Starting phenix.real_space_refine on Sat Apr 4 21:35:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m9w_63742/04_2026/9m9w_63742.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m9w_63742/04_2026/9m9w_63742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m9w_63742/04_2026/9m9w_63742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m9w_63742/04_2026/9m9w_63742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m9w_63742/04_2026/9m9w_63742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m9w_63742/04_2026/9m9w_63742.map" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 2664 2.51 5 N 672 2.21 5 O 697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4059 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2041 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 250} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2018 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 248} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.13, per 1000 atoms: 0.28 Number of scatterers: 4059 At special positions: 0 Unit cell: (81.608, 67.872, 88.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 697 8.00 N 672 7.00 C 2664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 161.3 milliseconds 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 944 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 81.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 14 through 61 removed outlier: 3.788A pdb=" N LEU A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 removed outlier: 3.567A pdb=" N PHE A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.756A pdb=" N TYR A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 164 removed outlier: 3.531A pdb=" N VAL A 133 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 221 Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 253 through 293 removed outlier: 3.729A pdb=" N LYS A 293 " --> pdb=" O TRP A 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 42 removed outlier: 3.609A pdb=" N LEU B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 64 removed outlier: 3.504A pdb=" N HIS B 64 " --> pdb=" O PHE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 85 Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.826A pdb=" N TYR B 102 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 163 removed outlier: 3.806A pdb=" N SER B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 221 Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 223 through 236 Processing helix chain 'B' and resid 253 through 291 335 hydrogen bonds defined for protein. 1005 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: 0.70 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1251 1.34 - 1.46: 808 1.46 - 1.57: 2066 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 4161 Sorted by residual: bond pdb=" CG GLU A 55 " pdb=" CD GLU A 55 " ideal model delta sigma weight residual 1.516 1.474 0.042 2.50e-02 1.60e+03 2.81e+00 bond pdb=" CB LYS A 191 " pdb=" CG LYS A 191 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.02e+00 bond pdb=" CB GLU B 55 " pdb=" CG GLU B 55 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CG LYS A 191 " pdb=" CD LYS A 191 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.36e+00 bond pdb=" CB LYS B 191 " pdb=" CG LYS B 191 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.16e+00 ... (remaining 4156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 5447 1.56 - 3.12: 139 3.12 - 4.68: 25 4.68 - 6.24: 16 6.24 - 7.79: 6 Bond angle restraints: 5633 Sorted by residual: angle pdb=" CA GLU A 55 " pdb=" CB GLU A 55 " pdb=" CG GLU A 55 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+01 angle pdb=" CA LYS A 191 " pdb=" CB LYS A 191 " pdb=" CG LYS A 191 " ideal model delta sigma weight residual 114.10 121.33 -7.23 2.00e+00 2.50e-01 1.31e+01 angle pdb=" N GLU A 55 " pdb=" CA GLU A 55 " pdb=" CB GLU A 55 " ideal model delta sigma weight residual 110.39 116.23 -5.84 1.66e+00 3.63e-01 1.24e+01 angle pdb=" N GLY B 134 " pdb=" CA GLY B 134 " pdb=" C GLY B 134 " ideal model delta sigma weight residual 112.49 116.52 -4.03 1.21e+00 6.83e-01 1.11e+01 angle pdb=" CB LYS A 191 " pdb=" CG LYS A 191 " pdb=" CD LYS A 191 " ideal model delta sigma weight residual 111.30 118.94 -7.64 2.30e+00 1.89e-01 1.10e+01 ... (remaining 5628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 2052 17.69 - 35.38: 238 35.38 - 53.07: 81 53.07 - 70.76: 13 70.76 - 88.45: 1 Dihedral angle restraints: 2385 sinusoidal: 911 harmonic: 1474 Sorted by residual: dihedral pdb=" CA TRP A 95 " pdb=" C TRP A 95 " pdb=" N ASP A 96 " pdb=" CA ASP A 96 " ideal model delta harmonic sigma weight residual 180.00 160.91 19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA LEU A 43 " pdb=" C LEU A 43 " pdb=" N ALA A 44 " pdb=" CA ALA A 44 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP A 242 " pdb=" CB ASP A 242 " pdb=" CG ASP A 242 " pdb=" OD1 ASP A 242 " ideal model delta sinusoidal sigma weight residual -30.00 -89.81 59.81 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 2382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 458 0.039 - 0.078: 141 0.078 - 0.117: 24 0.117 - 0.156: 5 0.156 - 0.195: 2 Chirality restraints: 630 Sorted by residual: chirality pdb=" CA GLU A 55 " pdb=" N GLU A 55 " pdb=" C GLU A 55 " pdb=" CB GLU A 55 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CG LEU B 75 " pdb=" CB LEU B 75 " pdb=" CD1 LEU B 75 " pdb=" CD2 LEU B 75 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CA GLU A 42 " pdb=" N GLU A 42 " pdb=" C GLU A 42 " pdb=" CB GLU A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 627 not shown) Planarity restraints: 696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 216 " -0.015 2.00e-02 2.50e+03 2.17e-02 9.44e+00 pdb=" CG TYR B 216 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR B 216 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 216 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR B 216 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 216 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 216 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 216 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 45 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.09e+00 pdb=" C HIS B 45 " -0.046 2.00e-02 2.50e+03 pdb=" O HIS B 45 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU B 46 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 92 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 93 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.031 5.00e-02 4.00e+02 ... (remaining 693 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 124 2.71 - 3.25: 4541 3.25 - 3.80: 6869 3.80 - 4.35: 8313 4.35 - 4.90: 13732 Nonbonded interactions: 33579 Sorted by model distance: nonbonded pdb=" OE2 GLU A 220 " pdb=" OH TYR A 257 " model vdw 2.158 3.040 nonbonded pdb=" O SER B 245 " pdb=" NE2 GLN B 247 " model vdw 2.172 3.120 nonbonded pdb=" O VAL B 108 " pdb=" OG1 THR B 138 " model vdw 2.176 3.040 nonbonded pdb=" OH TYR A 273 " pdb=" OH TYR B 273 " model vdw 2.224 3.040 nonbonded pdb=" O SER A 245 " pdb=" NE2 GLN A 247 " model vdw 2.244 3.120 ... (remaining 33574 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 14 through 163 or resid 191 through 293)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.580 Find NCS groups from input model: 0.170 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:7.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 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 0.043 4161 Z= 0.174 Angle : 0.694 7.795 5633 Z= 0.394 Chirality : 0.039 0.195 630 Planarity : 0.005 0.056 696 Dihedral : 17.001 88.446 1441 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.20 % Favored : 96.20 % Rotamer: Outliers : 2.33 % Allowed : 26.05 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.38), residues: 500 helix: 1.99 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -1.58 (0.66), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 52 TYR 0.053 0.003 TYR B 216 PHE 0.022 0.002 PHE A 235 TRP 0.015 0.001 TRP A 53 HIS 0.016 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 4161) covalent geometry : angle 0.69382 ( 5633) hydrogen bonds : bond 0.17402 ( 335) hydrogen bonds : angle 6.45516 ( 1005) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.147 Fit side-chains REVERT: A 91 VAL cc_start: 0.7040 (m) cc_final: 0.6783 (t) REVERT: A 235 PHE cc_start: 0.8193 (m-10) cc_final: 0.7989 (m-10) REVERT: B 52 ARG cc_start: 0.7268 (ttp80) cc_final: 0.7038 (ttp80) REVERT: B 106 THR cc_start: 0.7722 (p) cc_final: 0.7493 (m) REVERT: B 215 MET cc_start: 0.7560 (ttp) cc_final: 0.7212 (ttp) outliers start: 10 outliers final: 4 residues processed: 97 average time/residue: 0.5217 time to fit residues: 52.2550 Evaluate side-chains 84 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.177589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.161926 restraints weight = 5587.872| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.08 r_work: 0.3970 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4161 Z= 0.214 Angle : 0.619 5.563 5633 Z= 0.349 Chirality : 0.043 0.193 630 Planarity : 0.005 0.055 696 Dihedral : 6.414 54.763 567 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.00 % Favored : 96.40 % Rotamer: Outliers : 6.51 % Allowed : 22.33 % Favored : 71.16 % 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 (0.37), residues: 500 helix: 1.72 (0.24), residues: 395 sheet: None (None), residues: 0 loop : -1.98 (0.61), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 56 TYR 0.040 0.003 TYR B 216 PHE 0.014 0.002 PHE A 230 TRP 0.014 0.002 TRP A 53 HIS 0.009 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 4161) covalent geometry : angle 0.61913 ( 5633) hydrogen bonds : bond 0.05803 ( 335) hydrogen bonds : angle 4.99018 ( 1005) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.115 Fit side-chains REVERT: A 79 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.7005 (mm-30) REVERT: A 156 ILE cc_start: 0.7464 (mm) cc_final: 0.7235 (mm) REVERT: A 235 PHE cc_start: 0.8518 (m-10) cc_final: 0.8215 (m-10) REVERT: B 27 ILE cc_start: 0.5689 (mt) cc_final: 0.5347 (mt) REVERT: B 52 ARG cc_start: 0.7422 (ttp80) cc_final: 0.7142 (ttp80) REVERT: B 146 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7401 (mp) REVERT: B 201 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7940 (mt) REVERT: B 215 MET cc_start: 0.8333 (ttp) cc_final: 0.8064 (ttp) outliers start: 28 outliers final: 8 residues processed: 105 average time/residue: 0.5368 time to fit residues: 58.1527 Evaluate side-chains 94 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 281 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.0670 chunk 5 optimal weight: 0.0070 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.179918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.164131 restraints weight = 5602.533| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.08 r_work: 0.4004 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3844 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4161 Z= 0.148 Angle : 0.538 5.385 5633 Z= 0.303 Chirality : 0.040 0.182 630 Planarity : 0.005 0.052 696 Dihedral : 5.903 57.691 565 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.60 % Favored : 96.80 % Rotamer: Outliers : 6.51 % Allowed : 22.56 % Favored : 70.93 % 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 (0.37), residues: 500 helix: 1.92 (0.25), residues: 395 sheet: None (None), residues: 0 loop : -2.00 (0.60), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 56 TYR 0.028 0.002 TYR B 216 PHE 0.012 0.001 PHE A 60 TRP 0.012 0.001 TRP A 53 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 4161) covalent geometry : angle 0.53796 ( 5633) hydrogen bonds : bond 0.04926 ( 335) hydrogen bonds : angle 4.67347 ( 1005) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.5501 (tt) REVERT: A 156 ILE cc_start: 0.7439 (mm) cc_final: 0.7227 (mm) REVERT: A 235 PHE cc_start: 0.8592 (m-10) cc_final: 0.8277 (m-10) REVERT: B 52 ARG cc_start: 0.7412 (ttp80) cc_final: 0.7083 (ttp80) REVERT: B 86 ILE cc_start: 0.8123 (mm) cc_final: 0.7874 (tt) REVERT: B 201 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7905 (mt) REVERT: B 215 MET cc_start: 0.8313 (ttp) cc_final: 0.8079 (ttp) outliers start: 28 outliers final: 15 residues processed: 96 average time/residue: 0.5421 time to fit residues: 53.6962 Evaluate side-chains 97 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 0.0470 chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.179919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.163570 restraints weight = 5551.211| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.14 r_work: 0.3996 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.2926 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= 0.152 Angle : 0.533 5.575 5633 Z= 0.299 Chirality : 0.040 0.179 630 Planarity : 0.005 0.057 696 Dihedral : 5.896 59.352 565 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.20 % Favored : 96.20 % Rotamer: Outliers : 6.05 % Allowed : 23.26 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.37), residues: 500 helix: 2.00 (0.25), residues: 395 sheet: None (None), residues: 0 loop : -2.01 (0.60), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 56 TYR 0.021 0.001 TYR B 216 PHE 0.010 0.001 PHE A 60 TRP 0.013 0.001 TRP A 53 HIS 0.003 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4161) covalent geometry : angle 0.53277 ( 5633) hydrogen bonds : bond 0.04715 ( 335) hydrogen bonds : angle 4.56932 ( 1005) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7651 (mtm110) REVERT: B 52 ARG cc_start: 0.7331 (ttp80) cc_final: 0.7031 (ttp80) outliers start: 26 outliers final: 13 residues processed: 95 average time/residue: 0.5408 time to fit residues: 53.0507 Evaluate side-chains 86 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 0.0670 chunk 23 optimal weight: 0.3980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.180539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.164250 restraints weight = 5538.356| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 2.06 r_work: 0.3999 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4161 Z= 0.151 Angle : 0.529 5.332 5633 Z= 0.298 Chirality : 0.040 0.198 630 Planarity : 0.005 0.065 696 Dihedral : 5.816 58.931 565 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.00 % Favored : 96.40 % Rotamer: Outliers : 5.12 % Allowed : 23.72 % Favored : 71.16 % 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: 1.91 (0.37), residues: 500 helix: 2.10 (0.25), residues: 393 sheet: None (None), residues: 0 loop : -2.04 (0.59), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 87 TYR 0.021 0.002 TYR B 30 PHE 0.013 0.001 PHE A 235 TRP 0.012 0.001 TRP A 53 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4161) covalent geometry : angle 0.52854 ( 5633) hydrogen bonds : bond 0.04678 ( 335) hydrogen bonds : angle 4.50381 ( 1005) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7816 (ttpt) REVERT: B 52 ARG cc_start: 0.7410 (ttp80) cc_final: 0.7096 (ttp80) outliers start: 22 outliers final: 14 residues processed: 91 average time/residue: 0.5652 time to fit residues: 53.0941 Evaluate side-chains 89 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 0.0050 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.181018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.164706 restraints weight = 5620.903| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.10 r_work: 0.4005 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4161 Z= 0.147 Angle : 0.538 5.906 5633 Z= 0.298 Chirality : 0.041 0.228 630 Planarity : 0.005 0.069 696 Dihedral : 5.777 57.164 565 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.80 % Favored : 96.60 % Rotamer: Outliers : 4.88 % Allowed : 24.88 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.37), residues: 500 helix: 2.08 (0.25), residues: 397 sheet: None (None), residues: 0 loop : -1.93 (0.62), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 56 TYR 0.026 0.002 TYR B 30 PHE 0.010 0.001 PHE B 103 TRP 0.011 0.001 TRP A 53 HIS 0.002 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4161) covalent geometry : angle 0.53847 ( 5633) hydrogen bonds : bond 0.04531 ( 335) hydrogen bonds : angle 4.48756 ( 1005) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7665 (ttpt) REVERT: B 52 ARG cc_start: 0.7295 (ttp80) cc_final: 0.7028 (ttp80) outliers start: 21 outliers final: 13 residues processed: 87 average time/residue: 0.5234 time to fit residues: 47.0746 Evaluate side-chains 88 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN B 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.178815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.162573 restraints weight = 5612.013| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.12 r_work: 0.3975 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4161 Z= 0.191 Angle : 0.584 6.320 5633 Z= 0.323 Chirality : 0.042 0.241 630 Planarity : 0.004 0.050 696 Dihedral : 5.940 57.025 565 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.60 % Favored : 96.00 % Rotamer: Outliers : 3.72 % Allowed : 26.51 % Favored : 69.77 % 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: 1.64 (0.37), residues: 500 helix: 1.88 (0.25), residues: 395 sheet: None (None), residues: 0 loop : -2.11 (0.59), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 56 TYR 0.025 0.002 TYR B 30 PHE 0.012 0.002 PHE A 230 TRP 0.013 0.001 TRP A 53 HIS 0.002 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 4161) covalent geometry : angle 0.58381 ( 5633) hydrogen bonds : bond 0.04931 ( 335) hydrogen bonds : angle 4.65732 ( 1005) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7803 (ttpt) REVERT: B 261 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.7064 (t160) outliers start: 16 outliers final: 10 residues processed: 85 average time/residue: 0.5854 time to fit residues: 51.2621 Evaluate side-chains 88 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 261 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 22 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.180797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.164552 restraints weight = 5533.211| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 2.11 r_work: 0.3992 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4161 Z= 0.171 Angle : 0.584 8.174 5633 Z= 0.321 Chirality : 0.043 0.249 630 Planarity : 0.005 0.058 696 Dihedral : 5.878 55.493 565 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.00 % Favored : 95.60 % Rotamer: Outliers : 3.95 % Allowed : 26.98 % Favored : 69.07 % 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: 1.73 (0.37), residues: 500 helix: 1.93 (0.25), residues: 396 sheet: None (None), residues: 0 loop : -2.03 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 56 TYR 0.024 0.001 TYR B 30 PHE 0.011 0.001 PHE A 230 TRP 0.013 0.001 TRP A 53 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4161) covalent geometry : angle 0.58390 ( 5633) hydrogen bonds : bond 0.04755 ( 335) hydrogen bonds : angle 4.59558 ( 1005) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7752 (ttpt) REVERT: B 27 ILE cc_start: 0.5643 (mt) cc_final: 0.5405 (mt) REVERT: B 261 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.7115 (t160) outliers start: 17 outliers final: 11 residues processed: 86 average time/residue: 0.5822 time to fit residues: 51.6820 Evaluate side-chains 88 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 261 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.181177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.164952 restraints weight = 5595.909| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.13 r_work: 0.4002 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4161 Z= 0.163 Angle : 0.596 9.669 5633 Z= 0.324 Chirality : 0.043 0.257 630 Planarity : 0.005 0.049 696 Dihedral : 5.828 53.804 565 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.60 % Favored : 96.00 % Rotamer: Outliers : 3.26 % Allowed : 28.14 % 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: 1.78 (0.37), residues: 500 helix: 1.95 (0.25), residues: 397 sheet: None (None), residues: 0 loop : -1.97 (0.60), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 56 TYR 0.023 0.001 TYR B 30 PHE 0.011 0.001 PHE A 230 TRP 0.012 0.001 TRP A 53 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4161) covalent geometry : angle 0.59627 ( 5633) hydrogen bonds : bond 0.04655 ( 335) hydrogen bonds : angle 4.55530 ( 1005) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7743 (ttpt) REVERT: B 261 ASN cc_start: 0.7503 (OUTLIER) cc_final: 0.7078 (t160) outliers start: 14 outliers final: 10 residues processed: 84 average time/residue: 0.5684 time to fit residues: 49.1963 Evaluate side-chains 89 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 261 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 0.0670 chunk 33 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.181536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.165413 restraints weight = 5481.483| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 2.10 r_work: 0.4008 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4161 Z= 0.167 Angle : 0.608 12.134 5633 Z= 0.327 Chirality : 0.044 0.266 630 Planarity : 0.006 0.080 696 Dihedral : 5.832 52.534 565 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.60 % Favored : 96.00 % Rotamer: Outliers : 3.26 % Allowed : 28.60 % Favored : 68.14 % 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: 1.79 (0.37), residues: 500 helix: 1.96 (0.25), residues: 395 sheet: None (None), residues: 0 loop : -1.95 (0.60), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 52 TYR 0.023 0.001 TYR B 30 PHE 0.011 0.001 PHE A 230 TRP 0.014 0.001 TRP A 53 HIS 0.003 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4161) covalent geometry : angle 0.60830 ( 5633) hydrogen bonds : bond 0.04690 ( 335) hydrogen bonds : angle 4.55471 ( 1005) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7747 (ttpt) REVERT: B 261 ASN cc_start: 0.7496 (OUTLIER) cc_final: 0.7081 (t160) outliers start: 14 outliers final: 11 residues processed: 83 average time/residue: 0.5412 time to fit residues: 46.4738 Evaluate side-chains 87 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 261 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.179343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.162838 restraints weight = 5501.733| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.17 r_work: 0.3974 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4161 Z= 0.211 Angle : 0.640 11.233 5633 Z= 0.344 Chirality : 0.046 0.283 630 Planarity : 0.005 0.050 696 Dihedral : 5.957 51.909 565 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.20 % Favored : 95.40 % Rotamer: Outliers : 3.26 % Allowed : 28.60 % Favored : 68.14 % 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: 1.55 (0.37), residues: 500 helix: 1.78 (0.25), residues: 396 sheet: None (None), residues: 0 loop : -2.01 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 52 TYR 0.026 0.001 TYR B 30 PHE 0.013 0.002 PHE A 230 TRP 0.014 0.001 TRP A 53 HIS 0.005 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 4161) covalent geometry : angle 0.64022 ( 5633) hydrogen bonds : bond 0.05023 ( 335) hydrogen bonds : angle 4.68396 ( 1005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1541.17 seconds wall clock time: 26 minutes 58.19 seconds (1618.19 seconds total)