Starting phenix.real_space_refine on Tue Mar 3 11:40:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e94_47768/03_2026/9e94_47768.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e94_47768/03_2026/9e94_47768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e94_47768/03_2026/9e94_47768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e94_47768/03_2026/9e94_47768.map" model { file = "/net/cci-nas-00/data/ceres_data/9e94_47768/03_2026/9e94_47768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e94_47768/03_2026/9e94_47768.cif" } resolution = 3.67 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= 0.003 sd= 0.032 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 K 3 8.98 5 S 10 5.16 5 C 2266 2.51 5 N 532 2.21 5 O 570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1654 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1654 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {' K': 2, 'D10': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' K': 1, 'D10': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 0.88, per 1000 atoms: 0.26 Number of scatterers: 3381 At special positions: 0 Unit cell: (68.06, 86.32, 68.06, 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) K 3 19.00 S 10 16.00 O 570 8.00 N 532 7.00 C 2266 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: 0.29 Conformation dependent library (CDL) restraints added in 138.0 milliseconds 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 820 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 75.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 8 through 37 removed outlier: 3.577A pdb=" N ARG A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 4.288A pdb=" N ARG A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 48 Processing helix chain 'A' and resid 56 through 67 Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 116 through 130 Processing helix chain 'A' and resid 131 through 149 Processing helix chain 'A' and resid 172 through 179 Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 200 through 213 Processing helix chain 'A' and resid 231 through 257 Processing helix chain 'B' and resid 8 through 37 removed outlier: 3.576A pdb=" N ARG B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) Proline residue: B 31 - end of helix removed outlier: 4.288A pdb=" N ARG B 37 " --> pdb=" O GLU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 48 Processing helix chain 'B' and resid 56 through 67 Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 116 through 130 Processing helix chain 'B' and resid 131 through 149 Processing helix chain 'B' and resid 172 through 179 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 200 through 213 Processing helix chain 'B' and resid 231 through 257 234 hydrogen bonds defined for protein. 702 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: 0.48 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 928 1.34 - 1.46: 615 1.46 - 1.57: 1888 1.57 - 1.69: 0 1.69 - 1.80: 14 Bond restraints: 3445 Sorted by residual: bond pdb=" CG LEU A 253 " pdb=" CD1 LEU A 253 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.65e+00 bond pdb=" C ALA B 56 " pdb=" N PRO B 57 " ideal model delta sigma weight residual 1.334 1.381 -0.047 1.51e-02 4.39e+03 9.63e+00 bond pdb=" CG LEU B 253 " pdb=" CD1 LEU B 253 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.57e+00 bond pdb=" C ALA A 56 " pdb=" N PRO A 57 " ideal model delta sigma weight residual 1.334 1.380 -0.046 1.51e-02 4.39e+03 9.38e+00 bond pdb=" CG LEU A 103 " pdb=" CD2 LEU A 103 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.23e+00 ... (remaining 3440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 4392 3.21 - 6.42: 234 6.42 - 9.64: 43 9.64 - 12.85: 8 12.85 - 16.06: 3 Bond angle restraints: 4680 Sorted by residual: angle pdb=" OG1 THR A 106 " pdb=" CB THR A 106 " pdb=" CG2 THR A 106 " ideal model delta sigma weight residual 109.30 93.95 15.35 2.00e+00 2.50e-01 5.89e+01 angle pdb=" OG1 THR B 106 " pdb=" CB THR B 106 " pdb=" CG2 THR B 106 " ideal model delta sigma weight residual 109.30 93.99 15.31 2.00e+00 2.50e-01 5.86e+01 angle pdb=" C LEU A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta sigma weight residual 122.77 117.03 5.74 1.05e+00 9.07e-01 2.99e+01 angle pdb=" C LEU B 103 " pdb=" N ILE B 104 " pdb=" CA ILE B 104 " ideal model delta sigma weight residual 122.77 117.06 5.71 1.05e+00 9.07e-01 2.96e+01 angle pdb=" C4 D10 A 405 " pdb=" C5 D10 A 405 " pdb=" C6 D10 A 405 " ideal model delta sigma weight residual 113.31 129.37 -16.06 3.00e+00 1.11e-01 2.87e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.94: 1729 13.94 - 27.89: 201 27.89 - 41.83: 57 41.83 - 55.77: 4 55.77 - 69.71: 10 Dihedral angle restraints: 2001 sinusoidal: 729 harmonic: 1272 Sorted by residual: dihedral pdb=" CD ARG B 71 " pdb=" NE ARG B 71 " pdb=" CZ ARG B 71 " pdb=" NH1 ARG B 71 " ideal model delta sinusoidal sigma weight residual 0.00 52.86 -52.86 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CD ARG A 71 " pdb=" NE ARG A 71 " pdb=" CZ ARG A 71 " pdb=" NH1 ARG A 71 " ideal model delta sinusoidal sigma weight residual 0.00 52.81 -52.81 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CA THR A 182 " pdb=" C THR A 182 " pdb=" N VAL A 183 " pdb=" CA VAL A 183 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 470 0.106 - 0.212: 92 0.212 - 0.318: 10 0.318 - 0.424: 2 0.424 - 0.530: 2 Chirality restraints: 576 Sorted by residual: chirality pdb=" CG LEU A 103 " pdb=" CB LEU A 103 " pdb=" CD1 LEU A 103 " pdb=" CD2 LEU A 103 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 7.02e+00 chirality pdb=" CG LEU B 103 " pdb=" CB LEU B 103 " pdb=" CD1 LEU B 103 " pdb=" CD2 LEU B 103 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 7.02e+00 chirality pdb=" CB VAL B 252 " pdb=" CA VAL B 252 " pdb=" CG1 VAL B 252 " pdb=" CG2 VAL B 252 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.27e+00 ... (remaining 573 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 71 " 0.712 9.50e-02 1.11e+02 3.20e-01 7.32e+01 pdb=" NE ARG B 71 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG B 71 " 0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG B 71 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG B 71 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 71 " 0.710 9.50e-02 1.11e+02 3.20e-01 7.31e+01 pdb=" NE ARG A 71 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 71 " 0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG A 71 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG A 71 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 109 " 0.001 2.00e-02 2.50e+03 3.78e-02 2.86e+01 pdb=" CG TYR A 109 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR A 109 " 0.073 2.00e-02 2.50e+03 pdb=" CD2 TYR A 109 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 109 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR A 109 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 109 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 109 " -0.005 2.00e-02 2.50e+03 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.67: 84 2.67 - 3.28: 3495 3.28 - 3.90: 6326 3.90 - 4.52: 8082 4.52 - 5.14: 12426 Nonbonded interactions: 30413 Sorted by model distance: nonbonded pdb=" O VAL A 107 " pdb=" K K A 406 " model vdw 2.047 2.850 nonbonded pdb=" O LEU B 217 " pdb=" K K A 407 " model vdw 2.121 2.850 nonbonded pdb=" O THR B 106 " pdb=" K K B 401 " model vdw 2.248 2.850 nonbonded pdb=" O LEU A 217 " pdb=" K K A 407 " model vdw 2.339 2.850 nonbonded pdb=" O GLY A 73 " pdb=" NH2 ARG B 44 " model vdw 2.368 3.120 ... (remaining 30408 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' and (resid 5 through 261 or resid 402 through 403)) selection = (chain 'B' and (resid 5 through 261 or resid 402 through 403)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.230 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 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 : 0.010 0.103 3445 Z= 0.455 Angle : 1.694 16.060 4680 Z= 0.911 Chirality : 0.090 0.530 576 Planarity : 0.025 0.320 566 Dihedral : 14.022 69.715 1181 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.49 % 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 are not related in a simple way. whole: -4.00 (0.32), residues: 428 helix: -1.66 (0.24), residues: 326 sheet: None (None), residues: 0 loop : -5.64 (0.31), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.008 ARG A 71 TYR 0.073 0.005 TYR B 109 PHE 0.064 0.008 PHE A 256 TRP 0.047 0.007 TRP B 91 HIS 0.004 0.002 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.01011 ( 3445) covalent geometry : angle 1.69363 ( 4680) hydrogen bonds : bond 0.10782 ( 234) hydrogen bonds : angle 6.14224 ( 702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1171 time to fit residues: 13.1686 Evaluate side-chains 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.194791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.163215 restraints weight = 3758.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.162750 restraints weight = 4121.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.162700 restraints weight = 4254.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.162660 restraints weight = 4193.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.162608 restraints weight = 4242.896| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 3445 Z= 0.171 Angle : 0.783 10.102 4680 Z= 0.384 Chirality : 0.043 0.162 576 Planarity : 0.006 0.038 566 Dihedral : 6.724 56.161 521 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.41 % Allowed : 8.73 % Favored : 88.86 % 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 are not related in a simple way. whole: -1.29 (0.39), residues: 428 helix: 0.39 (0.27), residues: 334 sheet: None (None), residues: 0 loop : -5.56 (0.31), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 65 TYR 0.013 0.001 TYR B 17 PHE 0.017 0.002 PHE A 207 TRP 0.009 0.001 TRP A 91 HIS 0.003 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 3445) covalent geometry : angle 0.78337 ( 4680) hydrogen bonds : bond 0.04711 ( 234) hydrogen bonds : angle 4.27676 ( 702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7096 (mpp80) cc_final: 0.6543 (mtm110) REVERT: A 29 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 44 ARG cc_start: 0.7665 (ttm110) cc_final: 0.7398 (ttm110) REVERT: B 104 ILE cc_start: 0.8157 (tt) cc_final: 0.7814 (tt) REVERT: B 213 SER cc_start: 0.8753 (t) cc_final: 0.8497 (m) outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 0.1396 time to fit residues: 9.4068 Evaluate side-chains 51 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 231 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.202755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.159989 restraints weight = 3868.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.156737 restraints weight = 3858.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.156791 restraints weight = 4103.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.157172 restraints weight = 4066.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.157243 restraints weight = 3929.973| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3445 Z= 0.164 Angle : 0.662 9.128 4680 Z= 0.330 Chirality : 0.040 0.142 576 Planarity : 0.005 0.038 566 Dihedral : 6.521 56.812 521 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.22 % Allowed : 12.05 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.41), residues: 428 helix: 1.32 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -5.10 (0.39), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 65 TYR 0.012 0.001 TYR B 17 PHE 0.015 0.002 PHE B 185 TRP 0.011 0.001 TRP B 91 HIS 0.002 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 3445) covalent geometry : angle 0.66172 ( 4680) hydrogen bonds : bond 0.04200 ( 234) hydrogen bonds : angle 3.87321 ( 702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.111 Fit side-chains REVERT: A 27 ARG cc_start: 0.7000 (mpp80) cc_final: 0.6327 (mtm110) REVERT: B 74 ARG cc_start: 0.6975 (ptm160) cc_final: 0.6657 (ptm160) REVERT: B 104 ILE cc_start: 0.8415 (tt) cc_final: 0.8106 (tt) REVERT: B 213 SER cc_start: 0.8927 (t) cc_final: 0.8704 (m) outliers start: 14 outliers final: 6 residues processed: 58 average time/residue: 0.1220 time to fit residues: 7.9382 Evaluate side-chains 48 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 231 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.203990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.167104 restraints weight = 3804.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.163007 restraints weight = 5679.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.164292 restraints weight = 6118.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.162381 restraints weight = 4864.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.162791 restraints weight = 4620.224| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3445 Z= 0.135 Angle : 0.600 8.620 4680 Z= 0.296 Chirality : 0.038 0.137 576 Planarity : 0.005 0.039 566 Dihedral : 6.128 53.760 521 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.52 % Allowed : 13.25 % Favored : 82.23 % 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 are not related in a simple way. whole: 0.70 (0.43), residues: 428 helix: 1.78 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -4.73 (0.45), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 65 TYR 0.011 0.001 TYR B 17 PHE 0.013 0.002 PHE B 185 TRP 0.006 0.001 TRP B 91 HIS 0.002 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 3445) covalent geometry : angle 0.59988 ( 4680) hydrogen bonds : bond 0.03778 ( 234) hydrogen bonds : angle 3.60657 ( 702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7053 (mpp80) cc_final: 0.6412 (mtm110) REVERT: A 106 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7917 (m) REVERT: B 74 ARG cc_start: 0.7289 (ptm160) cc_final: 0.6997 (ptm160) REVERT: B 104 ILE cc_start: 0.8411 (tt) cc_final: 0.8128 (tt) REVERT: B 106 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7734 (m) outliers start: 15 outliers final: 8 residues processed: 57 average time/residue: 0.1107 time to fit residues: 7.1369 Evaluate side-chains 50 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 231 ARG Chi-restraints excluded: chain B residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 7 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.205362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.168909 restraints weight = 3780.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.165935 restraints weight = 5993.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.167169 restraints weight = 6707.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.167660 restraints weight = 5248.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.167302 restraints weight = 5042.483| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3445 Z= 0.125 Angle : 0.591 9.660 4680 Z= 0.286 Chirality : 0.038 0.131 576 Planarity : 0.004 0.043 566 Dihedral : 5.839 50.942 521 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.52 % Allowed : 14.16 % Favored : 81.33 % 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 are not related in a simple way. whole: 1.19 (0.43), residues: 428 helix: 2.11 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -4.49 (0.48), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 65 TYR 0.010 0.001 TYR B 17 PHE 0.009 0.001 PHE B 122 TRP 0.012 0.001 TRP B 91 HIS 0.002 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3445) covalent geometry : angle 0.59088 ( 4680) hydrogen bonds : bond 0.03658 ( 234) hydrogen bonds : angle 3.44869 ( 702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.103 Fit side-chains REVERT: A 27 ARG cc_start: 0.7056 (mpp80) cc_final: 0.6528 (mtm110) REVERT: A 106 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7888 (m) REVERT: A 111 TYR cc_start: 0.6692 (OUTLIER) cc_final: 0.6100 (t80) REVERT: B 106 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7618 (m) REVERT: B 231 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7281 (tpt-90) outliers start: 15 outliers final: 6 residues processed: 52 average time/residue: 0.1429 time to fit residues: 8.1906 Evaluate side-chains 49 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 231 ARG Chi-restraints excluded: chain B residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.199765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.163581 restraints weight = 3803.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.159919 restraints weight = 6193.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.161356 restraints weight = 6352.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.160932 restraints weight = 5009.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.161116 restraints weight = 4794.024| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3445 Z= 0.161 Angle : 0.640 10.700 4680 Z= 0.309 Chirality : 0.039 0.137 576 Planarity : 0.005 0.041 566 Dihedral : 6.008 50.345 521 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.92 % Allowed : 14.46 % Favored : 81.63 % 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 are not related in a simple way. whole: 1.39 (0.42), residues: 428 helix: 2.20 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -4.18 (0.51), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 65 TYR 0.009 0.001 TYR B 17 PHE 0.014 0.002 PHE A 122 TRP 0.020 0.002 TRP B 91 HIS 0.002 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 3445) covalent geometry : angle 0.64043 ( 4680) hydrogen bonds : bond 0.03953 ( 234) hydrogen bonds : angle 3.59873 ( 702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7298 (mpp80) cc_final: 0.6764 (mtm110) REVERT: A 106 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7894 (m) REVERT: B 106 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7778 (m) REVERT: B 231 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7320 (tpt-90) outliers start: 13 outliers final: 7 residues processed: 53 average time/residue: 0.1501 time to fit residues: 8.8196 Evaluate side-chains 49 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 231 ARG Chi-restraints excluded: chain B residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.0270 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.187865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.143660 restraints weight = 3724.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142664 restraints weight = 3034.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.144624 restraints weight = 3034.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.146245 restraints weight = 2500.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.146483 restraints weight = 2255.975| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3445 Z= 0.178 Angle : 0.666 11.389 4680 Z= 0.319 Chirality : 0.040 0.135 576 Planarity : 0.005 0.040 566 Dihedral : 6.105 48.580 521 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.12 % Allowed : 14.16 % Favored : 80.72 % 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 are not related in a simple way. whole: 1.40 (0.42), residues: 428 helix: 2.16 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -4.15 (0.52), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 65 TYR 0.009 0.001 TYR A 206 PHE 0.014 0.002 PHE A 122 TRP 0.020 0.002 TRP B 91 HIS 0.001 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 3445) covalent geometry : angle 0.66611 ( 4680) hydrogen bonds : bond 0.04057 ( 234) hydrogen bonds : angle 3.65991 ( 702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7225 (mpp80) cc_final: 0.6563 (mtm110) REVERT: A 106 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7933 (m) REVERT: B 106 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7842 (m) REVERT: B 231 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7682 (tpt-90) outliers start: 17 outliers final: 10 residues processed: 54 average time/residue: 0.1378 time to fit residues: 8.2649 Evaluate side-chains 54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 231 ARG Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 256 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 0.0980 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.192643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142611 restraints weight = 3702.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.145867 restraints weight = 2738.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.147920 restraints weight = 2282.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.148604 restraints weight = 2044.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.149705 restraints weight = 1945.386| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3445 Z= 0.119 Angle : 0.602 10.855 4680 Z= 0.282 Chirality : 0.037 0.125 576 Planarity : 0.004 0.039 566 Dihedral : 5.540 42.595 521 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.31 % Allowed : 15.06 % Favored : 81.63 % 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 are not related in a simple way. whole: 1.92 (0.43), residues: 428 helix: 2.52 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -3.86 (0.55), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 65 TYR 0.009 0.001 TYR B 17 PHE 0.015 0.001 PHE B 209 TRP 0.007 0.001 TRP B 91 HIS 0.001 0.000 HIS B 172 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 3445) covalent geometry : angle 0.60223 ( 4680) hydrogen bonds : bond 0.03460 ( 234) hydrogen bonds : angle 3.53880 ( 702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.118 Fit side-chains REVERT: A 27 ARG cc_start: 0.7232 (mpp80) cc_final: 0.6619 (mtm110) REVERT: A 106 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7879 (m) REVERT: A 111 TYR cc_start: 0.6750 (OUTLIER) cc_final: 0.6108 (t80) REVERT: B 231 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7304 (tpt-90) outliers start: 11 outliers final: 6 residues processed: 49 average time/residue: 0.1436 time to fit residues: 7.9320 Evaluate side-chains 47 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 231 ARG Chi-restraints excluded: chain B residue 256 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 36 optimal weight: 0.1980 chunk 14 optimal weight: 0.0970 chunk 6 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 0.0040 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.194900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.146569 restraints weight = 3622.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.150792 restraints weight = 2669.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.151966 restraints weight = 2155.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.153030 restraints weight = 1922.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.153610 restraints weight = 1819.862| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3445 Z= 0.106 Angle : 0.589 10.448 4680 Z= 0.272 Chirality : 0.036 0.119 576 Planarity : 0.004 0.038 566 Dihedral : 5.082 38.241 521 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.41 % Allowed : 16.27 % Favored : 81.33 % 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 are not related in a simple way. whole: 2.26 (0.43), residues: 428 helix: 2.73 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -3.66 (0.58), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 35 TYR 0.009 0.001 TYR B 220 PHE 0.010 0.001 PHE B 185 TRP 0.003 0.001 TRP B 91 HIS 0.001 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 3445) covalent geometry : angle 0.58897 ( 4680) hydrogen bonds : bond 0.03231 ( 234) hydrogen bonds : angle 3.42025 ( 702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.118 Fit side-chains REVERT: A 27 ARG cc_start: 0.7219 (mpp80) cc_final: 0.6574 (mtm110) REVERT: A 106 THR cc_start: 0.8038 (OUTLIER) cc_final: 0.7806 (m) REVERT: A 111 TYR cc_start: 0.6598 (OUTLIER) cc_final: 0.5997 (t80) REVERT: B 194 HIS cc_start: 0.6491 (t-90) cc_final: 0.5698 (t-170) outliers start: 8 outliers final: 5 residues processed: 46 average time/residue: 0.1470 time to fit residues: 7.5557 Evaluate side-chains 44 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 256 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.0370 chunk 42 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.192738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144993 restraints weight = 3688.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147906 restraints weight = 2723.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.148845 restraints weight = 2271.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.150430 restraints weight = 2012.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150738 restraints weight = 1827.834| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3445 Z= 0.118 Angle : 0.630 10.740 4680 Z= 0.286 Chirality : 0.037 0.119 576 Planarity : 0.005 0.063 566 Dihedral : 5.140 38.445 521 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.11 % Allowed : 17.17 % Favored : 80.72 % 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 are not related in a simple way. whole: 2.39 (0.43), residues: 428 helix: 2.80 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -3.47 (0.59), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 65 TYR 0.008 0.001 TYR B 17 PHE 0.010 0.001 PHE A 122 TRP 0.007 0.001 TRP B 91 HIS 0.001 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 3445) covalent geometry : angle 0.63004 ( 4680) hydrogen bonds : bond 0.03338 ( 234) hydrogen bonds : angle 3.40090 ( 702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.122 Fit side-chains REVERT: A 27 ARG cc_start: 0.7151 (mpp80) cc_final: 0.6447 (mtm110) REVERT: A 106 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7765 (m) REVERT: A 111 TYR cc_start: 0.6575 (OUTLIER) cc_final: 0.5969 (t80) REVERT: A 220 TYR cc_start: 0.8750 (m-80) cc_final: 0.8544 (m-10) REVERT: B 194 HIS cc_start: 0.6584 (t-90) cc_final: 0.5730 (t-170) REVERT: B 230 TYR cc_start: 0.7256 (m-10) cc_final: 0.7049 (m-10) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 0.1340 time to fit residues: 6.8360 Evaluate side-chains 46 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 256 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 6 optimal weight: 0.1980 chunk 39 optimal weight: 0.0070 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.194272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.145596 restraints weight = 3703.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.150343 restraints weight = 2786.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.152678 restraints weight = 2206.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.153155 restraints weight = 1807.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.153367 restraints weight = 1746.747| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3445 Z= 0.111 Angle : 0.611 10.533 4680 Z= 0.278 Chirality : 0.037 0.120 576 Planarity : 0.005 0.062 566 Dihedral : 4.983 35.603 521 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.71 % Allowed : 17.17 % Favored : 80.12 % 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 are not related in a simple way. whole: 2.55 (0.43), residues: 428 helix: 2.92 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -3.32 (0.61), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 65 TYR 0.009 0.001 TYR B 17 PHE 0.008 0.001 PHE A 207 TRP 0.004 0.001 TRP A 91 HIS 0.001 0.000 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 3445) covalent geometry : angle 0.61130 ( 4680) hydrogen bonds : bond 0.03223 ( 234) hydrogen bonds : angle 3.39557 ( 702) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 809.63 seconds wall clock time: 14 minutes 31.42 seconds (871.42 seconds total)