Starting phenix.real_space_refine on Wed Jul 1 23:33:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dbr_46725/07_2026/9dbr_46725.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dbr_46725/07_2026/9dbr_46725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dbr_46725/07_2026/9dbr_46725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dbr_46725/07_2026/9dbr_46725.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dbr_46725/07_2026/9dbr_46725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dbr_46725/07_2026/9dbr_46725.map" } resolution = 3.94 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= 0.000 sd= 0.006 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 2 8.98 5 S 14 5.16 5 C 2709 2.51 5 N 618 2.21 5 O 694 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: 4037 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2006 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "B" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2006 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Ad-hoc single atom residues: {' K': 2} Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 1.10, per 1000 atoms: 0.27 Number of scatterers: 4037 At special positions: 0 Unit cell: (95.824, 64.448, 86.496, 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 2 19.00 S 14 16.00 O 694 8.00 N 618 7.00 C 2709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS B 93 " distance=2.03 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: 0.36 Conformation dependent library (CDL) restraints added in 142.8 milliseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 924 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 79.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 43 through 91 Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 95 through 113 Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 152 through 194 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 202 through 223 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 237 through 251 Processing helix chain 'A' and resid 269 through 297 removed outlier: 3.512A pdb=" N ILE A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 68 Processing helix chain 'B' and resid 69 through 91 removed outlier: 3.566A pdb=" N GLU B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 113 Processing helix chain 'B' and resid 128 through 141 Processing helix chain 'B' and resid 152 through 193 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 202 through 223 Processing helix chain 'B' and resid 223 through 235 Processing helix chain 'B' and resid 237 through 250 Processing helix chain 'B' and resid 269 through 297 326 hydrogen bonds defined for protein. 978 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: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 874 1.33 - 1.45: 960 1.45 - 1.57: 2286 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4142 Sorted by residual: bond pdb=" N VAL A 148 " pdb=" CA VAL A 148 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N GLU B 69 " pdb=" CA GLU B 69 " ideal model delta sigma weight residual 1.460 1.490 -0.030 1.14e-02 7.69e+03 6.85e+00 bond pdb=" N LEU B 68 " pdb=" CA LEU B 68 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.82e+00 bond pdb=" N THR A 152 " pdb=" CA THR A 152 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.48e+00 bond pdb=" N SER A 149 " pdb=" CA SER A 149 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.25e-02 6.40e+03 6.20e+00 ... (remaining 4137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 5367 1.11 - 2.22: 199 2.22 - 3.33: 41 3.33 - 4.44: 13 4.44 - 5.55: 11 Bond angle restraints: 5631 Sorted by residual: angle pdb=" N ASN A 147 " pdb=" CA ASN A 147 " pdb=" C ASN A 147 " ideal model delta sigma weight residual 111.82 107.87 3.95 1.16e+00 7.43e-01 1.16e+01 angle pdb=" N GLU B 263 " pdb=" CA GLU B 263 " pdb=" C GLU B 263 " ideal model delta sigma weight residual 111.17 115.75 -4.58 1.41e+00 5.03e-01 1.05e+01 angle pdb=" N GLU B 69 " pdb=" CA GLU B 69 " pdb=" C GLU B 69 " ideal model delta sigma weight residual 114.62 111.04 3.58 1.14e+00 7.69e-01 9.86e+00 angle pdb=" N HIS A 151 " pdb=" CA HIS A 151 " pdb=" C HIS A 151 " ideal model delta sigma weight residual 112.90 109.09 3.81 1.31e+00 5.83e-01 8.47e+00 angle pdb=" CA THR A 152 " pdb=" C THR A 152 " pdb=" O THR A 152 " ideal model delta sigma weight residual 121.19 118.09 3.10 1.10e+00 8.26e-01 7.92e+00 ... (remaining 5626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.69: 2287 23.69 - 47.38: 61 47.38 - 71.08: 5 71.08 - 94.77: 7 94.77 - 118.46: 2 Dihedral angle restraints: 2362 sinusoidal: 914 harmonic: 1448 Sorted by residual: dihedral pdb=" C04 P0T A 403 " pdb=" C03 P0T A 403 " pdb=" C05 P0T A 403 " pdb=" C06 P0T A 403 " ideal model delta sinusoidal sigma weight residual -61.60 56.86 -118.46 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C06 P0T A 403 " pdb=" C03 P0T A 403 " pdb=" C05 P0T A 403 " pdb=" C10 P0T A 403 " ideal model delta sinusoidal sigma weight residual 186.18 67.81 118.37 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C05 P0T A 403 " pdb=" C03 P0T A 403 " pdb=" C04 P0T A 403 " pdb=" C07 P0T A 403 " ideal model delta sinusoidal sigma weight residual 41.58 -43.72 85.30 1 3.00e+01 1.11e-03 9.79e+00 ... (remaining 2359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 445 0.034 - 0.068: 146 0.068 - 0.102: 51 0.102 - 0.136: 12 0.136 - 0.170: 2 Chirality restraints: 656 Sorted by residual: chirality pdb=" CA VAL A 148 " pdb=" N VAL A 148 " pdb=" C VAL A 148 " pdb=" CB VAL A 148 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA GLU B 263 " pdb=" N GLU B 263 " pdb=" C GLU B 263 " pdb=" CB GLU B 263 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" C04 P0T A 403 " pdb=" C03 P0T A 403 " pdb=" C07 P0T A 403 " pdb=" C08 P0T A 403 " both_signs ideal model delta sigma weight residual False -2.48 -2.34 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 653 not shown) Planarity restraints: 678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 82 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.33e+00 pdb=" C GLN A 82 " -0.020 2.00e-02 2.50e+03 pdb=" O GLN A 82 " 0.007 2.00e-02 2.50e+03 pdb=" N GLU A 83 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 115 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO B 116 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 116 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 116 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 271 " -0.018 5.00e-02 4.00e+02 2.70e-02 1.16e+00 pdb=" N PRO B 272 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " -0.015 5.00e-02 4.00e+02 ... (remaining 675 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.79: 920 2.79 - 3.38: 4815 3.38 - 3.96: 7613 3.96 - 4.55: 10309 4.55 - 5.14: 14607 Nonbonded interactions: 38264 Sorted by model distance: nonbonded pdb=" O GLY A 137 " pdb=" OG1 THR A 141 " model vdw 2.200 3.040 nonbonded pdb=" OE2 GLU A 73 " pdb=" OG SER B 125 " model vdw 2.251 3.040 nonbonded pdb=" O ALA B 112 " pdb=" NE2 HIS B 151 " model vdw 2.350 3.120 nonbonded pdb=" O ALA B 227 " pdb=" OG SER B 241 " model vdw 2.369 3.040 nonbonded pdb=" O THR A 250 " pdb=" OG1 THR A 251 " model vdw 2.398 3.040 ... (remaining 38259 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 43 through 297) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.470 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 : 0.004 0.078 4143 Z= 0.218 Angle : 0.567 5.547 5633 Z= 0.341 Chirality : 0.041 0.170 656 Planarity : 0.003 0.028 678 Dihedral : 12.741 118.459 1435 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.36), residues: 506 helix: 2.72 (0.24), residues: 400 sheet: None (None), residues: 0 loop : -1.82 (0.54), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 111 TYR 0.009 0.001 TYR A 57 PHE 0.010 0.001 PHE A 158 TRP 0.005 0.001 TRP A 127 HIS 0.002 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.22 ( 4142) covalent geometry : angle 0.56669 / 0.34 ( 5631) SS BOND : bond 0.00196 / 0.10 ( 1) SS BOND : angle 0.71142 / 0.41 ( 2) hydrogen bonds : bond 0.08093 / 5.31 ( 326) hydrogen bonds : angle 4.09181 / 2.99 ( 978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 HIS cc_start: 0.5820 (m-70) cc_final: 0.5008 (m90) REVERT: A 195 MET cc_start: 0.0921 (mmm) cc_final: 0.0692 (ptm) REVERT: B 44 TRP cc_start: 0.7543 (m-90) cc_final: 0.6920 (m-90) REVERT: B 123 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7887 (mp0) REVERT: B 165 LEU cc_start: 0.8598 (mp) cc_final: 0.8229 (tt) REVERT: B 195 MET cc_start: 0.4871 (mmm) cc_final: 0.4472 (mtm) REVERT: B 216 LEU cc_start: 0.8889 (tp) cc_final: 0.8615 (mp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0608 time to fit residues: 14.2770 Evaluate side-chains 102 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.163872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129255 restraints weight = 7406.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133552 restraints weight = 4260.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136544 restraints weight = 2942.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.138224 restraints weight = 2281.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139807 restraints weight = 1951.489| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4143 Z= 0.226 Angle : 0.725 8.116 5633 Z= 0.377 Chirality : 0.046 0.252 656 Planarity : 0.004 0.029 678 Dihedral : 8.531 78.491 557 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.51 % Allowed : 15.35 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.37), residues: 506 helix: 2.59 (0.25), residues: 401 sheet: None (None), residues: 0 loop : -1.56 (0.56), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 79 TYR 0.030 0.002 TYR B 243 PHE 0.014 0.002 PHE B 214 TRP 0.008 0.001 TRP A 127 HIS 0.004 0.002 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 ( 4142) covalent geometry : angle 0.72490 / 0.38 ( 5631) SS BOND : bond 0.00085 / 0.04 ( 1) SS BOND : angle 0.63284 / 0.36 ( 2) hydrogen bonds : bond 0.05263 / 3.36 ( 326) hydrogen bonds : angle 4.06595 / 2.98 ( 978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.8923 (mtmm) cc_final: 0.8567 (pttp) REVERT: A 131 SER cc_start: 0.8030 (t) cc_final: 0.7604 (p) REVERT: A 132 SER cc_start: 0.9014 (m) cc_final: 0.8457 (p) REVERT: A 222 PHE cc_start: 0.9078 (m-80) cc_final: 0.8802 (m-10) REVERT: B 44 TRP cc_start: 0.7595 (m-90) cc_final: 0.6618 (p90) REVERT: B 195 MET cc_start: 0.4623 (mmm) cc_final: 0.4396 (mtp) REVERT: B 213 LEU cc_start: 0.8147 (mt) cc_final: 0.7883 (tt) outliers start: 28 outliers final: 22 residues processed: 132 average time/residue: 0.0429 time to fit residues: 7.7492 Evaluate side-chains 118 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 288 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.164316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130078 restraints weight = 7480.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.134328 restraints weight = 4360.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137218 restraints weight = 3038.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138945 restraints weight = 2381.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.140336 restraints weight = 2045.675| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4143 Z= 0.148 Angle : 0.617 8.849 5633 Z= 0.312 Chirality : 0.042 0.165 656 Planarity : 0.003 0.032 678 Dihedral : 7.874 81.380 557 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.58 % Allowed : 19.07 % Favored : 75.35 % 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: 3.14 (0.37), residues: 506 helix: 2.90 (0.25), residues: 399 sheet: None (None), residues: 0 loop : -1.36 (0.58), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 111 TYR 0.021 0.002 TYR B 243 PHE 0.018 0.001 PHE B 214 TRP 0.008 0.001 TRP A 277 HIS 0.003 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 4142) covalent geometry : angle 0.61666 / 0.31 ( 5631) SS BOND : bond 0.00024 / 0.01 ( 1) SS BOND : angle 0.32934 / 0.19 ( 2) hydrogen bonds : bond 0.04519 / 2.91 ( 326) hydrogen bonds : angle 3.71606 / 2.72 ( 978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 131 SER cc_start: 0.7979 (t) cc_final: 0.7577 (p) REVERT: A 132 SER cc_start: 0.8953 (m) cc_final: 0.8384 (p) REVERT: A 222 PHE cc_start: 0.9078 (m-80) cc_final: 0.8783 (m-10) REVERT: B 44 TRP cc_start: 0.7516 (m-90) cc_final: 0.6589 (p90) REVERT: B 195 MET cc_start: 0.4753 (mmm) cc_final: 0.4436 (mtp) REVERT: B 249 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.8995 (tt) outliers start: 24 outliers final: 18 residues processed: 122 average time/residue: 0.0477 time to fit residues: 7.7896 Evaluate side-chains 115 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 288 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.0070 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.164960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130432 restraints weight = 7271.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.134863 restraints weight = 4195.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.137816 restraints weight = 2888.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139773 restraints weight = 2250.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.140952 restraints weight = 1905.610| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4143 Z= 0.128 Angle : 0.608 11.185 5633 Z= 0.302 Chirality : 0.041 0.151 656 Planarity : 0.003 0.032 678 Dihedral : 7.151 76.900 557 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.95 % Allowed : 23.72 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.38), residues: 506 helix: 2.92 (0.25), residues: 402 sheet: None (None), residues: 0 loop : -1.30 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 111 TYR 0.020 0.002 TYR B 243 PHE 0.022 0.001 PHE B 214 TRP 0.007 0.001 TRP A 275 HIS 0.002 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 4142) covalent geometry : angle 0.60776 / 0.30 ( 5631) SS BOND : bond 0.00097 / 0.05 ( 1) SS BOND : angle 0.39885 / 0.23 ( 2) hydrogen bonds : bond 0.04213 / 2.71 ( 326) hydrogen bonds : angle 3.57095 / 2.61 ( 978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 57 TYR cc_start: 0.8675 (t80) cc_final: 0.8026 (t80) REVERT: A 131 SER cc_start: 0.7988 (t) cc_final: 0.7519 (p) REVERT: A 132 SER cc_start: 0.8911 (m) cc_final: 0.8295 (p) REVERT: A 222 PHE cc_start: 0.9008 (m-80) cc_final: 0.8732 (m-10) REVERT: B 44 TRP cc_start: 0.7458 (m-90) cc_final: 0.6536 (p90) REVERT: B 195 MET cc_start: 0.4765 (mmm) cc_final: 0.4506 (mtp) REVERT: B 216 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8482 (mp) REVERT: B 249 LEU cc_start: 0.9419 (mp) cc_final: 0.8880 (tt) REVERT: B 257 PHE cc_start: 0.8967 (m-80) cc_final: 0.8425 (m-80) outliers start: 17 outliers final: 14 residues processed: 120 average time/residue: 0.0507 time to fit residues: 8.1802 Evaluate side-chains 112 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 241 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.162938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.129015 restraints weight = 7273.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133261 restraints weight = 4194.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136107 restraints weight = 2902.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.138070 restraints weight = 2264.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.139356 restraints weight = 1917.467| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 4143 Z= 0.140 Angle : 0.604 10.428 5633 Z= 0.307 Chirality : 0.041 0.156 656 Planarity : 0.003 0.032 678 Dihedral : 6.354 73.638 557 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.81 % Allowed : 23.72 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.28 (0.38), residues: 506 helix: 2.95 (0.25), residues: 402 sheet: None (None), residues: 0 loop : -1.20 (0.62), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 111 TYR 0.021 0.002 TYR B 243 PHE 0.019 0.001 PHE B 214 TRP 0.006 0.001 TRP A 277 HIS 0.002 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 4142) covalent geometry : angle 0.60426 / 0.31 ( 5631) SS BOND : bond 0.00152 / 0.08 ( 1) SS BOND : angle 0.28658 / 0.17 ( 2) hydrogen bonds : bond 0.04265 / 2.74 ( 326) hydrogen bonds : angle 3.61424 / 2.64 ( 978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.156 Fit side-chains REVERT: A 57 TYR cc_start: 0.8783 (t80) cc_final: 0.8048 (t80) REVERT: A 131 SER cc_start: 0.7947 (t) cc_final: 0.7494 (p) REVERT: A 132 SER cc_start: 0.8950 (m) cc_final: 0.8319 (p) REVERT: A 216 LEU cc_start: 0.8040 (tt) cc_final: 0.7785 (pp) REVERT: A 222 PHE cc_start: 0.9004 (m-80) cc_final: 0.8519 (m-10) REVERT: B 44 TRP cc_start: 0.7540 (m-90) cc_final: 0.6644 (p90) REVERT: B 195 MET cc_start: 0.4765 (mmm) cc_final: 0.4509 (mtp) REVERT: B 216 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8485 (mp) REVERT: B 257 PHE cc_start: 0.8979 (m-80) cc_final: 0.8396 (m-80) outliers start: 25 outliers final: 18 residues processed: 116 average time/residue: 0.0577 time to fit residues: 8.9510 Evaluate side-chains 115 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 241 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 GLN B 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.161499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128231 restraints weight = 7368.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.132564 restraints weight = 4190.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.135473 restraints weight = 2868.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.137390 restraints weight = 2211.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.138712 restraints weight = 1862.589| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4143 Z= 0.137 Angle : 0.601 8.957 5633 Z= 0.302 Chirality : 0.041 0.155 656 Planarity : 0.003 0.034 678 Dihedral : 5.877 73.958 557 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.56 % Favored : 96.25 % Rotamer: Outliers : 5.58 % Allowed : 25.81 % Favored : 68.60 % 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: 3.27 (0.38), residues: 506 helix: 2.97 (0.25), residues: 402 sheet: None (None), residues: 0 loop : -1.34 (0.62), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 111 TYR 0.018 0.002 TYR B 243 PHE 0.012 0.001 PHE B 214 TRP 0.007 0.001 TRP A 277 HIS 0.002 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 4142) covalent geometry : angle 0.60089 / 0.30 ( 5631) SS BOND : bond 0.00131 / 0.07 ( 1) SS BOND : angle 0.24864 / 0.15 ( 2) hydrogen bonds : bond 0.04196 / 2.69 ( 326) hydrogen bonds : angle 3.56306 / 2.59 ( 978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.159 Fit side-chains REVERT: A 57 TYR cc_start: 0.8789 (t80) cc_final: 0.8032 (t80) REVERT: A 131 SER cc_start: 0.7991 (t) cc_final: 0.7555 (p) REVERT: A 132 SER cc_start: 0.8940 (m) cc_final: 0.8320 (p) REVERT: A 222 PHE cc_start: 0.8989 (m-80) cc_final: 0.8469 (m-10) REVERT: B 44 TRP cc_start: 0.7537 (m-90) cc_final: 0.6605 (p90) REVERT: B 195 MET cc_start: 0.4888 (mmm) cc_final: 0.4640 (mtp) REVERT: B 216 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8521 (mp) REVERT: B 257 PHE cc_start: 0.8950 (m-80) cc_final: 0.8445 (m-80) outliers start: 24 outliers final: 21 residues processed: 122 average time/residue: 0.0491 time to fit residues: 8.1648 Evaluate side-chains 122 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 249 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 0.0470 chunk 15 optimal weight: 0.0020 overall best weight: 0.4686 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.162353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.128717 restraints weight = 7438.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133109 restraints weight = 4280.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136048 restraints weight = 2928.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.137865 restraints weight = 2268.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.139294 restraints weight = 1928.118| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 4143 Z= 0.127 Angle : 0.594 8.305 5633 Z= 0.302 Chirality : 0.041 0.153 656 Planarity : 0.003 0.033 678 Dihedral : 5.759 75.568 557 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.37 % Favored : 97.43 % Rotamer: Outliers : 4.88 % Allowed : 26.51 % Favored : 68.60 % 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: 3.36 (0.38), residues: 506 helix: 3.06 (0.25), residues: 402 sheet: None (None), residues: 0 loop : -1.42 (0.63), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 111 TYR 0.017 0.002 TYR B 243 PHE 0.012 0.001 PHE B 214 TRP 0.007 0.001 TRP A 277 HIS 0.002 0.000 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 4142) covalent geometry : angle 0.59388 / 0.30 ( 5631) SS BOND : bond 0.00250 / 0.13 ( 1) SS BOND : angle 0.42004 / 0.25 ( 2) hydrogen bonds : bond 0.04015 / 2.58 ( 326) hydrogen bonds : angle 3.54644 / 2.57 ( 978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 57 TYR cc_start: 0.8687 (t80) cc_final: 0.8041 (t80) REVERT: A 131 SER cc_start: 0.8002 (t) cc_final: 0.7582 (p) REVERT: A 132 SER cc_start: 0.8925 (m) cc_final: 0.8249 (p) REVERT: A 222 PHE cc_start: 0.8937 (m-80) cc_final: 0.8425 (m-10) REVERT: B 44 TRP cc_start: 0.7515 (m-90) cc_final: 0.6574 (p90) REVERT: B 195 MET cc_start: 0.4837 (mmm) cc_final: 0.4555 (mtp) REVERT: B 216 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8509 (mp) REVERT: B 256 ASP cc_start: 0.8068 (p0) cc_final: 0.7746 (p0) REVERT: B 257 PHE cc_start: 0.8985 (m-80) cc_final: 0.8291 (m-80) REVERT: B 291 MET cc_start: 0.7633 (mmp) cc_final: 0.7418 (mmt) outliers start: 21 outliers final: 17 residues processed: 119 average time/residue: 0.0440 time to fit residues: 7.1519 Evaluate side-chains 118 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 252 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.160233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126623 restraints weight = 7277.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.130880 restraints weight = 4153.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.133786 restraints weight = 2851.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.135541 restraints weight = 2208.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.136674 restraints weight = 1877.288| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4143 Z= 0.130 Angle : 0.605 9.864 5633 Z= 0.305 Chirality : 0.041 0.154 656 Planarity : 0.003 0.033 678 Dihedral : 5.725 77.262 557 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.57 % Favored : 97.23 % Rotamer: Outliers : 5.35 % Allowed : 26.28 % Favored : 68.37 % 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: 3.39 (0.38), residues: 506 helix: 3.05 (0.25), residues: 403 sheet: None (None), residues: 0 loop : -1.34 (0.62), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 111 TYR 0.017 0.002 TYR B 243 PHE 0.022 0.001 PHE B 185 TRP 0.007 0.001 TRP A 277 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 4142) covalent geometry : angle 0.60558 / 0.30 ( 5631) SS BOND : bond 0.00210 / 0.11 ( 1) SS BOND : angle 0.26149 / 0.15 ( 2) hydrogen bonds : bond 0.04077 / 2.59 ( 326) hydrogen bonds : angle 3.56635 / 2.58 ( 978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.149 Fit side-chains REVERT: A 57 TYR cc_start: 0.8697 (t80) cc_final: 0.8040 (t80) REVERT: A 131 SER cc_start: 0.8011 (t) cc_final: 0.7549 (p) REVERT: A 132 SER cc_start: 0.8941 (m) cc_final: 0.8290 (p) REVERT: B 44 TRP cc_start: 0.7529 (m-90) cc_final: 0.6588 (p90) REVERT: B 195 MET cc_start: 0.4888 (mmm) cc_final: 0.4589 (mtp) REVERT: B 216 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8480 (mp) REVERT: B 256 ASP cc_start: 0.8107 (p0) cc_final: 0.7850 (p0) REVERT: B 257 PHE cc_start: 0.9010 (m-80) cc_final: 0.8320 (m-80) REVERT: B 291 MET cc_start: 0.7632 (mmp) cc_final: 0.7424 (mmt) outliers start: 23 outliers final: 19 residues processed: 119 average time/residue: 0.0393 time to fit residues: 6.3452 Evaluate side-chains 121 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 252 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122922 restraints weight = 7579.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127050 restraints weight = 4298.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129823 restraints weight = 2958.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.131629 restraints weight = 2299.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.132782 restraints weight = 1948.392| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4143 Z= 0.165 Angle : 0.639 10.278 5633 Z= 0.328 Chirality : 0.042 0.161 656 Planarity : 0.003 0.031 678 Dihedral : 6.006 84.324 557 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.35 % Allowed : 26.74 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.38), residues: 506 helix: 2.94 (0.25), residues: 402 sheet: None (None), residues: 0 loop : -1.53 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 111 TYR 0.017 0.002 TYR B 243 PHE 0.012 0.001 PHE A 158 TRP 0.008 0.001 TRP A 199 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 4142) covalent geometry : angle 0.63890 / 0.33 ( 5631) SS BOND : bond 0.00126 / 0.07 ( 1) SS BOND : angle 0.27066 / 0.16 ( 2) hydrogen bonds : bond 0.04621 / 2.93 ( 326) hydrogen bonds : angle 3.76229 / 2.71 ( 978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.148 Fit side-chains REVERT: A 57 TYR cc_start: 0.8742 (t80) cc_final: 0.8098 (t80) REVERT: A 77 LYS cc_start: 0.8618 (pttp) cc_final: 0.8247 (pttt) REVERT: A 131 SER cc_start: 0.8028 (t) cc_final: 0.7549 (p) REVERT: A 132 SER cc_start: 0.9017 (m) cc_final: 0.8402 (p) REVERT: A 138 THR cc_start: 0.9231 (p) cc_final: 0.8981 (t) REVERT: B 68 LEU cc_start: 0.8736 (tp) cc_final: 0.8531 (tt) REVERT: B 70 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7999 (mt0) REVERT: B 257 PHE cc_start: 0.8997 (m-80) cc_final: 0.8451 (m-80) outliers start: 23 outliers final: 21 residues processed: 120 average time/residue: 0.0526 time to fit residues: 8.3951 Evaluate side-chains 121 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 241 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 46 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.159188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125432 restraints weight = 7311.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129703 restraints weight = 4223.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132490 restraints weight = 2927.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134292 restraints weight = 2293.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.134858 restraints weight = 1952.406| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4143 Z= 0.134 Angle : 0.623 10.575 5633 Z= 0.316 Chirality : 0.042 0.163 656 Planarity : 0.003 0.033 678 Dihedral : 6.037 84.083 557 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.57 % Favored : 97.23 % Rotamer: Outliers : 4.65 % Allowed : 27.91 % Favored : 67.44 % 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: 3.25 (0.38), residues: 506 helix: 2.95 (0.25), residues: 402 sheet: None (None), residues: 0 loop : -1.30 (0.63), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 111 TYR 0.016 0.002 TYR B 243 PHE 0.025 0.001 PHE B 214 TRP 0.023 0.001 TRP B 44 HIS 0.002 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 4142) covalent geometry : angle 0.62306 / 0.32 ( 5631) SS BOND : bond 0.00173 / 0.09 ( 1) SS BOND : angle 0.19568 / 0.11 ( 2) hydrogen bonds : bond 0.04126 / 2.63 ( 326) hydrogen bonds : angle 3.64238 / 2.64 ( 978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.130 Fit side-chains REVERT: A 57 TYR cc_start: 0.8674 (t80) cc_final: 0.8058 (t80) REVERT: A 131 SER cc_start: 0.8036 (t) cc_final: 0.7763 (p) REVERT: A 132 SER cc_start: 0.8972 (m) cc_final: 0.8320 (p) REVERT: A 138 THR cc_start: 0.9139 (p) cc_final: 0.8879 (t) REVERT: B 44 TRP cc_start: 0.8060 (m-90) cc_final: 0.7837 (m-90) REVERT: B 70 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7932 (mt0) REVERT: B 78 TYR cc_start: 0.8143 (m-80) cc_final: 0.7930 (m-80) REVERT: B 83 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8640 (tm-30) REVERT: B 257 PHE cc_start: 0.8880 (m-80) cc_final: 0.8450 (m-80) outliers start: 20 outliers final: 18 residues processed: 119 average time/residue: 0.0478 time to fit residues: 7.6662 Evaluate side-chains 118 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 241 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 3 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.159277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.124691 restraints weight = 7542.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.128859 restraints weight = 4355.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131643 restraints weight = 3032.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133317 restraints weight = 2379.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134542 restraints weight = 2042.684| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.6046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4143 Z= 0.137 Angle : 0.632 10.727 5633 Z= 0.319 Chirality : 0.042 0.156 656 Planarity : 0.003 0.032 678 Dihedral : 5.992 85.973 557 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.36 % Favored : 96.44 % Rotamer: Outliers : 4.65 % Allowed : 28.37 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.20 (0.38), residues: 506 helix: 2.93 (0.25), residues: 401 sheet: None (None), residues: 0 loop : -1.38 (0.62), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 111 TYR 0.017 0.002 TYR B 243 PHE 0.015 0.001 PHE B 214 TRP 0.020 0.001 TRP B 44 HIS 0.002 0.000 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 4142) covalent geometry : angle 0.63260 / 0.32 ( 5631) SS BOND : bond 0.00179 / 0.09 ( 1) SS BOND : angle 0.20204 / 0.12 ( 2) hydrogen bonds : bond 0.04168 / 2.66 ( 326) hydrogen bonds : angle 3.60368 / 2.61 ( 978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 866.38 seconds wall clock time: 15 minutes 35.40 seconds (935.40 seconds total)