Starting phenix.real_space_refine on Fri Aug 22 14:21:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1z_36806/08_2025/8k1z_36806.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1z_36806/08_2025/8k1z_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_36806/08_2025/8k1z_36806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1z_36806/08_2025/8k1z_36806.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1z_36806/08_2025/8k1z_36806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1z_36806/08_2025/8k1z_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-2.0-5787/lib/python3.9/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, 109 Unusual residues: {' K': 4, 'Y01': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' K': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 0.93, per 1000 atoms: 0.23 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: 0.22 Conformation dependent library (CDL) restraints added in 145.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.08 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: 0.46 Time building geometry restraints manager: 0.32 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: 0.460 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: 0.000 Set scattering table: 0.010 Process input model: 4.870 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 aren 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 covalent geometry : bond 0.00213 ( 4156) covalent geometry : angle 0.42000 ( 5644) hydrogen bonds : bond 0.13129 ( 328) hydrogen bonds : angle 3.98302 ( 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 : 0.115 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: 0.0949 time to fit residues: 11.6647 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 : 0.118 ------------------------------------------------------------------------------- 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: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.200119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.156237 restraints weight = 4285.402| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.03 r_work: 0.3250 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4156 Z= 0.160 Angle : 0.559 6.352 5644 Z= 0.292 Chirality : 0.038 0.140 650 Planarity : 0.004 0.040 664 Dihedral : 5.790 42.088 952 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.96 % Allowed : 8.82 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.27 (0.40), residues: 476 helix: 3.91 (0.25), residues: 400 sheet: None (None), residues: 0 loop : 0.69 (0.87), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 137 TYR 0.020 0.002 TYR B 85 PHE 0.011 0.001 PHE B 223 TRP 0.004 0.001 TRP A 184 HIS 0.001 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 4156) covalent geometry : angle 0.55910 ( 5644) hydrogen bonds : bond 0.04357 ( 328) hydrogen bonds : angle 3.08103 ( 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 100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7478 (m-80) cc_final: 0.6340 (t80) REVERT: A 47 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7404 (ttp80) REVERT: A 135 PHE cc_start: 0.7171 (t80) cc_final: 0.6018 (m-10) REVERT: B 16 PHE cc_start: 0.7435 (m-80) cc_final: 0.6326 (t80) REVERT: B 38 GLU cc_start: 0.8048 (tp30) cc_final: 0.7766 (tp30) REVERT: B 42 LYS cc_start: 0.8234 (ttmm) cc_final: 0.8023 (tppt) REVERT: B 47 ARG cc_start: 0.7776 (ttp80) cc_final: 0.7405 (ttp80) REVERT: B 135 PHE cc_start: 0.7175 (t80) cc_final: 0.6000 (m-10) outliers start: 8 outliers final: 4 residues processed: 95 average time/residue: 0.0978 time to fit residues: 11.0464 Evaluate side-chains 82 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 198 THR 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: 0.7980 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 26 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4101 r_free = 0.4101 target = 0.199527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.152292 restraints weight = 4333.855| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.97 r_work: 0.3167 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4156 Z= 0.123 Angle : 0.511 6.565 5644 Z= 0.264 Chirality : 0.036 0.148 650 Planarity : 0.003 0.019 664 Dihedral : 5.208 41.175 952 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.21 % Allowed : 11.76 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.28 (0.40), residues: 476 helix: 3.94 (0.25), residues: 400 sheet: None (None), residues: 0 loop : 0.56 (0.85), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.014 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 A 72 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 4156) covalent geometry : angle 0.51099 ( 5644) hydrogen bonds : bond 0.03855 ( 328) hydrogen bonds : angle 2.87718 ( 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 94 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7512 (m-80) cc_final: 0.6346 (t80) REVERT: A 42 LYS cc_start: 0.8847 (tppt) cc_final: 0.8631 (tppt) REVERT: A 47 ARG cc_start: 0.7704 (ttp80) cc_final: 0.7496 (ttp80) REVERT: A 135 PHE cc_start: 0.7110 (t80) cc_final: 0.5961 (m-10) REVERT: B 16 PHE cc_start: 0.7472 (m-80) cc_final: 0.6366 (t80) REVERT: B 47 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7459 (ttp80) REVERT: B 135 PHE cc_start: 0.7029 (t80) cc_final: 0.5823 (m-10) REVERT: B 198 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.9001 (t) outliers start: 9 outliers final: 6 residues processed: 89 average time/residue: 0.0902 time to fit residues: 9.4652 Evaluate side-chains 84 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 156 MET 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 Chi-restraints excluded: chain B residue 198 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.189178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.143534 restraints weight = 4253.139| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.10 r_work: 0.3146 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4156 Z= 0.143 Angle : 0.542 6.692 5644 Z= 0.284 Chirality : 0.038 0.171 650 Planarity : 0.003 0.015 664 Dihedral : 4.719 35.758 952 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.45 % Allowed : 14.71 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.96 (0.39), residues: 476 helix: 3.75 (0.25), residues: 400 sheet: None (None), residues: 0 loop : 0.24 (0.83), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 73 TYR 0.018 0.002 TYR B 85 PHE 0.010 0.001 PHE B 223 TRP 0.006 0.001 TRP B 184 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4156) covalent geometry : angle 0.54201 ( 5644) hydrogen bonds : bond 0.04233 ( 328) hydrogen bonds : angle 2.98645 ( 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 95 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8040 (tp30) cc_final: 0.7697 (tp30) REVERT: A 135 PHE cc_start: 0.7363 (t80) cc_final: 0.6118 (m-10) REVERT: B 135 PHE cc_start: 0.7288 (t80) cc_final: 0.6128 (m-10) outliers start: 10 outliers final: 8 residues processed: 87 average time/residue: 0.0963 time to fit residues: 9.8837 Evaluate side-chains 85 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 156 MET 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 Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 7 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.187474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.138811 restraints weight = 4244.743| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.11 r_work: 0.3071 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3996 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= 0.140 Angle : 0.539 7.213 5644 Z= 0.282 Chirality : 0.038 0.163 650 Planarity : 0.002 0.016 664 Dihedral : 4.629 33.633 952 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.94 % Allowed : 14.95 % 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 aren not related in a simple way. whole: 4.76 (0.39), residues: 476 helix: 3.64 (0.25), residues: 400 sheet: None (None), residues: 0 loop : 0.02 (0.82), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 73 TYR 0.016 0.002 TYR B 85 PHE 0.009 0.001 PHE B 246 TRP 0.008 0.001 TRP A 184 HIS 0.001 0.000 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4156) covalent geometry : angle 0.53925 ( 5644) hydrogen bonds : bond 0.04199 ( 328) hydrogen bonds : angle 2.99870 ( 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 105 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8038 (tt) REVERT: A 135 PHE cc_start: 0.7390 (t80) cc_final: 0.6161 (m-10) REVERT: A 226 MET cc_start: 0.8598 (mmp) cc_final: 0.8132 (mmm) REVERT: A 227 TYR cc_start: 0.8707 (t80) cc_final: 0.8171 (t80) REVERT: B 29 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8111 (tt) REVERT: B 135 PHE cc_start: 0.7379 (t80) cc_final: 0.6180 (m-10) REVERT: B 227 TYR cc_start: 0.8703 (t80) cc_final: 0.8166 (t80) outliers start: 12 outliers final: 8 residues processed: 99 average time/residue: 0.0870 time to fit residues: 10.1926 Evaluate side-chains 102 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 156 MET 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 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: 0.9980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.184026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.138196 restraints weight = 4355.545| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.10 r_work: 0.3081 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4287 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= 0.158 Angle : 0.562 7.443 5644 Z= 0.297 Chirality : 0.038 0.157 650 Planarity : 0.003 0.016 664 Dihedral : 4.653 36.267 952 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.94 % Allowed : 17.40 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.64 (0.39), residues: 476 helix: 3.58 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -0.12 (0.80), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 73 TYR 0.016 0.002 TYR B 85 PHE 0.009 0.001 PHE A 109 TRP 0.008 0.001 TRP B 184 HIS 0.001 0.000 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4156) covalent geometry : angle 0.56207 ( 5644) hydrogen bonds : bond 0.04498 ( 328) hydrogen bonds : angle 3.08967 ( 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 108 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8106 (tt) REVERT: A 38 GLU cc_start: 0.8130 (tp30) cc_final: 0.7913 (tp30) REVERT: A 226 MET cc_start: 0.8652 (mmp) cc_final: 0.8208 (mmm) REVERT: A 227 TYR cc_start: 0.8803 (t80) cc_final: 0.8187 (t80) REVERT: B 29 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8148 (tt) REVERT: B 135 PHE cc_start: 0.7449 (t80) cc_final: 0.6162 (m-10) REVERT: B 227 TYR cc_start: 0.8743 (t80) cc_final: 0.8284 (t80) outliers start: 12 outliers final: 9 residues processed: 100 average time/residue: 0.0823 time to fit residues: 9.8127 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 : 0.161 ------------------------------------------------------------------------------- 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 156 MET 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 34 GLU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 229 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: 0.4980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.185093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.138874 restraints weight = 4369.558| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.07 r_work: 0.3061 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4156 Z= 0.140 Angle : 0.556 9.150 5644 Z= 0.294 Chirality : 0.037 0.148 650 Planarity : 0.003 0.017 664 Dihedral : 4.650 38.985 952 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.43 % Allowed : 17.65 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.71 (0.39), residues: 476 helix: 3.62 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -0.07 (0.80), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 73 TYR 0.014 0.001 TYR B 113 PHE 0.031 0.001 PHE A 112 TRP 0.012 0.001 TRP A 184 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4156) covalent geometry : angle 0.55614 ( 5644) hydrogen bonds : bond 0.04238 ( 328) hydrogen bonds : angle 3.05054 ( 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 112 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8084 (tt) REVERT: A 38 GLU cc_start: 0.8084 (tp30) cc_final: 0.7813 (tp30) REVERT: A 135 PHE cc_start: 0.7034 (t80) cc_final: 0.5918 (m-10) REVERT: A 227 TYR cc_start: 0.8770 (t80) cc_final: 0.8179 (t80) REVERT: B 29 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8121 (tt) REVERT: B 135 PHE cc_start: 0.7516 (t80) cc_final: 0.6160 (m-10) REVERT: B 227 TYR cc_start: 0.8766 (t80) cc_final: 0.8300 (t80) outliers start: 14 outliers final: 10 residues processed: 102 average time/residue: 0.0744 time to fit residues: 9.1211 Evaluate side-chains 99 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 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 156 MET Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 116 LEU 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: 0.9980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 0.0040 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN B 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.185564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.141848 restraints weight = 4261.652| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.17 r_work: 0.3109 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4587 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= 0.134 Angle : 0.564 9.021 5644 Z= 0.299 Chirality : 0.037 0.180 650 Planarity : 0.003 0.016 664 Dihedral : 4.663 40.204 952 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.70 % Allowed : 18.14 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.80 (0.39), residues: 476 helix: 3.68 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -0.05 (0.81), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 73 TYR 0.020 0.001 TYR B 113 PHE 0.028 0.001 PHE A 112 TRP 0.007 0.001 TRP B 184 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4156) covalent geometry : angle 0.56381 ( 5644) hydrogen bonds : bond 0.04057 ( 328) hydrogen bonds : angle 3.04804 ( 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 107 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8117 (tt) REVERT: A 135 PHE cc_start: 0.7048 (t80) cc_final: 0.5788 (m-10) REVERT: A 227 TYR cc_start: 0.8756 (t80) cc_final: 0.8228 (t80) REVERT: B 29 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8136 (tt) REVERT: B 70 GLU cc_start: 0.7502 (pt0) cc_final: 0.7092 (pm20) REVERT: B 135 PHE cc_start: 0.7553 (t80) cc_final: 0.6243 (m-10) REVERT: B 227 TYR cc_start: 0.8771 (t80) cc_final: 0.8332 (t80) outliers start: 11 outliers final: 9 residues processed: 100 average time/residue: 0.0910 time to fit residues: 10.8067 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 : 0.143 ------------------------------------------------------------------------------- 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 156 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.182201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.135684 restraints weight = 4354.572| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.09 r_work: 0.3045 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4843 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= 0.160 Angle : 0.590 7.538 5644 Z= 0.314 Chirality : 0.038 0.180 650 Planarity : 0.003 0.017 664 Dihedral : 4.724 40.956 952 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.43 % Allowed : 18.63 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.72 (0.39), residues: 476 helix: 3.63 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -0.10 (0.81), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 137 TYR 0.017 0.002 TYR B 113 PHE 0.027 0.001 PHE B 112 TRP 0.012 0.001 TRP A 184 HIS 0.002 0.000 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 4156) covalent geometry : angle 0.58977 ( 5644) hydrogen bonds : bond 0.04534 ( 328) hydrogen bonds : angle 3.17177 ( 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 101 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8101 (tt) REVERT: A 38 GLU cc_start: 0.8161 (tp30) cc_final: 0.7883 (tp30) REVERT: A 42 LYS cc_start: 0.8946 (tppt) cc_final: 0.8713 (tppt) REVERT: A 135 PHE cc_start: 0.6913 (t80) cc_final: 0.5758 (m-10) REVERT: B 29 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8143 (tt) REVERT: B 38 GLU cc_start: 0.8126 (tp30) cc_final: 0.7837 (tp30) REVERT: B 42 LYS cc_start: 0.8975 (tppt) cc_final: 0.8768 (tppt) REVERT: B 70 GLU cc_start: 0.7800 (pt0) cc_final: 0.7196 (pm20) REVERT: B 227 TYR cc_start: 0.8841 (t80) cc_final: 0.8328 (t80) outliers start: 14 outliers final: 11 residues processed: 92 average time/residue: 0.0904 time to fit residues: 9.8254 Evaluate side-chains 100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.085 ------------------------------------------------------------------------------- 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 156 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 116 LEU 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: 2.9990 chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.0270 chunk 1 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.180671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.136835 restraints weight = 4264.281| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.05 r_work: 0.3115 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4156 Z= 0.134 Angle : 0.566 7.739 5644 Z= 0.298 Chirality : 0.037 0.173 650 Planarity : 0.002 0.017 664 Dihedral : 4.688 42.475 952 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.19 % Allowed : 18.87 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.85 (0.39), residues: 476 helix: 3.72 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -0.06 (0.82), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 73 TYR 0.017 0.001 TYR B 113 PHE 0.029 0.001 PHE A 112 TRP 0.011 0.001 TRP B 184 HIS 0.000 0.000 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4156) covalent geometry : angle 0.56609 ( 5644) hydrogen bonds : bond 0.04112 ( 328) hydrogen bonds : angle 3.10106 ( 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 100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8129 (tt) REVERT: A 38 GLU cc_start: 0.8192 (tp30) cc_final: 0.7915 (tp30) REVERT: A 135 PHE cc_start: 0.6978 (t80) cc_final: 0.5743 (m-10) REVERT: A 227 TYR cc_start: 0.8813 (t80) cc_final: 0.8362 (t80) REVERT: B 29 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8152 (tt) REVERT: B 38 GLU cc_start: 0.8146 (tp30) cc_final: 0.7870 (tp30) REVERT: B 42 LYS cc_start: 0.8991 (tppt) cc_final: 0.8786 (tppt) REVERT: B 70 GLU cc_start: 0.7726 (pt0) cc_final: 0.7167 (pm20) REVERT: B 135 PHE cc_start: 0.7124 (t80) cc_final: 0.5897 (m-10) REVERT: B 227 TYR cc_start: 0.8821 (t80) cc_final: 0.8240 (t80) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 0.0824 time to fit residues: 9.1504 Evaluate side-chains 96 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 156 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 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 = 0.3898 r_free = 0.3898 target = 0.178177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.131887 restraints weight = 4299.330| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.10 r_work: 0.3034 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5015 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= 0.156 Angle : 0.609 9.401 5644 Z= 0.321 Chirality : 0.039 0.184 650 Planarity : 0.003 0.020 664 Dihedral : 4.751 42.809 952 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.94 % Allowed : 19.36 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.77 (0.39), residues: 476 helix: 3.67 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -0.13 (0.82), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 73 TYR 0.017 0.002 TYR B 113 PHE 0.029 0.001 PHE A 112 TRP 0.009 0.002 TRP B 184 HIS 0.003 0.000 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4156) covalent geometry : angle 0.60862 ( 5644) hydrogen bonds : bond 0.04434 ( 328) hydrogen bonds : angle 3.16574 ( 972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 953.99 seconds wall clock time: 17 minutes 2.07 seconds (1022.07 seconds total)