Starting phenix.real_space_refine on Tue Aug 4 14:52:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ov9_70894/08_2026/9ov9_70894.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ov9_70894/08_2026/9ov9_70894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ov9_70894/08_2026/9ov9_70894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ov9_70894/08_2026/9ov9_70894.map" model { file = "/net/cci-nas-00/data/ceres_data/9ov9_70894/08_2026/9ov9_70894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ov9_70894/08_2026/9ov9_70894.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 16 5.16 5 C 2682 2.51 5 N 668 2.21 5 O 686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4055 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2028 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 15, 'TRANS': 250} Chain breaks: 1 Chain: "A" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2024 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 15, 'TRANS': 250} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.91, per 1000 atoms: 0.22 Number of scatterers: 4055 At special positions: 0 Unit cell: (69.7, 80.36, 98.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 16 16.00 O 686 8.00 N 668 7.00 C 2682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS A 53 " 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: 0.22 Conformation dependent library (CDL) restraints added in 130.0 milliseconds 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 990 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 78.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'B' and resid 6 through 51 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 55 through 70 Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 116 through 152 Proline residue: B 132 - end of helix Processing helix chain 'B' and resid 166 through 185 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 200 through 213 removed outlier: 4.040A pdb=" N LEU B 212 " --> pdb=" O CYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 264 Processing helix chain 'B' and resid 264 through 270 removed outlier: 3.586A pdb=" N LEU B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 51 Proline residue: A 31 - end of helix removed outlier: 3.516A pdb=" N SER A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.715A pdb=" N LEU A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 removed outlier: 3.589A pdb=" N ARG A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 116 through 151 Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 165 through 185 Processing helix chain 'A' and resid 185 through 196 removed outlier: 3.726A pdb=" N ALA A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 213 Processing helix chain 'A' and resid 230 through 263 removed outlier: 3.783A pdb=" N HIS A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 269 removed outlier: 3.733A pdb=" N GLU A 267 " --> pdb=" O GLY A 264 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 957 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: 0.52 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1256 1.35 - 1.47: 1052 1.47 - 1.59: 1830 1.59 - 1.71: 0 1.71 - 1.83: 22 Bond restraints: 4160 Sorted by residual: bond pdb=" C PRO A 273 " pdb=" N PRO A 274 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.10e+00 bond pdb=" CA VAL B 131 " pdb=" CB VAL B 131 " ideal model delta sigma weight residual 1.537 1.543 -0.006 5.00e-03 4.00e+04 1.44e+00 bond pdb=" CA VAL A 131 " pdb=" CB VAL A 131 " ideal model delta sigma weight residual 1.537 1.542 -0.005 5.00e-03 4.00e+04 1.21e+00 bond pdb=" CB VAL B 25 " pdb=" CG1 VAL B 25 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" CA GLY A 70 " pdb=" C GLY A 70 " ideal model delta sigma weight residual 1.530 1.520 0.011 1.04e-02 9.25e+03 1.10e+00 ... (remaining 4155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 5570 1.87 - 3.73: 94 3.73 - 5.60: 27 5.60 - 7.47: 7 7.47 - 9.34: 3 Bond angle restraints: 5701 Sorted by residual: angle pdb=" CA LEU B 36 " pdb=" CB LEU B 36 " pdb=" CG LEU B 36 " ideal model delta sigma weight residual 116.30 125.64 -9.34 3.50e+00 8.16e-02 7.12e+00 angle pdb=" C LEU B 77 " pdb=" N ALA B 78 " pdb=" CA ALA B 78 " ideal model delta sigma weight residual 120.38 123.91 -3.53 1.37e+00 5.33e-01 6.65e+00 angle pdb=" C PHE B 209 " pdb=" N ILE B 210 " pdb=" CA ILE B 210 " ideal model delta sigma weight residual 121.97 117.53 4.44 1.80e+00 3.09e-01 6.07e+00 angle pdb=" CA PRO A 274 " pdb=" N PRO A 274 " pdb=" CD PRO A 274 " ideal model delta sigma weight residual 112.00 108.70 3.30 1.40e+00 5.10e-01 5.55e+00 angle pdb=" N GLY B 30 " pdb=" CA GLY B 30 " pdb=" C GLY B 30 " ideal model delta sigma weight residual 112.34 117.06 -4.72 2.04e+00 2.40e-01 5.35e+00 ... (remaining 5696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.99: 2078 10.99 - 21.98: 177 21.98 - 32.97: 100 32.97 - 43.97: 41 43.97 - 54.96: 11 Dihedral angle restraints: 2407 sinusoidal: 871 harmonic: 1536 Sorted by residual: dihedral pdb=" CA PRO A 52 " pdb=" C PRO A 52 " pdb=" N CYS A 53 " pdb=" CA CYS A 53 " ideal model delta harmonic sigma weight residual 180.00 152.84 27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA PRO A 273 " pdb=" C PRO A 273 " pdb=" N PRO A 274 " pdb=" CA PRO A 274 " ideal model delta harmonic sigma weight residual -180.00 -152.88 -27.12 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ILE B 210 " pdb=" C ILE B 210 " pdb=" N SER B 211 " pdb=" CA SER B 211 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 2404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 462 0.034 - 0.067: 171 0.067 - 0.101: 44 0.101 - 0.135: 11 0.135 - 0.168: 3 Chirality restraints: 691 Sorted by residual: chirality pdb=" CA PRO A 274 " pdb=" N PRO A 274 " pdb=" C PRO A 274 " pdb=" CB PRO A 274 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CB VAL A 54 " pdb=" CA VAL A 54 " pdb=" CG1 VAL A 54 " pdb=" CG2 VAL A 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA VAL A 187 " pdb=" N VAL A 187 " pdb=" C VAL A 187 " pdb=" CB VAL A 187 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 688 not shown) Planarity restraints: 700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 273 " 0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO A 274 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 273 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C PRO A 273 " -0.041 2.00e-02 2.50e+03 pdb=" O PRO A 273 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO A 274 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 164 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 165 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " -0.021 5.00e-02 4.00e+02 ... (remaining 697 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.06: 2986 3.06 - 3.58: 5851 3.58 - 4.10: 6605 4.10 - 4.62: 10408 4.62 - 5.14: 12415 Nonbonded interactions: 38265 Sorted by model distance: nonbonded pdb=" O HIS A 258 " pdb=" OD1 ASP A 261 " model vdw 2.545 3.040 nonbonded pdb=" O SER A 213 " pdb=" OG1 THR A 214 " model vdw 2.575 3.040 nonbonded pdb=" CB ARG A 71 " pdb=" NE ARG A 71 " model vdw 2.588 2.816 nonbonded pdb=" O VAL B 131 " pdb=" OG1 THR B 134 " model vdw 2.598 3.040 nonbonded pdb=" O VAL A 252 " pdb=" OG1 THR A 255 " model vdw 2.599 3.040 ... (remaining 38260 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 4 through 81 or resid 89 through 301)) selection = (chain 'B' and (resid 4 through 81 or resid 89 through 301)) } 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: 1.500 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: 5.710 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.003 0.041 4161 Z= 0.168 Angle : 0.708 9.336 5703 Z= 0.340 Chirality : 0.038 0.168 691 Planarity : 0.006 0.090 700 Dihedral : 12.489 54.957 1414 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.92 % Favored : 93.89 % Rotamer: Outliers : 2.65 % Allowed : 8.92 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.38), residues: 524 helix: 2.02 (0.25), residues: 404 sheet: None (None), residues: 0 loop : -2.10 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.009 0.001 TYR B 17 PHE 0.021 0.002 PHE A 122 TRP 0.006 0.001 TRP A 156 HIS 0.002 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 ( 4160) covalent geometry : angle 0.70775 / 0.34 ( 5701) SS BOND : bond 0.00264 / 0.17 ( 1) SS BOND : angle 1.37052 / 0.65 ( 2) hydrogen bonds : bond 0.08734 / 6.41 ( 321) hydrogen bonds : angle 4.22365 / 3.24 ( 957) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 LEU cc_start: 0.8219 (mp) cc_final: 0.7857 (tp) REVERT: B 74 ARG cc_start: 0.9201 (mtp85) cc_final: 0.8580 (mtm180) REVERT: B 122 PHE cc_start: 0.9309 (t80) cc_final: 0.9073 (t80) REVERT: B 199 TRP cc_start: 0.8527 (m-10) cc_final: 0.8213 (m-10) REVERT: B 212 LEU cc_start: 0.8149 (mt) cc_final: 0.7949 (mt) REVERT: B 246 LEU cc_start: 0.9521 (mt) cc_final: 0.9041 (mt) REVERT: A 74 ARG cc_start: 0.9221 (mtp85) cc_final: 0.8754 (ttt-90) REVERT: A 122 PHE cc_start: 0.9239 (t80) cc_final: 0.8909 (t80) REVERT: A 126 PHE cc_start: 0.9374 (t80) cc_final: 0.9011 (t80) outliers start: 11 outliers final: 4 residues processed: 143 average time/residue: 0.0602 time to fit residues: 11.0034 Evaluate side-chains 113 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 266 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.105641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.084082 restraints weight = 14185.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.086874 restraints weight = 8613.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.088949 restraints weight = 6022.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.090472 restraints weight = 4593.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.091552 restraints weight = 3697.717| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4161 Z= 0.145 Angle : 0.842 11.569 5703 Z= 0.377 Chirality : 0.044 0.199 691 Planarity : 0.006 0.077 700 Dihedral : 6.144 51.702 585 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.34 % Favored : 94.47 % Rotamer: Outliers : 3.13 % Allowed : 16.87 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.37), residues: 524 helix: 1.78 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -1.53 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 50 TYR 0.022 0.002 TYR B 17 PHE 0.040 0.002 PHE A 192 TRP 0.006 0.001 TRP A 156 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 4160) covalent geometry : angle 0.84209 / 0.38 ( 5701) SS BOND : bond 0.00283 / 0.18 ( 1) SS BOND : angle 0.97668 / 0.34 ( 2) hydrogen bonds : bond 0.04019 / 2.80 ( 321) hydrogen bonds : angle 3.86123 / 2.95 ( 957) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 LEU cc_start: 0.8184 (mp) cc_final: 0.7804 (tp) REVERT: B 122 PHE cc_start: 0.9297 (t80) cc_final: 0.9052 (t80) REVERT: B 159 MET cc_start: 0.2963 (mmp) cc_final: 0.2740 (mmp) REVERT: B 201 PHE cc_start: 0.9154 (t80) cc_final: 0.8072 (m-80) REVERT: B 228 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8434 (tm-30) REVERT: B 246 LEU cc_start: 0.9504 (mt) cc_final: 0.8970 (mt) REVERT: A 74 ARG cc_start: 0.9163 (mtp85) cc_final: 0.8701 (ttt-90) REVERT: A 120 LYS cc_start: 0.9382 (mttt) cc_final: 0.9105 (mttm) REVERT: A 122 PHE cc_start: 0.9250 (t80) cc_final: 0.8750 (t80) REVERT: A 219 ASP cc_start: 0.7903 (p0) cc_final: 0.7608 (p0) REVERT: A 220 TYR cc_start: 0.8585 (m-80) cc_final: 0.8258 (m-80) outliers start: 13 outliers final: 9 residues processed: 131 average time/residue: 0.0505 time to fit residues: 8.5109 Evaluate side-chains 120 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 266 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 0.0050 chunk 2 optimal weight: 2.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.104516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.082860 restraints weight = 14522.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.085448 restraints weight = 9192.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.087380 restraints weight = 6586.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.088728 restraints weight = 5098.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.089741 restraints weight = 4205.429| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4161 Z= 0.151 Angle : 0.830 10.773 5703 Z= 0.383 Chirality : 0.045 0.285 691 Planarity : 0.005 0.077 700 Dihedral : 5.969 48.883 585 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.15 % Favored : 94.47 % Rotamer: Outliers : 3.37 % Allowed : 22.17 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.37), residues: 524 helix: 1.70 (0.25), residues: 411 sheet: None (None), residues: 0 loop : -1.46 (0.62), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 50 TYR 0.030 0.002 TYR A 17 PHE 0.023 0.002 PHE B 98 TRP 0.007 0.001 TRP A 156 HIS 0.003 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 4160) covalent geometry : angle 0.82940 / 0.38 ( 5701) SS BOND : bond 0.00259 / 0.16 ( 1) SS BOND : angle 1.12904 / 0.41 ( 2) hydrogen bonds : bond 0.03885 / 2.69 ( 321) hydrogen bonds : angle 3.87258 / 2.92 ( 957) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 LEU cc_start: 0.8176 (mp) cc_final: 0.7832 (tp) REVERT: B 122 PHE cc_start: 0.9323 (t80) cc_final: 0.8875 (t80) REVERT: B 212 LEU cc_start: 0.7864 (mt) cc_final: 0.7605 (mt) REVERT: B 228 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8332 (tm-30) REVERT: B 246 LEU cc_start: 0.9425 (mt) cc_final: 0.8990 (mt) REVERT: A 74 ARG cc_start: 0.9120 (mtp85) cc_final: 0.8646 (ttt-90) REVERT: A 120 LYS cc_start: 0.9300 (mttt) cc_final: 0.9098 (mttm) REVERT: A 122 PHE cc_start: 0.9328 (t80) cc_final: 0.8983 (t80) outliers start: 14 outliers final: 9 residues processed: 122 average time/residue: 0.0394 time to fit residues: 6.3147 Evaluate side-chains 124 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 266 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.0050 chunk 37 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.104933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.083602 restraints weight = 14098.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.086193 restraints weight = 8888.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.088070 restraints weight = 6360.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.089450 restraints weight = 4943.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.090453 restraints weight = 4048.427| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4161 Z= 0.137 Angle : 0.876 12.349 5703 Z= 0.385 Chirality : 0.045 0.224 691 Planarity : 0.005 0.075 700 Dihedral : 5.504 46.914 581 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.58 % Favored : 95.04 % Rotamer: Outliers : 3.61 % Allowed : 22.17 % Favored : 74.22 % 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 are not related in a simple way. whole: 1.54 (0.37), residues: 524 helix: 1.73 (0.25), residues: 408 sheet: None (None), residues: 0 loop : -1.58 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 50 TYR 0.019 0.002 TYR A 17 PHE 0.020 0.002 PHE A 209 TRP 0.007 0.001 TRP A 156 HIS 0.002 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 4160) covalent geometry : angle 0.87580 / 0.38 ( 5701) SS BOND : bond 0.00130 / 0.08 ( 1) SS BOND : angle 0.93487 / 0.36 ( 2) hydrogen bonds : bond 0.03701 / 2.53 ( 321) hydrogen bonds : angle 3.76852 / 2.82 ( 957) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 LEU cc_start: 0.8134 (mp) cc_final: 0.7786 (tp) REVERT: B 74 ARG cc_start: 0.9045 (mtp85) cc_final: 0.8614 (mtt180) REVERT: B 201 PHE cc_start: 0.9216 (t80) cc_final: 0.8247 (m-80) REVERT: B 212 LEU cc_start: 0.7863 (mt) cc_final: 0.7416 (mt) REVERT: B 228 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8245 (tm-30) REVERT: B 246 LEU cc_start: 0.9404 (mt) cc_final: 0.8902 (mt) REVERT: A 74 ARG cc_start: 0.9087 (mtp85) cc_final: 0.8609 (ttt-90) REVERT: A 122 PHE cc_start: 0.9308 (t80) cc_final: 0.9048 (t80) REVERT: A 219 ASP cc_start: 0.7753 (p0) cc_final: 0.7342 (p0) REVERT: A 220 TYR cc_start: 0.8520 (m-80) cc_final: 0.8295 (m-80) outliers start: 15 outliers final: 11 residues processed: 128 average time/residue: 0.0341 time to fit residues: 5.8196 Evaluate side-chains 120 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 266 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.103971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.082563 restraints weight = 14410.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.085233 restraints weight = 8789.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.087189 restraints weight = 6170.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.088601 restraints weight = 4703.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.089635 restraints weight = 3829.680| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4161 Z= 0.144 Angle : 0.880 11.867 5703 Z= 0.391 Chirality : 0.047 0.440 691 Planarity : 0.005 0.076 700 Dihedral : 5.494 44.636 581 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.34 % Favored : 94.27 % Rotamer: Outliers : 3.13 % Allowed : 26.99 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.38), residues: 524 helix: 1.73 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -1.53 (0.62), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.018 0.002 TYR B 17 PHE 0.025 0.002 PHE B 122 TRP 0.013 0.001 TRP B 91 HIS 0.002 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 4160) covalent geometry : angle 0.87964 / 0.39 ( 5701) SS BOND : bond 0.00250 / 0.16 ( 1) SS BOND : angle 0.96137 / 0.36 ( 2) hydrogen bonds : bond 0.03659 / 2.50 ( 321) hydrogen bonds : angle 3.85710 / 2.90 ( 957) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 LEU cc_start: 0.8249 (mp) cc_final: 0.7836 (tp) REVERT: B 74 ARG cc_start: 0.9109 (mtp85) cc_final: 0.8720 (mtt180) REVERT: B 212 LEU cc_start: 0.8060 (mt) cc_final: 0.7774 (mt) REVERT: B 228 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8391 (tm-30) REVERT: B 242 LEU cc_start: 0.9549 (tp) cc_final: 0.9318 (tp) REVERT: B 246 LEU cc_start: 0.9499 (mt) cc_final: 0.8833 (mp) REVERT: A 47 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8826 (tt) REVERT: A 74 ARG cc_start: 0.9119 (mtp85) cc_final: 0.8685 (ttt-90) REVERT: A 122 PHE cc_start: 0.9209 (t80) cc_final: 0.8994 (t80) REVERT: A 234 TYR cc_start: 0.9391 (t80) cc_final: 0.8931 (t80) outliers start: 13 outliers final: 9 residues processed: 124 average time/residue: 0.0548 time to fit residues: 8.9707 Evaluate side-chains 118 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 266 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 0.0470 chunk 9 optimal weight: 0.1980 chunk 41 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.8484 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.104122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.082687 restraints weight = 14433.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.085352 restraints weight = 8806.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.087308 restraints weight = 6197.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.088705 restraints weight = 4742.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.089749 restraints weight = 3870.826| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4161 Z= 0.146 Angle : 0.923 12.435 5703 Z= 0.410 Chirality : 0.046 0.273 691 Planarity : 0.005 0.075 700 Dihedral : 5.067 36.443 579 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.34 % Favored : 94.27 % Rotamer: Outliers : 3.61 % Allowed : 27.95 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.38), residues: 524 helix: 1.80 (0.26), residues: 406 sheet: None (None), residues: 0 loop : -1.66 (0.60), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.018 0.001 TYR A 17 PHE 0.026 0.002 PHE B 122 TRP 0.008 0.001 TRP A 91 HIS 0.002 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 4160) covalent geometry : angle 0.92281 / 0.41 ( 5701) SS BOND : bond 0.00203 / 0.13 ( 1) SS BOND : angle 0.87773 / 0.34 ( 2) hydrogen bonds : bond 0.03676 / 2.51 ( 321) hydrogen bonds : angle 3.88906 / 2.92 ( 957) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 LEU cc_start: 0.8279 (mp) cc_final: 0.7875 (tp) REVERT: B 64 GLU cc_start: 0.9755 (tm-30) cc_final: 0.9414 (tm-30) REVERT: B 159 MET cc_start: 0.2895 (mmp) cc_final: 0.2574 (mmt) REVERT: B 201 PHE cc_start: 0.9147 (t80) cc_final: 0.8228 (m-80) REVERT: B 212 LEU cc_start: 0.8104 (mt) cc_final: 0.7871 (mt) REVERT: B 228 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8340 (tm-30) REVERT: B 242 LEU cc_start: 0.9552 (tp) cc_final: 0.9305 (tp) REVERT: B 246 LEU cc_start: 0.9497 (mt) cc_final: 0.8786 (mp) REVERT: A 74 ARG cc_start: 0.9113 (mtp85) cc_final: 0.8662 (ttt-90) REVERT: A 122 PHE cc_start: 0.9225 (t80) cc_final: 0.9010 (t80) REVERT: A 219 ASP cc_start: 0.7751 (p0) cc_final: 0.7459 (p0) REVERT: A 234 TYR cc_start: 0.9405 (t80) cc_final: 0.8947 (t80) REVERT: A 254 GLN cc_start: 0.9468 (tt0) cc_final: 0.9199 (tm-30) outliers start: 15 outliers final: 9 residues processed: 123 average time/residue: 0.0345 time to fit residues: 5.7219 Evaluate side-chains 114 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 266 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.098677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.077072 restraints weight = 15033.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.079702 restraints weight = 9560.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.081220 restraints weight = 6877.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.082857 restraints weight = 5485.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.083777 restraints weight = 4515.477| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4161 Z= 0.168 Angle : 0.949 14.241 5703 Z= 0.427 Chirality : 0.049 0.455 691 Planarity : 0.005 0.076 700 Dihedral : 5.157 35.776 579 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.92 % Favored : 93.70 % Rotamer: Outliers : 4.10 % Allowed : 28.43 % Favored : 67.47 % 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: 1.54 (0.38), residues: 524 helix: 1.75 (0.26), residues: 407 sheet: None (None), residues: 0 loop : -1.63 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.019 0.002 TYR A 17 PHE 0.028 0.002 PHE B 122 TRP 0.010 0.001 TRP A 91 HIS 0.002 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 4160) covalent geometry : angle 0.94920 / 0.43 ( 5701) SS BOND : bond 0.00197 / 0.12 ( 1) SS BOND : angle 0.92211 / 0.34 ( 2) hydrogen bonds : bond 0.03867 / 2.61 ( 321) hydrogen bonds : angle 4.01346 / 3.03 ( 957) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.148 Fit side-chains REVERT: B 20 LEU cc_start: 0.8391 (mp) cc_final: 0.7937 (tp) REVERT: B 64 GLU cc_start: 0.9730 (tm-30) cc_final: 0.9394 (tm-30) REVERT: B 74 ARG cc_start: 0.9124 (mtp85) cc_final: 0.8708 (mtt180) REVERT: B 102 THR cc_start: 0.9474 (p) cc_final: 0.9192 (t) REVERT: B 212 LEU cc_start: 0.8208 (mt) cc_final: 0.8001 (mt) REVERT: B 228 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8346 (tm-30) REVERT: B 242 LEU cc_start: 0.9548 (tp) cc_final: 0.9302 (tp) REVERT: B 246 LEU cc_start: 0.9507 (mt) cc_final: 0.8825 (mp) REVERT: A 74 ARG cc_start: 0.9118 (mtp85) cc_final: 0.8640 (ttt-90) REVERT: A 122 PHE cc_start: 0.9259 (t80) cc_final: 0.9054 (t80) REVERT: A 234 TYR cc_start: 0.9432 (t80) cc_final: 0.9000 (t80) REVERT: A 254 GLN cc_start: 0.9482 (tt0) cc_final: 0.9193 (tm-30) outliers start: 17 outliers final: 10 residues processed: 123 average time/residue: 0.0403 time to fit residues: 6.7257 Evaluate side-chains 121 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 241 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 10 optimal weight: 0.0370 chunk 51 optimal weight: 0.4980 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.0170 chunk 50 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.102391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.081788 restraints weight = 13994.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.084389 restraints weight = 8539.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.086283 restraints weight = 5996.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.087623 restraints weight = 4603.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.088623 restraints weight = 3747.305| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4161 Z= 0.152 Angle : 1.042 16.689 5703 Z= 0.447 Chirality : 0.049 0.345 691 Planarity : 0.005 0.075 700 Dihedral : 5.051 37.361 578 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.53 % Favored : 94.08 % Rotamer: Outliers : 2.41 % Allowed : 31.57 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.38), residues: 524 helix: 1.76 (0.26), residues: 405 sheet: None (None), residues: 0 loop : -1.68 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.018 0.001 TYR A 17 PHE 0.025 0.002 PHE B 209 TRP 0.004 0.000 TRP A 156 HIS 0.002 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 4160) covalent geometry : angle 1.04177 / 0.45 ( 5701) SS BOND : bond 0.00176 / 0.11 ( 1) SS BOND : angle 1.05654 / 0.41 ( 2) hydrogen bonds : bond 0.03901 / 2.66 ( 321) hydrogen bonds : angle 3.95868 / 2.99 ( 957) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 LEU cc_start: 0.8356 (mp) cc_final: 0.8042 (tt) REVERT: B 64 GLU cc_start: 0.9731 (tm-30) cc_final: 0.9391 (tm-30) REVERT: B 105 THR cc_start: 0.9686 (OUTLIER) cc_final: 0.9444 (t) REVERT: B 159 MET cc_start: 0.2915 (mmp) cc_final: 0.2563 (mmt) REVERT: B 192 PHE cc_start: 0.9617 (m-80) cc_final: 0.9282 (m-80) REVERT: B 201 PHE cc_start: 0.9147 (t80) cc_final: 0.8250 (m-80) REVERT: B 212 LEU cc_start: 0.8130 (mt) cc_final: 0.7918 (mt) REVERT: B 228 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8300 (tm-30) REVERT: B 242 LEU cc_start: 0.9529 (tp) cc_final: 0.9276 (tp) REVERT: B 246 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.8733 (mp) REVERT: A 74 ARG cc_start: 0.9086 (mtp85) cc_final: 0.8617 (ttt-90) REVERT: A 122 PHE cc_start: 0.9235 (t80) cc_final: 0.9032 (t80) REVERT: A 234 TYR cc_start: 0.9410 (t80) cc_final: 0.8962 (t80) REVERT: A 254 GLN cc_start: 0.9487 (tt0) cc_final: 0.9175 (tm-30) outliers start: 10 outliers final: 7 residues processed: 120 average time/residue: 0.0434 time to fit residues: 6.9555 Evaluate side-chains 120 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 241 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 9.9990 chunk 31 optimal weight: 0.0170 chunk 47 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.0010 chunk 11 optimal weight: 0.8980 overall best weight: 0.4824 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.098834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.077968 restraints weight = 14547.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.080609 restraints weight = 9089.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.082521 restraints weight = 6476.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.083884 restraints weight = 5004.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.084938 restraints weight = 4124.015| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4161 Z= 0.157 Angle : 1.052 16.294 5703 Z= 0.454 Chirality : 0.050 0.421 691 Planarity : 0.005 0.075 700 Dihedral : 5.001 36.212 578 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.15 % Favored : 94.47 % Rotamer: Outliers : 2.17 % Allowed : 33.73 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.38), residues: 524 helix: 1.75 (0.26), residues: 404 sheet: None (None), residues: 0 loop : -1.76 (0.61), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.015 0.001 TYR A 17 PHE 0.027 0.002 PHE B 122 TRP 0.010 0.001 TRP B 91 HIS 0.001 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 4160) covalent geometry : angle 1.05197 / 0.45 ( 5701) SS BOND : bond 0.00109 / 0.07 ( 1) SS BOND : angle 1.10134 / 0.43 ( 2) hydrogen bonds : bond 0.03956 / 2.74 ( 321) hydrogen bonds : angle 3.97194 / 3.00 ( 957) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.138 Fit side-chains REVERT: B 20 LEU cc_start: 0.8323 (mp) cc_final: 0.8036 (tt) REVERT: B 64 GLU cc_start: 0.9729 (tm-30) cc_final: 0.9382 (tm-30) REVERT: B 74 ARG cc_start: 0.9080 (mtp85) cc_final: 0.8668 (mtt180) REVERT: B 105 THR cc_start: 0.9675 (OUTLIER) cc_final: 0.9424 (t) REVERT: B 228 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8274 (tm-30) REVERT: B 242 LEU cc_start: 0.9518 (tp) cc_final: 0.9274 (tp) REVERT: B 246 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.8736 (mp) REVERT: A 74 ARG cc_start: 0.9088 (mtp85) cc_final: 0.8605 (ttt-90) REVERT: A 234 TYR cc_start: 0.9391 (t80) cc_final: 0.8962 (t80) REVERT: A 254 GLN cc_start: 0.9494 (tt0) cc_final: 0.9179 (tm-30) outliers start: 9 outliers final: 6 residues processed: 114 average time/residue: 0.0536 time to fit residues: 8.1496 Evaluate side-chains 115 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.0060 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.0030 overall best weight: 0.5408 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.102140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.081433 restraints weight = 13767.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.083981 restraints weight = 8464.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.085869 restraints weight = 5965.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.087201 restraints weight = 4553.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.088210 restraints weight = 3721.006| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4161 Z= 0.167 Angle : 1.086 16.734 5703 Z= 0.475 Chirality : 0.052 0.444 691 Planarity : 0.005 0.075 700 Dihedral : 5.070 36.346 578 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.96 % Favored : 94.66 % Rotamer: Outliers : 2.17 % Allowed : 33.73 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.38), residues: 524 helix: 1.64 (0.26), residues: 404 sheet: None (None), residues: 0 loop : -1.83 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.018 0.002 TYR A 17 PHE 0.043 0.002 PHE A 122 TRP 0.009 0.001 TRP B 91 HIS 0.002 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 4160) covalent geometry : angle 1.08563 / 0.47 ( 5701) SS BOND : bond 0.00066 / 0.04 ( 1) SS BOND : angle 0.93813 / 0.36 ( 2) hydrogen bonds : bond 0.04060 / 2.82 ( 321) hydrogen bonds : angle 3.98028 / 2.99 ( 957) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.085 Fit side-chains REVERT: B 20 LEU cc_start: 0.8301 (mp) cc_final: 0.8021 (tt) REVERT: B 64 GLU cc_start: 0.9732 (tm-30) cc_final: 0.9394 (tm-30) REVERT: B 74 ARG cc_start: 0.9104 (mtp85) cc_final: 0.8681 (mtt180) REVERT: B 105 THR cc_start: 0.9684 (OUTLIER) cc_final: 0.9464 (t) REVERT: B 159 MET cc_start: 0.3087 (mmp) cc_final: 0.2703 (mmt) REVERT: B 228 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8258 (tm-30) REVERT: B 242 LEU cc_start: 0.9505 (tp) cc_final: 0.9289 (tp) REVERT: B 246 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.8911 (mp) REVERT: A 42 THR cc_start: 0.9033 (m) cc_final: 0.8779 (p) REVERT: A 74 ARG cc_start: 0.9074 (mtp85) cc_final: 0.8610 (ttt-90) REVERT: A 234 TYR cc_start: 0.9404 (t80) cc_final: 0.9007 (t80) REVERT: A 254 GLN cc_start: 0.9504 (tt0) cc_final: 0.9164 (tm-30) outliers start: 9 outliers final: 7 residues processed: 114 average time/residue: 0.0338 time to fit residues: 5.1416 Evaluate side-chains 116 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 0.0000 chunk 21 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.101542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.081519 restraints weight = 14086.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.084040 restraints weight = 8535.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.085889 restraints weight = 5996.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.087184 restraints weight = 4591.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.088182 restraints weight = 3756.341| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 4161 Z= 0.166 Angle : 1.064 16.524 5703 Z= 0.468 Chirality : 0.051 0.440 691 Planarity : 0.005 0.075 700 Dihedral : 5.009 36.051 578 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.96 % Favored : 94.66 % Rotamer: Outliers : 2.17 % Allowed : 33.73 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.38), residues: 524 helix: 1.60 (0.26), residues: 404 sheet: None (None), residues: 0 loop : -1.79 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.016 0.002 TYR A 17 PHE 0.036 0.002 PHE A 122 TRP 0.009 0.001 TRP B 91 HIS 0.001 0.000 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 4160) covalent geometry : angle 1.06445 / 0.47 ( 5701) SS BOND : bond 0.00091 / 0.06 ( 1) SS BOND : angle 0.99251 / 0.38 ( 2) hydrogen bonds : bond 0.04007 / 2.77 ( 321) hydrogen bonds : angle 3.96850 / 2.99 ( 957) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 818.37 seconds wall clock time: 14 minutes 44.27 seconds (884.27 seconds total)