Starting phenix.real_space_refine on Tue Feb 3 15:28:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ls0_63349/02_2026/9ls0_63349.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ls0_63349/02_2026/9ls0_63349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ls0_63349/02_2026/9ls0_63349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ls0_63349/02_2026/9ls0_63349.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ls0_63349/02_2026/9ls0_63349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ls0_63349/02_2026/9ls0_63349.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 22 5.16 5 C 2677 2.51 5 N 765 2.21 5 O 816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4280 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2182 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 2, 'TRANS': 278} Chain: "B" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2098 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 9, 'TRANS': 234} Chain breaks: 1 Time building chain proxies: 1.27, per 1000 atoms: 0.30 Number of scatterers: 4280 At special positions: 0 Unit cell: (100.57, 76.84, 171.76, 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 22 16.00 O 816 8.00 N 765 7.00 C 2677 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: 0.36 Conformation dependent library (CDL) restraints added in 148.5 milliseconds 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1014 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 79.4% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 42 through 98 removed outlier: 3.943A pdb=" N GLU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 128 removed outlier: 3.698A pdb=" N GLU A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 243 removed outlier: 3.951A pdb=" N GLY A 197 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 274 removed outlier: 4.338A pdb=" N SER A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 281 removed outlier: 3.535A pdb=" N ARG A 279 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 42 Processing helix chain 'B' and resid 51 through 57 removed outlier: 4.634A pdb=" N GLN B 55 " --> pdb=" O ASN B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 61 through 99 Processing helix chain 'B' and resid 107 through 146 removed outlier: 3.625A pdb=" N LYS B 111 " --> pdb=" O TRP B 107 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 146 " --> pdb=" O ASN B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 154 Processing helix chain 'B' and resid 155 through 176 Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.828A pdb=" N THR B 182 " --> pdb=" O ASN B 178 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Proline residue: B 184 - end of helix Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 198 through 220 removed outlier: 3.888A pdb=" N HIS B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 246 Processing helix chain 'B' and resid 249 through 263 Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 152 removed outlier: 4.300A pdb=" N MET A 149 " --> pdb=" O VAL A 163 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 999 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: 0.73 Time building geometry restraints manager: 0.47 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: 1447 1.34 - 1.46: 926 1.46 - 1.58: 1932 1.58 - 1.70: 0 1.70 - 1.82: 43 Bond restraints: 4348 Sorted by residual: bond pdb=" CB ARG A 60 " pdb=" CG ARG A 60 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" C TYR B 199 " pdb=" N PRO B 200 " ideal model delta sigma weight residual 1.335 1.347 -0.013 1.28e-02 6.10e+03 9.64e-01 bond pdb=" CG ARG A 219 " pdb=" CD ARG A 219 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.31e-01 bond pdb=" CB THR A 244 " pdb=" CG2 THR A 244 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.77e-01 bond pdb=" CG ARG A 255 " pdb=" CD ARG A 255 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.02e-01 ... (remaining 4343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 5789 1.90 - 3.81: 45 3.81 - 5.71: 5 5.71 - 7.62: 2 7.62 - 9.52: 2 Bond angle restraints: 5843 Sorted by residual: angle pdb=" CB MET B 225 " pdb=" CG MET B 225 " pdb=" SD MET B 225 " ideal model delta sigma weight residual 112.70 122.22 -9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CB MET B 84 " pdb=" CG MET B 84 " pdb=" SD MET B 84 " ideal model delta sigma weight residual 112.70 122.13 -9.43 3.00e+00 1.11e-01 9.87e+00 angle pdb=" CB MET A 266 " pdb=" CG MET A 266 " pdb=" SD MET A 266 " ideal model delta sigma weight residual 112.70 120.13 -7.43 3.00e+00 1.11e-01 6.14e+00 angle pdb=" CA MET B 225 " pdb=" CB MET B 225 " pdb=" CG MET B 225 " ideal model delta sigma weight residual 114.10 118.76 -4.66 2.00e+00 2.50e-01 5.43e+00 angle pdb=" N TYR B 199 " pdb=" CA TYR B 199 " pdb=" C TYR B 199 " ideal model delta sigma weight residual 109.81 114.76 -4.95 2.21e+00 2.05e-01 5.02e+00 ... (remaining 5838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2260 17.94 - 35.88: 324 35.88 - 53.82: 90 53.82 - 71.76: 17 71.76 - 89.70: 8 Dihedral angle restraints: 2699 sinusoidal: 1140 harmonic: 1559 Sorted by residual: dihedral pdb=" CA ASN A 156 " pdb=" C ASN A 156 " pdb=" N MET A 157 " pdb=" CA MET A 157 " ideal model delta harmonic sigma weight residual -180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA GLN B 177 " pdb=" CB GLN B 177 " pdb=" CG GLN B 177 " pdb=" CD GLN B 177 " ideal model delta sinusoidal sigma weight residual -180.00 -120.15 -59.85 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 168 " pdb=" CG MET A 168 " pdb=" SD MET A 168 " pdb=" CE MET A 168 " ideal model delta sinusoidal sigma weight residual 180.00 121.08 58.92 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 329 0.024 - 0.047: 183 0.047 - 0.071: 83 0.071 - 0.094: 21 0.094 - 0.118: 17 Chirality restraints: 633 Sorted by residual: chirality pdb=" CA TYR B 199 " pdb=" N TYR B 199 " pdb=" C TYR B 199 " pdb=" CB TYR B 199 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA LEU B 179 " pdb=" N LEU B 179 " pdb=" C LEU B 179 " pdb=" CB LEU B 179 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.37e-01 chirality pdb=" CA ILE B 147 " pdb=" N ILE B 147 " pdb=" C ILE B 147 " pdb=" CB ILE B 147 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.22e-01 ... (remaining 630 not shown) Planarity restraints: 759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 137 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" C THR A 137 " 0.018 2.00e-02 2.50e+03 pdb=" O THR A 137 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY A 138 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 16 " 0.005 2.00e-02 2.50e+03 9.95e-03 9.89e-01 pdb=" C VAL B 16 " -0.017 2.00e-02 2.50e+03 pdb=" O VAL B 16 " 0.006 2.00e-02 2.50e+03 pdb=" N PRO B 17 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 16 " -0.015 5.00e-02 4.00e+02 2.34e-02 8.76e-01 pdb=" N PRO B 17 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 17 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 17 " -0.013 5.00e-02 4.00e+02 ... (remaining 756 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 223 2.74 - 3.28: 4225 3.28 - 3.82: 7315 3.82 - 4.36: 8050 4.36 - 4.90: 13814 Nonbonded interactions: 33627 Sorted by model distance: nonbonded pdb=" OG SER A 49 " pdb=" OE2 GLU A 238 " model vdw 2.196 3.040 nonbonded pdb=" OD1 ASP A 26 " pdb=" NE2 GLN A 249 " model vdw 2.251 3.120 nonbonded pdb=" OE2 GLU B 187 " pdb=" OH TYR B 209 " model vdw 2.419 3.040 nonbonded pdb=" NH1 ARG A 123 " pdb=" OE1 GLN A 127 " model vdw 2.435 3.120 nonbonded pdb=" O THR A 260 " pdb=" OG1 THR A 264 " model vdw 2.444 3.040 ... (remaining 33622 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.140 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.690 Find NCS groups from input model: 0.020 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:10.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 0.035 4348 Z= 0.144 Angle : 0.501 9.523 5843 Z= 0.266 Chirality : 0.037 0.118 633 Planarity : 0.003 0.031 759 Dihedral : 18.347 89.704 1685 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.60 % Allowed : 20.61 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.41 (0.36), residues: 519 helix: 3.03 (0.24), residues: 397 sheet: None (None), residues: 0 loop : -0.53 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 255 TYR 0.014 0.002 TYR A 256 PHE 0.010 0.002 PHE A 183 TRP 0.007 0.001 TRP B 109 HIS 0.004 0.002 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4348) covalent geometry : angle 0.50119 ( 5843) hydrogen bonds : bond 0.17544 ( 339) hydrogen bonds : angle 4.73101 ( 999) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.177 Fit side-chains REVERT: A 77 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: A 81 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8343 (mt0) REVERT: A 91 ARG cc_start: 0.8643 (tpt90) cc_final: 0.8179 (tpt90) REVERT: A 228 MET cc_start: 0.8895 (mmm) cc_final: 0.8660 (mmp) REVERT: A 255 ARG cc_start: 0.6286 (ttt180) cc_final: 0.5657 (ttm-80) REVERT: B 67 ASN cc_start: 0.7266 (m-40) cc_final: 0.6887 (t0) REVERT: B 91 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: B 154 GLU cc_start: 0.7912 (tp30) cc_final: 0.7340 (mp0) REVERT: B 217 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7695 (ttmt) REVERT: B 228 LYS cc_start: 0.8246 (ttmm) cc_final: 0.8021 (ttpt) outliers start: 12 outliers final: 9 residues processed: 92 average time/residue: 0.7716 time to fit residues: 72.6520 Evaluate side-chains 97 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 217 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.158120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.127845 restraints weight = 4267.318| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 0.90 r_work: 0.3219 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4348 Z= 0.173 Angle : 0.508 6.053 5843 Z= 0.283 Chirality : 0.038 0.123 633 Planarity : 0.004 0.036 759 Dihedral : 7.499 52.085 615 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.82 % Allowed : 19.31 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.96 (0.36), residues: 519 helix: 3.51 (0.23), residues: 405 sheet: None (None), residues: 0 loop : -0.99 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 153 TYR 0.010 0.002 TYR A 216 PHE 0.010 0.001 PHE A 183 TRP 0.008 0.001 TRP B 109 HIS 0.005 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4348) covalent geometry : angle 0.50791 ( 5843) hydrogen bonds : bond 0.07747 ( 339) hydrogen bonds : angle 3.67068 ( 999) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.105 Fit side-chains REVERT: A 77 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: A 81 GLN cc_start: 0.8552 (tp-100) cc_final: 0.8237 (mt0) REVERT: A 91 ARG cc_start: 0.8657 (tpt90) cc_final: 0.8138 (tpt90) REVERT: A 255 ARG cc_start: 0.6367 (ttt180) cc_final: 0.5408 (ttm-80) REVERT: B 154 GLU cc_start: 0.7906 (tp30) cc_final: 0.7302 (mp0) REVERT: B 187 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: B 228 LYS cc_start: 0.8287 (ttmm) cc_final: 0.8007 (ttpt) outliers start: 13 outliers final: 5 residues processed: 97 average time/residue: 0.6442 time to fit residues: 63.9781 Evaluate side-chains 90 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 218 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.157771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.129469 restraints weight = 4299.121| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 0.94 r_work: 0.3237 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4348 Z= 0.151 Angle : 0.467 6.003 5843 Z= 0.258 Chirality : 0.036 0.118 633 Planarity : 0.003 0.027 759 Dihedral : 5.498 51.883 587 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.82 % Allowed : 20.39 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.15 (0.36), residues: 519 helix: 3.66 (0.23), residues: 405 sheet: None (None), residues: 0 loop : -1.04 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 255 TYR 0.009 0.001 TYR B 189 PHE 0.009 0.001 PHE A 183 TRP 0.008 0.001 TRP B 109 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 4348) covalent geometry : angle 0.46721 ( 5843) hydrogen bonds : bond 0.06920 ( 339) hydrogen bonds : angle 3.47901 ( 999) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.103 Fit side-chains REVERT: A 77 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: A 81 GLN cc_start: 0.8510 (tp-100) cc_final: 0.8218 (mt0) REVERT: A 255 ARG cc_start: 0.6400 (ttt180) cc_final: 0.5394 (ttt180) REVERT: A 275 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7548 (mm-40) REVERT: A 278 MET cc_start: 0.7479 (mmm) cc_final: 0.6714 (tpp) REVERT: B 91 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7160 (tm-30) REVERT: B 99 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7073 (mt-10) REVERT: B 154 GLU cc_start: 0.7901 (tp30) cc_final: 0.7298 (mp0) REVERT: B 217 LYS cc_start: 0.7891 (ttmt) cc_final: 0.7343 (mtmt) REVERT: B 228 LYS cc_start: 0.8323 (ttmm) cc_final: 0.8073 (ttpt) outliers start: 13 outliers final: 6 residues processed: 93 average time/residue: 0.6096 time to fit residues: 58.0233 Evaluate side-chains 89 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 218 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 48 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 0.0370 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.158270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.129694 restraints weight = 4231.324| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 0.97 r_work: 0.3231 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4348 Z= 0.151 Angle : 0.467 6.093 5843 Z= 0.257 Chirality : 0.036 0.117 633 Planarity : 0.003 0.027 759 Dihedral : 5.502 51.721 587 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.69 % Allowed : 19.74 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.17 (0.36), residues: 519 helix: 3.70 (0.23), residues: 405 sheet: None (None), residues: 0 loop : -1.08 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 255 TYR 0.012 0.001 TYR A 256 PHE 0.009 0.001 PHE A 183 TRP 0.008 0.001 TRP B 109 HIS 0.004 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4348) covalent geometry : angle 0.46701 ( 5843) hydrogen bonds : bond 0.06772 ( 339) hydrogen bonds : angle 3.43511 ( 999) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.158 Fit side-chains REVERT: A 2 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8507 (mp) REVERT: A 77 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: A 81 GLN cc_start: 0.8518 (tp-100) cc_final: 0.8178 (mt0) REVERT: A 200 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8231 (t70) REVERT: A 255 ARG cc_start: 0.6406 (ttt180) cc_final: 0.5364 (ttt180) REVERT: A 275 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7512 (mm-40) REVERT: B 91 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: B 154 GLU cc_start: 0.7901 (tp30) cc_final: 0.7285 (mp0) REVERT: B 217 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7317 (mtmt) REVERT: B 228 LYS cc_start: 0.8299 (ttmm) cc_final: 0.8044 (ttpt) outliers start: 17 outliers final: 7 residues processed: 91 average time/residue: 0.6519 time to fit residues: 60.7657 Evaluate side-chains 92 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 218 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.158685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.130136 restraints weight = 4308.850| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 0.92 r_work: 0.3223 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4348 Z= 0.175 Angle : 0.504 6.538 5843 Z= 0.278 Chirality : 0.038 0.122 633 Planarity : 0.003 0.032 759 Dihedral : 5.614 52.034 587 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.47 % Allowed : 20.39 % Favored : 76.14 % 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: 4.04 (0.36), residues: 519 helix: 3.59 (0.23), residues: 405 sheet: None (None), residues: 0 loop : -1.09 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 255 TYR 0.009 0.002 TYR B 252 PHE 0.010 0.002 PHE A 183 TRP 0.007 0.001 TRP B 109 HIS 0.005 0.002 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 4348) covalent geometry : angle 0.50394 ( 5843) hydrogen bonds : bond 0.07265 ( 339) hydrogen bonds : angle 3.50915 ( 999) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.184 Fit side-chains REVERT: A 2 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8524 (mp) REVERT: A 77 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: A 81 GLN cc_start: 0.8545 (tp-100) cc_final: 0.8219 (mt0) REVERT: A 200 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8257 (t70) REVERT: A 255 ARG cc_start: 0.6429 (ttt180) cc_final: 0.5363 (ttt180) REVERT: A 275 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7492 (mm-40) REVERT: B 91 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: B 154 GLU cc_start: 0.7906 (tp30) cc_final: 0.7286 (mp0) REVERT: B 187 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: B 228 LYS cc_start: 0.8279 (ttmm) cc_final: 0.8026 (ttpt) outliers start: 16 outliers final: 8 residues processed: 92 average time/residue: 0.7710 time to fit residues: 72.6940 Evaluate side-chains 95 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 218 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 51 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.0070 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.157324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.128642 restraints weight = 4299.159| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 0.90 r_work: 0.3233 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4348 Z= 0.157 Angle : 0.486 7.440 5843 Z= 0.264 Chirality : 0.037 0.118 633 Planarity : 0.003 0.028 759 Dihedral : 5.573 51.810 587 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.47 % Allowed : 21.04 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.10 (0.36), residues: 519 helix: 3.66 (0.23), residues: 405 sheet: None (None), residues: 0 loop : -1.17 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 255 TYR 0.022 0.002 TYR A 231 PHE 0.009 0.001 PHE A 183 TRP 0.008 0.001 TRP B 109 HIS 0.004 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4348) covalent geometry : angle 0.48595 ( 5843) hydrogen bonds : bond 0.06876 ( 339) hydrogen bonds : angle 3.44340 ( 999) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.104 Fit side-chains REVERT: A 2 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 77 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: A 81 GLN cc_start: 0.8506 (tp-100) cc_final: 0.8184 (mt0) REVERT: A 157 MET cc_start: 0.7924 (ttp) cc_final: 0.7609 (tpp) REVERT: A 255 ARG cc_start: 0.6387 (ttt180) cc_final: 0.5357 (ttt180) REVERT: A 275 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7477 (mm-40) REVERT: B 91 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7025 (tm-30) REVERT: B 154 GLU cc_start: 0.7901 (tp30) cc_final: 0.7276 (mp0) outliers start: 16 outliers final: 10 residues processed: 94 average time/residue: 0.6162 time to fit residues: 59.3741 Evaluate side-chains 94 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 259 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.157182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.128535 restraints weight = 4316.677| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 0.90 r_work: 0.3224 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4348 Z= 0.168 Angle : 0.512 8.308 5843 Z= 0.277 Chirality : 0.038 0.120 633 Planarity : 0.003 0.030 759 Dihedral : 5.618 51.952 587 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.90 % Allowed : 21.04 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.02 (0.36), residues: 519 helix: 3.60 (0.23), residues: 405 sheet: None (None), residues: 0 loop : -1.18 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 255 TYR 0.010 0.002 TYR B 252 PHE 0.010 0.001 PHE A 183 TRP 0.007 0.001 TRP B 109 HIS 0.004 0.002 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 4348) covalent geometry : angle 0.51196 ( 5843) hydrogen bonds : bond 0.07098 ( 339) hydrogen bonds : angle 3.46792 ( 999) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.176 Fit side-chains REVERT: A 2 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8516 (mp) REVERT: A 77 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: A 81 GLN cc_start: 0.8515 (tp-100) cc_final: 0.8201 (mt0) REVERT: A 200 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8234 (t70) REVERT: A 255 ARG cc_start: 0.6602 (ttt180) cc_final: 0.5280 (ttt180) REVERT: A 275 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7471 (mm-40) REVERT: B 91 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: B 154 GLU cc_start: 0.7906 (tp30) cc_final: 0.7286 (mp0) outliers start: 18 outliers final: 10 residues processed: 95 average time/residue: 0.6986 time to fit residues: 68.0337 Evaluate side-chains 95 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 259 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 4 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.159931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.131563 restraints weight = 4268.643| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 0.91 r_work: 0.3238 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4348 Z= 0.150 Angle : 0.489 8.625 5843 Z= 0.262 Chirality : 0.036 0.116 633 Planarity : 0.003 0.027 759 Dihedral : 5.551 51.638 587 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.47 % Allowed : 21.48 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.15 (0.36), residues: 519 helix: 3.70 (0.23), residues: 405 sheet: None (None), residues: 0 loop : -1.20 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 255 TYR 0.013 0.001 TYR A 256 PHE 0.009 0.001 PHE A 183 TRP 0.009 0.001 TRP B 109 HIS 0.003 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4348) covalent geometry : angle 0.48883 ( 5843) hydrogen bonds : bond 0.06674 ( 339) hydrogen bonds : angle 3.39401 ( 999) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.173 Fit side-chains REVERT: A 2 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 74 GLN cc_start: 0.8542 (tt0) cc_final: 0.8312 (tt0) REVERT: A 77 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: A 81 GLN cc_start: 0.8508 (tp-100) cc_final: 0.8173 (mt0) REVERT: A 157 MET cc_start: 0.7958 (ttp) cc_final: 0.7685 (tpp) REVERT: A 200 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8230 (t70) REVERT: A 255 ARG cc_start: 0.6390 (ttt180) cc_final: 0.5369 (ttt180) REVERT: A 275 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7541 (mm-40) REVERT: A 278 MET cc_start: 0.7358 (mmm) cc_final: 0.6783 (tpp) REVERT: B 91 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: B 154 GLU cc_start: 0.7906 (tp30) cc_final: 0.7280 (mp0) REVERT: B 217 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7318 (mtmt) REVERT: B 228 LYS cc_start: 0.8253 (ttmm) cc_final: 0.7997 (ttpt) outliers start: 16 outliers final: 10 residues processed: 94 average time/residue: 0.6953 time to fit residues: 66.9007 Evaluate side-chains 95 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 259 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.158270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.129786 restraints weight = 4309.689| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 0.89 r_work: 0.3240 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4348 Z= 0.156 Angle : 0.502 8.903 5843 Z= 0.270 Chirality : 0.037 0.118 633 Planarity : 0.003 0.027 759 Dihedral : 5.579 51.728 587 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.25 % Allowed : 21.69 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.11 (0.36), residues: 519 helix: 3.68 (0.23), residues: 405 sheet: None (None), residues: 0 loop : -1.20 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 255 TYR 0.013 0.002 TYR A 231 PHE 0.010 0.001 PHE A 183 TRP 0.008 0.001 TRP B 109 HIS 0.004 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4348) covalent geometry : angle 0.50219 ( 5843) hydrogen bonds : bond 0.06811 ( 339) hydrogen bonds : angle 3.40010 ( 999) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.160 Fit side-chains REVERT: A 2 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8517 (mp) REVERT: A 74 GLN cc_start: 0.8535 (tt0) cc_final: 0.8319 (tt0) REVERT: A 77 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: A 81 GLN cc_start: 0.8501 (tp-100) cc_final: 0.8175 (mt0) REVERT: A 157 MET cc_start: 0.7948 (ttp) cc_final: 0.7653 (tpp) REVERT: A 200 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8240 (t70) REVERT: A 255 ARG cc_start: 0.6366 (ttt180) cc_final: 0.5358 (ttt180) REVERT: A 275 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7519 (mm-40) REVERT: B 91 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: B 146 GLU cc_start: 0.7906 (pt0) cc_final: 0.7591 (pt0) REVERT: B 154 GLU cc_start: 0.7901 (tp30) cc_final: 0.7279 (mp0) outliers start: 15 outliers final: 10 residues processed: 92 average time/residue: 0.7477 time to fit residues: 70.3444 Evaluate side-chains 95 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 218 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 0.3980 chunk 27 optimal weight: 0.1980 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 38 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.0270 chunk 32 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 overall best weight: 0.2038 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.163560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.135810 restraints weight = 4343.279| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 0.99 r_work: 0.3293 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4348 Z= 0.123 Angle : 0.455 9.254 5843 Z= 0.240 Chirality : 0.034 0.121 633 Planarity : 0.002 0.023 759 Dihedral : 5.309 51.690 587 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.82 % Allowed : 21.91 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.50 (0.36), residues: 519 helix: 3.97 (0.23), residues: 405 sheet: None (None), residues: 0 loop : -1.14 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 61 TYR 0.014 0.001 TYR A 256 PHE 0.008 0.001 PHE A 253 TRP 0.010 0.001 TRP B 109 HIS 0.002 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 4348) covalent geometry : angle 0.45530 ( 5843) hydrogen bonds : bond 0.05694 ( 339) hydrogen bonds : angle 3.24201 ( 999) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.171 Fit side-chains REVERT: A 77 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: A 255 ARG cc_start: 0.6341 (ttt180) cc_final: 0.5176 (ttt180) REVERT: A 275 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7543 (mm-40) REVERT: A 278 MET cc_start: 0.7353 (mmm) cc_final: 0.6749 (tpp) REVERT: B 91 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: B 146 GLU cc_start: 0.7932 (pt0) cc_final: 0.7623 (pt0) REVERT: B 154 GLU cc_start: 0.7902 (tp30) cc_final: 0.7291 (mp0) REVERT: B 157 GLU cc_start: 0.7260 (mp0) cc_final: 0.6911 (pm20) REVERT: B 217 LYS cc_start: 0.7842 (ttmt) cc_final: 0.7306 (mtmt) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.7610 time to fit residues: 70.9231 Evaluate side-chains 94 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 259 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 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 = 0.3715 r_free = 0.3715 target = 0.156863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128244 restraints weight = 4280.113| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 0.89 r_work: 0.3222 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4348 Z= 0.189 Angle : 0.544 9.006 5843 Z= 0.293 Chirality : 0.039 0.124 633 Planarity : 0.003 0.032 759 Dihedral : 5.656 51.929 587 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.60 % Allowed : 22.34 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.07 (0.36), residues: 519 helix: 3.62 (0.23), residues: 405 sheet: None (None), residues: 0 loop : -1.12 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 255 TYR 0.025 0.002 TYR B 252 PHE 0.011 0.002 PHE A 183 TRP 0.007 0.001 TRP B 109 HIS 0.005 0.002 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 4348) covalent geometry : angle 0.54373 ( 5843) hydrogen bonds : bond 0.07366 ( 339) hydrogen bonds : angle 3.46181 ( 999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2711.24 seconds wall clock time: 46 minutes 45.88 seconds (2805.88 seconds total)