Starting phenix.real_space_refine on Wed Jul 1 23:15:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1z_36806/07_2026/8k1z_36806.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1z_36806/07_2026/8k1z_36806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1z_36806/07_2026/8k1z_36806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1z_36806/07_2026/8k1z_36806.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1z_36806/07_2026/8k1z_36806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1z_36806/07_2026/8k1z_36806.cif" } resolution = 3.41 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= -0.001 sd= 0.074 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 5 8.98 5 S 32 5.16 5 C 2706 2.51 5 N 616 2.21 5 O 700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4059 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1921 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "B" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1921 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 105 Ad-hoc single atom residues: {' K': 4} Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 4 Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 105 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 0.87, per 1000 atoms: 0.21 Number of scatterers: 4059 At special positions: 0 Unit cell: (64.9, 73.7, 89.1, 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 5 19.00 S 32 16.00 O 700 8.00 N 616 7.00 C 2706 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: 0.24 Conformation dependent library (CDL) restraints added in 185.6 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 896 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 87.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 2 through 53 removed outlier: 5.621A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.707A pdb=" N ARG A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 147 Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 183 removed outlier: 3.791A pdb=" N GLU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 241 removed outlier: 3.511A pdb=" N ASN A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.611A pdb=" N THR A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 53 removed outlier: 5.619A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 removed outlier: 3.680A pdb=" N ARG B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 147 Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 180 Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 248 removed outlier: 4.307A pdb=" N ARG B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 972 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: 0.59 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 673 1.33 - 1.45: 1085 1.45 - 1.57: 2350 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4156 Sorted by residual: bond pdb=" CA MET A 156 " pdb=" C MET A 156 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.26e-02 6.30e+03 1.17e+01 bond pdb=" CA GLU B 157 " pdb=" C GLU B 157 " ideal model delta sigma weight residual 1.524 1.486 0.038 1.29e-02 6.01e+03 8.55e+00 bond pdb=" C GLU B 157 " pdb=" N ASN B 158 " ideal model delta sigma weight residual 1.335 1.296 0.039 1.36e-02 5.41e+03 8.03e+00 bond pdb=" N MET A 156 " pdb=" CA MET A 156 " ideal model delta sigma weight residual 1.459 1.425 0.034 1.20e-02 6.94e+03 7.97e+00 bond pdb=" C MET A 156 " pdb=" N GLU A 157 " ideal model delta sigma weight residual 1.335 1.310 0.025 1.30e-02 5.92e+03 3.81e+00 ... (remaining 4151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 5483 0.98 - 1.96: 114 1.96 - 2.94: 24 2.94 - 3.92: 12 3.92 - 4.90: 11 Bond angle restraints: 5644 Sorted by residual: angle pdb=" N VAL A 242 " pdb=" CA VAL A 242 " pdb=" C VAL A 242 " ideal model delta sigma weight residual 113.71 109.72 3.99 9.50e-01 1.11e+00 1.76e+01 angle pdb=" N MET A 156 " pdb=" CA MET A 156 " pdb=" C MET A 156 " ideal model delta sigma weight residual 111.14 107.73 3.41 1.08e+00 8.57e-01 9.95e+00 angle pdb=" C SER A 155 " pdb=" N MET A 156 " pdb=" CA MET A 156 " ideal model delta sigma weight residual 120.44 116.32 4.12 1.36e+00 5.41e-01 9.20e+00 angle pdb=" N VAL A 243 " pdb=" CA VAL A 243 " pdb=" C VAL A 243 " ideal model delta sigma weight residual 112.12 110.12 2.00 8.40e-01 1.42e+00 5.65e+00 angle pdb=" C LYS A 2 " pdb=" CA LYS A 2 " pdb=" CB LYS A 2 " ideal model delta sigma weight residual 110.10 114.41 -4.31 1.90e+00 2.77e-01 5.13e+00 ... (remaining 5639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 2396 16.09 - 32.18: 238 32.18 - 48.27: 55 48.27 - 64.36: 15 64.36 - 80.44: 8 Dihedral angle restraints: 2712 sinusoidal: 1310 harmonic: 1402 Sorted by residual: dihedral pdb=" CG ARG A 7 " pdb=" CD ARG A 7 " pdb=" NE ARG A 7 " pdb=" CZ ARG A 7 " ideal model delta sinusoidal sigma weight residual 90.00 130.50 -40.50 2 1.50e+01 4.44e-03 9.00e+00 dihedral pdb=" CB GLU B 130 " pdb=" CG GLU B 130 " pdb=" CD GLU B 130 " pdb=" OE1 GLU B 130 " ideal model delta sinusoidal sigma weight residual 0.00 79.79 -79.79 1 3.00e+01 1.11e-03 8.78e+00 dihedral pdb=" CB GLU A 130 " pdb=" CG GLU A 130 " pdb=" CD GLU A 130 " pdb=" OE1 GLU A 130 " ideal model delta sinusoidal sigma weight residual 0.00 79.69 -79.69 1 3.00e+01 1.11e-03 8.76e+00 ... (remaining 2709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 450 0.022 - 0.043: 72 0.043 - 0.065: 86 0.065 - 0.087: 27 0.087 - 0.108: 15 Chirality restraints: 650 Sorted by residual: chirality pdb=" CA VAL B 76 " pdb=" N VAL B 76 " pdb=" C VAL B 76 " pdb=" CB VAL B 76 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.94e-01 chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.79e-01 chirality pdb=" CA VAL A 206 " pdb=" N VAL A 206 " pdb=" C VAL A 206 " pdb=" CB VAL A 206 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.58e-01 ... (remaining 647 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 2 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C LYS A 2 " 0.033 2.00e-02 2.50e+03 pdb=" O LYS A 2 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG A 3 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 156 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C MET B 156 " 0.028 2.00e-02 2.50e+03 pdb=" O MET B 156 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU B 157 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 156 " 0.005 2.00e-02 2.50e+03 9.51e-03 9.05e-01 pdb=" C MET A 156 " -0.016 2.00e-02 2.50e+03 pdb=" O MET A 156 " 0.006 2.00e-02 2.50e+03 pdb=" N GLU A 157 " 0.006 2.00e-02 2.50e+03 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 1154 2.82 - 3.40: 4506 3.40 - 3.98: 7281 3.98 - 4.56: 10210 4.56 - 5.14: 14419 Nonbonded interactions: 37570 Sorted by model distance: nonbonded pdb=" OG SER B 179 " pdb=" O TRP B 184 " model vdw 2.241 3.040 nonbonded pdb=" OE1 GLN A 126 " pdb=" ND2 ASN A 240 " model vdw 2.246 3.120 nonbonded pdb=" OH TYR A 52 " pdb=" OD2 ASP B 58 " model vdw 2.302 3.040 nonbonded pdb=" OG SER A 179 " pdb=" O TRP A 184 " model vdw 2.303 3.040 nonbonded pdb=" OD2 ASP A 58 " pdb=" OH TYR B 52 " model vdw 2.313 3.040 ... (remaining 37565 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 2 through 304) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.090 Find NCS groups from input model: 0.190 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 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 0.043 4156 Z= 0.148 Angle : 0.420 4.902 5644 Z= 0.247 Chirality : 0.032 0.108 650 Planarity : 0.002 0.019 664 Dihedral : 13.664 80.444 1816 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 5.04 (0.38), residues: 476 helix: 3.84 (0.25), residues: 394 sheet: None (None), residues: 0 loop : 0.42 (0.71), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 131 TYR 0.007 0.001 TYR B 18 PHE 0.004 0.000 PHE B 109 TRP 0.002 0.000 TRP B 184 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.15 ( 4156) covalent geometry : angle 0.42000 / 0.25 ( 5644) hydrogen bonds : bond 0.13129 / 8.09 ( 328) hydrogen bonds : angle 3.98302 / 3.03 ( 972) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.6915 (m-80) cc_final: 0.6458 (t80) REVERT: A 42 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8046 (tppt) REVERT: A 47 ARG cc_start: 0.7749 (ttp80) cc_final: 0.7485 (ttp80) REVERT: A 111 MET cc_start: 0.7869 (mtm) cc_final: 0.7653 (mtp) REVERT: A 135 PHE cc_start: 0.7010 (t80) cc_final: 0.5929 (m-10) REVERT: B 16 PHE cc_start: 0.6839 (m-80) cc_final: 0.6434 (t80) REVERT: B 42 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8030 (tppt) REVERT: B 47 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7448 (ttp80) REVERT: B 111 MET cc_start: 0.7910 (mtm) cc_final: 0.7710 (mtp) REVERT: B 135 PHE cc_start: 0.7018 (t80) cc_final: 0.5917 (m-10) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.0895 time to fit residues: 11.0075 Evaluate side-chains 80 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.200563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.154266 restraints weight = 4290.860| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.28 r_work: 0.3227 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4156 Z= 0.161 Angle : 0.577 6.571 5644 Z= 0.300 Chirality : 0.039 0.145 650 Planarity : 0.004 0.037 664 Dihedral : 5.834 41.777 952 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.96 % Allowed : 8.33 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 5.31 (0.40), residues: 476 helix: 3.85 (0.25), residues: 400 sheet: None (None), residues: 0 loop : 1.29 (0.91), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 137 TYR 0.020 0.002 TYR A 85 PHE 0.012 0.001 PHE B 223 TRP 0.007 0.002 TRP A 184 HIS 0.002 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 4156) covalent geometry : angle 0.57717 / 0.30 ( 5644) hydrogen bonds : bond 0.04237 / 2.85 ( 328) hydrogen bonds : angle 3.09615 / 2.31 ( 972) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7493 (m-80) cc_final: 0.6365 (t80) REVERT: A 38 GLU cc_start: 0.8045 (tp30) cc_final: 0.7814 (tp30) REVERT: A 42 LYS cc_start: 0.8237 (ttmm) cc_final: 0.8017 (tppt) REVERT: A 47 ARG cc_start: 0.7821 (ttp80) cc_final: 0.7404 (ttp80) REVERT: A 135 PHE cc_start: 0.7195 (t80) cc_final: 0.6060 (m-10) REVERT: B 16 PHE cc_start: 0.7464 (m-80) cc_final: 0.6354 (t80) REVERT: B 38 GLU cc_start: 0.8029 (tp30) cc_final: 0.7781 (tp30) REVERT: B 47 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7415 (ttp80) REVERT: B 135 PHE cc_start: 0.7203 (t80) cc_final: 0.6042 (m-10) outliers start: 8 outliers final: 2 residues processed: 96 average time/residue: 0.0803 time to fit residues: 9.2390 Evaluate side-chains 81 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 0.1980 chunk 24 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN B 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.198593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.151927 restraints weight = 4368.240| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.84 r_work: 0.3200 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4156 Z= 0.131 Angle : 0.525 6.722 5644 Z= 0.272 Chirality : 0.036 0.152 650 Planarity : 0.003 0.018 664 Dihedral : 5.240 40.445 952 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.47 % Allowed : 13.24 % Favored : 85.29 % 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: 5.28 (0.40), residues: 476 helix: 3.84 (0.25), residues: 400 sheet: None (None), residues: 0 loop : 1.22 (0.92), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 TYR 0.015 0.001 TYR A 85 PHE 0.009 0.001 PHE B 246 TRP 0.003 0.001 TRP B 184 HIS 0.001 0.000 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 4156) covalent geometry : angle 0.52455 / 0.27 ( 5644) hydrogen bonds : bond 0.03919 / 2.62 ( 328) hydrogen bonds : angle 2.93070 / 2.21 ( 972) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7554 (m-80) cc_final: 0.6403 (t80) REVERT: A 44 GLU cc_start: 0.8206 (tp30) cc_final: 0.7926 (tp30) REVERT: A 135 PHE cc_start: 0.7179 (t80) cc_final: 0.6046 (m-10) REVERT: A 168 MET cc_start: 0.7738 (mmm) cc_final: 0.7523 (mmm) REVERT: B 16 PHE cc_start: 0.7532 (m-80) cc_final: 0.6526 (t80) REVERT: B 44 GLU cc_start: 0.8085 (tp30) cc_final: 0.7776 (tp30) REVERT: B 135 PHE cc_start: 0.7195 (t80) cc_final: 0.6024 (m-10) outliers start: 6 outliers final: 6 residues processed: 89 average time/residue: 0.0939 time to fit residues: 9.9094 Evaluate side-chains 80 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 139 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.191557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.146092 restraints weight = 4276.882| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.19 r_work: 0.3187 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4156 Z= 0.132 Angle : 0.528 7.113 5644 Z= 0.275 Chirality : 0.037 0.160 650 Planarity : 0.002 0.017 664 Dihedral : 4.837 37.687 952 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.96 % Allowed : 15.44 % Favored : 82.60 % 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: 5.10 (0.40), residues: 476 helix: 3.74 (0.25), residues: 400 sheet: None (None), residues: 0 loop : 1.03 (0.91), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 TYR 0.015 0.001 TYR A 85 PHE 0.009 0.001 PHE B 223 TRP 0.007 0.001 TRP B 184 HIS 0.001 0.000 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 4156) covalent geometry : angle 0.52772 / 0.27 ( 5644) hydrogen bonds : bond 0.03902 / 2.64 ( 328) hydrogen bonds : angle 2.93433 / 2.21 ( 972) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7310 (t80) cc_final: 0.6107 (m-10) REVERT: A 168 MET cc_start: 0.8012 (mmm) cc_final: 0.7785 (mmm) REVERT: B 38 GLU cc_start: 0.7997 (tp30) cc_final: 0.7692 (tp30) REVERT: B 44 GLU cc_start: 0.7730 (tp30) cc_final: 0.7530 (tp30) REVERT: B 70 GLU cc_start: 0.7498 (pt0) cc_final: 0.7276 (pt0) REVERT: B 135 PHE cc_start: 0.7290 (t80) cc_final: 0.6100 (m-10) outliers start: 8 outliers final: 7 residues processed: 85 average time/residue: 0.0822 time to fit residues: 8.3326 Evaluate side-chains 90 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 139 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.184713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.138870 restraints weight = 4258.932| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.18 r_work: 0.3060 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4156 Z= 0.159 Angle : 0.556 6.277 5644 Z= 0.291 Chirality : 0.038 0.158 650 Planarity : 0.003 0.020 664 Dihedral : 4.670 33.433 952 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.70 % Allowed : 15.20 % Favored : 82.11 % 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: 4.77 (0.40), residues: 476 helix: 3.53 (0.25), residues: 400 sheet: None (None), residues: 0 loop : 0.83 (0.91), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 73 TYR 0.018 0.002 TYR A 85 PHE 0.009 0.001 PHE B 223 TRP 0.008 0.001 TRP B 184 HIS 0.001 0.000 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 4156) covalent geometry : angle 0.55562 / 0.29 ( 5644) hydrogen bonds : bond 0.04407 / 2.96 ( 328) hydrogen bonds : angle 3.05194 / 2.29 ( 972) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8098 (tt) REVERT: A 38 GLU cc_start: 0.8101 (tp30) cc_final: 0.7821 (tp30) REVERT: A 135 PHE cc_start: 0.7400 (t80) cc_final: 0.6183 (m-10) REVERT: A 168 MET cc_start: 0.8204 (mmm) cc_final: 0.7693 (mmt) REVERT: A 226 MET cc_start: 0.8627 (mmp) cc_final: 0.8170 (mmm) REVERT: A 227 TYR cc_start: 0.8725 (t80) cc_final: 0.8148 (t80) REVERT: B 29 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8146 (tt) REVERT: B 135 PHE cc_start: 0.7358 (t80) cc_final: 0.6150 (m-10) REVERT: B 227 TYR cc_start: 0.8702 (t80) cc_final: 0.8144 (t80) outliers start: 11 outliers final: 8 residues processed: 102 average time/residue: 0.0782 time to fit residues: 9.5720 Evaluate side-chains 100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 21 optimal weight: 0.0970 chunk 38 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.190969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.142786 restraints weight = 4404.376| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.31 r_work: 0.3143 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4156 Z= 0.123 Angle : 0.519 6.272 5644 Z= 0.271 Chirality : 0.036 0.158 650 Planarity : 0.002 0.015 664 Dihedral : 4.583 37.129 952 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.21 % Allowed : 16.42 % Favored : 81.37 % 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: 4.90 (0.40), residues: 476 helix: 3.62 (0.25), residues: 400 sheet: None (None), residues: 0 loop : 0.84 (0.92), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 TYR 0.014 0.001 TYR B 59 PHE 0.026 0.001 PHE A 112 TRP 0.010 0.001 TRP B 184 HIS 0.000 0.000 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 4156) covalent geometry : angle 0.51940 / 0.27 ( 5644) hydrogen bonds : bond 0.03862 / 2.63 ( 328) hydrogen bonds : angle 2.94700 / 2.23 ( 972) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8084 (tt) REVERT: A 135 PHE cc_start: 0.7378 (t80) cc_final: 0.6137 (m-10) REVERT: A 168 MET cc_start: 0.8201 (mmm) cc_final: 0.7786 (mmm) REVERT: A 227 TYR cc_start: 0.8667 (t80) cc_final: 0.8071 (t80) REVERT: B 29 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8074 (tt) REVERT: B 38 GLU cc_start: 0.8056 (tp30) cc_final: 0.7820 (tp30) REVERT: B 70 GLU cc_start: 0.7457 (pt0) cc_final: 0.7114 (pm20) REVERT: B 135 PHE cc_start: 0.7352 (t80) cc_final: 0.6135 (m-10) REVERT: B 227 TYR cc_start: 0.8705 (t80) cc_final: 0.8164 (t80) outliers start: 9 outliers final: 6 residues processed: 95 average time/residue: 0.0792 time to fit residues: 9.0191 Evaluate side-chains 90 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 139 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.186844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.139421 restraints weight = 4384.419| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.13 r_work: 0.3093 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4156 Z= 0.140 Angle : 0.542 8.049 5644 Z= 0.284 Chirality : 0.037 0.160 650 Planarity : 0.003 0.016 664 Dihedral : 4.628 38.341 952 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.70 % Allowed : 17.40 % Favored : 79.90 % 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 are not related in a simple way. whole: 4.98 (0.40), residues: 476 helix: 3.65 (0.25), residues: 398 sheet: None (None), residues: 0 loop : 1.11 (0.92), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 73 TYR 0.014 0.001 TYR A 85 PHE 0.024 0.001 PHE B 112 TRP 0.008 0.001 TRP A 184 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 4156) covalent geometry : angle 0.54242 / 0.28 ( 5644) hydrogen bonds : bond 0.04120 / 2.78 ( 328) hydrogen bonds : angle 3.00280 / 2.27 ( 972) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8086 (tt) REVERT: A 38 GLU cc_start: 0.8110 (tp30) cc_final: 0.7880 (tp30) REVERT: A 135 PHE cc_start: 0.7432 (t80) cc_final: 0.6131 (m-10) REVERT: A 168 MET cc_start: 0.8205 (mmm) cc_final: 0.7723 (mmm) REVERT: A 227 TYR cc_start: 0.8703 (t80) cc_final: 0.8177 (t80) REVERT: B 29 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8121 (tt) REVERT: B 38 GLU cc_start: 0.8039 (tp30) cc_final: 0.7814 (tp30) REVERT: B 135 PHE cc_start: 0.7421 (t80) cc_final: 0.6151 (m-10) REVERT: B 227 TYR cc_start: 0.8709 (t80) cc_final: 0.8285 (t80) outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 0.0785 time to fit residues: 8.8595 Evaluate side-chains 95 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.0770 chunk 43 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.185862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.140640 restraints weight = 4276.353| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.27 r_work: 0.3096 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4156 Z= 0.138 Angle : 0.531 6.329 5644 Z= 0.279 Chirality : 0.036 0.169 650 Planarity : 0.002 0.015 664 Dihedral : 4.626 40.402 952 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.70 % Allowed : 17.40 % Favored : 79.90 % 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 are not related in a simple way. whole: 4.90 (0.40), residues: 476 helix: 3.62 (0.25), residues: 400 sheet: None (None), residues: 0 loop : 0.83 (0.92), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 73 TYR 0.015 0.001 TYR B 59 PHE 0.023 0.001 PHE B 112 TRP 0.016 0.002 TRP B 184 HIS 0.001 0.000 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 4156) covalent geometry : angle 0.53070 / 0.28 ( 5644) hydrogen bonds : bond 0.04102 / 2.79 ( 328) hydrogen bonds : angle 3.00947 / 2.28 ( 972) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8097 (tt) REVERT: A 38 GLU cc_start: 0.8117 (tp30) cc_final: 0.7860 (tp30) REVERT: A 135 PHE cc_start: 0.7516 (t80) cc_final: 0.6195 (m-10) REVERT: A 168 MET cc_start: 0.8265 (mmm) cc_final: 0.7825 (mmm) REVERT: A 227 TYR cc_start: 0.8746 (t80) cc_final: 0.8190 (t80) REVERT: B 29 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8153 (tt) REVERT: B 135 PHE cc_start: 0.7485 (t80) cc_final: 0.6155 (m-10) REVERT: B 227 TYR cc_start: 0.8756 (t80) cc_final: 0.8293 (t80) outliers start: 11 outliers final: 8 residues processed: 95 average time/residue: 0.0685 time to fit residues: 7.7996 Evaluate side-chains 100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 139 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.184060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.137631 restraints weight = 4334.571| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.21 r_work: 0.3077 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4156 Z= 0.149 Angle : 0.575 9.482 5644 Z= 0.304 Chirality : 0.037 0.155 650 Planarity : 0.002 0.014 664 Dihedral : 4.674 41.395 952 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.94 % Allowed : 18.38 % Favored : 78.68 % 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: 4.89 (0.40), residues: 476 helix: 3.63 (0.25), residues: 400 sheet: None (None), residues: 0 loop : 0.74 (0.92), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 73 TYR 0.013 0.001 TYR B 85 PHE 0.023 0.001 PHE B 112 TRP 0.007 0.001 TRP A 184 HIS 0.001 0.000 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 4156) covalent geometry : angle 0.57526 / 0.30 ( 5644) hydrogen bonds : bond 0.04268 / 2.89 ( 328) hydrogen bonds : angle 3.06811 / 2.32 ( 972) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8097 (tt) REVERT: A 38 GLU cc_start: 0.8123 (tp30) cc_final: 0.7880 (tp30) REVERT: A 168 MET cc_start: 0.8280 (mmm) cc_final: 0.7839 (mmm) REVERT: A 227 TYR cc_start: 0.8789 (t80) cc_final: 0.8198 (t80) REVERT: B 29 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8131 (tt) REVERT: B 38 GLU cc_start: 0.8176 (tp30) cc_final: 0.7887 (tp30) REVERT: B 42 LYS cc_start: 0.8951 (tppt) cc_final: 0.8736 (tppt) REVERT: B 135 PHE cc_start: 0.7562 (t80) cc_final: 0.6222 (m-10) REVERT: B 227 TYR cc_start: 0.8761 (t80) cc_final: 0.8294 (t80) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.0785 time to fit residues: 8.7737 Evaluate side-chains 100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.182112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.137157 restraints weight = 4260.673| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.19 r_work: 0.3096 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4156 Z= 0.162 Angle : 0.578 6.301 5644 Z= 0.307 Chirality : 0.038 0.157 650 Planarity : 0.002 0.015 664 Dihedral : 4.777 42.754 952 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.70 % Allowed : 18.87 % Favored : 78.43 % 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: 4.83 (0.40), residues: 476 helix: 3.58 (0.25), residues: 400 sheet: None (None), residues: 0 loop : 0.78 (0.92), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 137 TYR 0.014 0.002 TYR B 85 PHE 0.024 0.001 PHE B 112 TRP 0.015 0.002 TRP B 184 HIS 0.001 0.000 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 4156) covalent geometry : angle 0.57786 / 0.31 ( 5644) hydrogen bonds : bond 0.04574 / 3.10 ( 328) hydrogen bonds : angle 3.15014 / 2.37 ( 972) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8112 (tt) REVERT: A 168 MET cc_start: 0.8316 (mmm) cc_final: 0.7925 (mmm) REVERT: B 29 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8148 (tt) REVERT: B 38 GLU cc_start: 0.8158 (tp30) cc_final: 0.7884 (tp30) outliers start: 11 outliers final: 7 residues processed: 96 average time/residue: 0.0855 time to fit residues: 9.6377 Evaluate side-chains 96 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.182729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.135531 restraints weight = 4270.716| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.32 r_work: 0.3067 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4156 Z= 0.150 Angle : 0.593 10.375 5644 Z= 0.317 Chirality : 0.038 0.164 650 Planarity : 0.002 0.015 664 Dihedral : 4.793 43.714 952 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.21 % Allowed : 19.61 % Favored : 78.19 % 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 are not related in a simple way. whole: 4.83 (0.40), residues: 476 helix: 3.59 (0.25), residues: 400 sheet: None (None), residues: 0 loop : 0.69 (0.91), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.013 0.001 TYR A 85 PHE 0.026 0.001 PHE B 112 TRP 0.007 0.001 TRP A 184 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 4156) covalent geometry : angle 0.59336 / 0.32 ( 5644) hydrogen bonds : bond 0.04401 / 2.98 ( 328) hydrogen bonds : angle 3.16944 / 2.38 ( 972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 911.22 seconds wall clock time: 16 minutes 22.00 seconds (982.00 seconds total)