 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.5318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6788 Z= 0.119 Angle : 0.574 6.645 9268 Z= 0.288 Chirality : 0.040 0.113 1112 Planarity : 0.004 0.035 1132 Dihedral : 3.972 20.864 924 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.73 % Allowed : 14.94 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.28), residues: 884 helix: 2.07 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.17 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 108 TYR 0.006 0.001 TYR A 233 PHE 0.007 0.001 PHE A 168 TRP 0.025 0.001 TRP A 35 HIS 0.002 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 6788) covalent geometry : angle 0.57361 ( 9268) hydrogen bonds : bond 0.03993 ( 485) hydrogen bonds : angle 4.51068 ( 1455) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2565.38 seconds wall clock time: 44 minutes 28.93 seconds (2668.93 seconds total)