Starting phenix.real_space_refine on Fri Oct 10 12:39:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p71_17514/10_2025/8p71_17514.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p71_17514/10_2025/8p71_17514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p71_17514/10_2025/8p71_17514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p71_17514/10_2025/8p71_17514.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p71_17514/10_2025/8p71_17514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p71_17514/10_2025/8p71_17514.map" } resolution = 2.0 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= 0.001 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 31 5.16 5 C 3289 2.51 5 N 870 2.21 5 O 1027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5217 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'X4F': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "I" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Time building chain proxies: 1.44, per 1000 atoms: 0.28 Number of scatterers: 5217 At special positions: 0 Unit cell: (84.7875, 94.05, 67.6875, 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 31 16.00 O 1027 8.00 N 870 7.00 C 3289 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: 0.45 Conformation dependent library (CDL) restraints added in 166.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 3 sheets defined 63.0% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'H' and resid 262 through 264 No H-bonds generated for 'chain 'H' and resid 262 through 264' Processing helix chain 'H' and resid 265 through 270 Processing helix chain 'H' and resid 271 through 275 removed outlier: 3.587A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 285 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.850A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.853A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.554A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.626A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 removed outlier: 3.772A pdb=" N ILE I 186 " --> pdb=" O ASN I 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 183 through 186' Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.543A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.897A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 261 Processing helix chain 'I' and resid 266 through 284 Processing helix chain 'J' and resid 56 through 68 removed outlier: 3.766A pdb=" N GLU J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 155 through 159 removed outlier: 4.262A pdb=" N LEU J 158 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 292 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.738A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 20 removed outlier: 6.616A pdb=" N LYS J 28 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE J 17 " --> pdb=" O VAL J 26 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL J 26 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 271 hydrogen bonds defined for protein. 765 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: 0.77 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1642 1.34 - 1.46: 1189 1.46 - 1.58: 2346 1.58 - 1.70: 1 1.70 - 1.82: 49 Bond restraints: 5227 Sorted by residual: bond pdb=" C08 X4F J 401 " pdb=" N09 X4F J 401 " ideal model delta sigma weight residual 1.342 1.491 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" C02 X4F J 401 " pdb=" C04 X4F J 401 " ideal model delta sigma weight residual 1.502 1.596 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C18 X4F J 401 " pdb=" N19 X4F J 401 " ideal model delta sigma weight residual 1.365 1.454 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C10 X4F J 401 " pdb=" N09 X4F J 401 " ideal model delta sigma weight residual 1.451 1.510 -0.059 2.00e-02 2.50e+03 8.85e+00 bond pdb=" C27 X4F J 401 " pdb=" N26 X4F J 401 " ideal model delta sigma weight residual 1.344 1.395 -0.051 2.00e-02 2.50e+03 6.59e+00 ... (remaining 5222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 6885 1.41 - 2.82: 135 2.82 - 4.23: 45 4.23 - 5.64: 8 5.64 - 7.04: 2 Bond angle restraints: 7075 Sorted by residual: angle pdb=" CB MET J 189 " pdb=" CG MET J 189 " pdb=" SD MET J 189 " ideal model delta sigma weight residual 112.70 119.74 -7.04 3.00e+00 1.11e-01 5.51e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.96 3.94 1.80e+00 3.09e-01 4.80e+00 angle pdb=" C04 X4F J 401 " pdb=" C05 X4F J 401 " pdb=" N06 X4F J 401 " ideal model delta sigma weight residual 113.81 107.42 6.39 3.00e+00 1.11e-01 4.54e+00 angle pdb=" CB GLU H 262 " pdb=" CG GLU H 262 " pdb=" CD GLU H 262 " ideal model delta sigma weight residual 112.60 116.04 -3.44 1.70e+00 3.46e-01 4.09e+00 angle pdb=" C17 X4F J 401 " pdb=" C08 X4F J 401 " pdb=" N09 X4F J 401 " ideal model delta sigma weight residual 126.29 120.82 5.47 3.00e+00 1.11e-01 3.32e+00 ... (remaining 7070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 2695 16.15 - 32.31: 325 32.31 - 48.46: 99 48.46 - 64.61: 35 64.61 - 80.76: 12 Dihedral angle restraints: 3166 sinusoidal: 1319 harmonic: 1847 Sorted by residual: dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA THR I 176 " pdb=" C THR I 176 " pdb=" N ARG I 177 " pdb=" CA ARG I 177 " ideal model delta harmonic sigma weight residual -180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA GLN H 281 " pdb=" CB GLN H 281 " pdb=" CG GLN H 281 " pdb=" CD GLN H 281 " ideal model delta sinusoidal sigma weight residual 60.00 119.99 -59.99 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 448 0.026 - 0.052: 192 0.052 - 0.077: 83 0.077 - 0.103: 40 0.103 - 0.129: 14 Chirality restraints: 777 Sorted by residual: chirality pdb=" CA TYR I 91 " pdb=" N TYR I 91 " pdb=" C TYR I 91 " pdb=" CB TYR I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE J 74 " pdb=" N ILE J 74 " pdb=" C ILE J 74 " pdb=" CB ILE J 74 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE J 255 " pdb=" N ILE J 255 " pdb=" C ILE J 255 " pdb=" CB ILE J 255 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 774 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.020 5.00e-02 4.00e+02 2.96e-02 1.41e+00 pdb=" N PRO J 140 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 210 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO J 211 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO J 211 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO J 211 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 49 " 0.017 5.00e-02 4.00e+02 2.59e-02 1.08e+00 pdb=" N PRO I 50 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO I 50 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO I 50 " 0.015 5.00e-02 4.00e+02 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 870 2.76 - 3.29: 5174 3.29 - 3.83: 9865 3.83 - 4.36: 11471 4.36 - 4.90: 19039 Nonbonded interactions: 46419 Sorted by model distance: nonbonded pdb=" O HOH J 503 " pdb=" O HOH J 551 " model vdw 2.223 3.040 nonbonded pdb=" O TRP I 11 " pdb=" O HOH I 401 " model vdw 2.228 3.040 nonbonded pdb=" OD2 ASP J 92 " pdb=" O HOH J 501 " model vdw 2.233 3.040 nonbonded pdb=" O HOH J 536 " pdb=" O HOH J 554 " model vdw 2.257 3.040 nonbonded pdb=" O HOH J 502 " pdb=" O HOH J 552 " model vdw 2.258 3.040 ... (remaining 46414 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.800 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 0.149 5227 Z= 0.206 Angle : 0.549 7.044 7075 Z= 0.265 Chirality : 0.039 0.129 777 Planarity : 0.004 0.030 903 Dihedral : 16.922 80.763 1970 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.72 % Allowed : 20.04 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.34), residues: 618 helix: 1.89 (0.28), residues: 346 sheet: -0.80 (1.11), residues: 20 loop : 0.37 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 188 TYR 0.014 0.001 TYR I 2 PHE 0.014 0.002 PHE J 91 TRP 0.011 0.002 TRP J 132 HIS 0.002 0.001 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 5227) covalent geometry : angle 0.54936 ( 7075) hydrogen bonds : bond 0.12377 ( 271) hydrogen bonds : angle 5.79837 ( 765) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.211 Fit side-chains REVERT: I 232 LEU cc_start: 0.8173 (mm) cc_final: 0.7884 (mm) REVERT: J 252 PHE cc_start: 0.6732 (m-80) cc_final: 0.6433 (m-10) outliers start: 4 outliers final: 3 residues processed: 94 average time/residue: 0.7783 time to fit residues: 75.4716 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 ASP Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 158 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.178650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.155782 restraints weight = 4686.788| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.00 r_work: 0.3785 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.0596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5227 Z= 0.137 Angle : 0.529 5.108 7075 Z= 0.272 Chirality : 0.040 0.130 777 Planarity : 0.004 0.033 903 Dihedral : 5.602 59.998 713 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 2.35 % Allowed : 18.59 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.34), residues: 618 helix: 1.99 (0.28), residues: 348 sheet: 0.84 (1.25), residues: 15 loop : 0.38 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 23 TYR 0.016 0.002 TYR I 2 PHE 0.015 0.002 PHE J 91 TRP 0.009 0.002 TRP J 132 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5227) covalent geometry : angle 0.52910 ( 7075) hydrogen bonds : bond 0.04778 ( 271) hydrogen bonds : angle 4.64145 ( 765) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.175 Fit side-chains REVERT: I 232 LEU cc_start: 0.8113 (mm) cc_final: 0.7809 (mm) REVERT: J 252 PHE cc_start: 0.6731 (m-80) cc_final: 0.6392 (m-10) outliers start: 13 outliers final: 8 residues processed: 104 average time/residue: 0.7332 time to fit residues: 78.7611 Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 48 optimal weight: 0.0870 chunk 36 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.176751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.153785 restraints weight = 4621.261| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 0.99 r_work: 0.3762 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5227 Z= 0.188 Angle : 0.594 6.170 7075 Z= 0.306 Chirality : 0.043 0.136 777 Planarity : 0.005 0.033 903 Dihedral : 5.572 58.893 709 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 3.07 % Allowed : 16.43 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.34), residues: 618 helix: 1.70 (0.27), residues: 351 sheet: 0.96 (1.31), residues: 15 loop : 0.26 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 23 TYR 0.021 0.002 TYR I 2 PHE 0.019 0.002 PHE J 91 TRP 0.012 0.002 TRP J 132 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 5227) covalent geometry : angle 0.59417 ( 7075) hydrogen bonds : bond 0.05243 ( 271) hydrogen bonds : angle 4.71414 ( 765) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.264 Fit side-chains REVERT: I 63 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7290 (mmm160) REVERT: I 85 MET cc_start: 0.7824 (tpp) cc_final: 0.7503 (tpp) outliers start: 17 outliers final: 11 residues processed: 102 average time/residue: 0.7479 time to fit residues: 78.7543 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 56 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.177009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.153973 restraints weight = 4631.664| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 0.99 r_work: 0.3763 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5227 Z= 0.182 Angle : 0.588 5.374 7075 Z= 0.303 Chirality : 0.042 0.137 777 Planarity : 0.005 0.033 903 Dihedral : 5.525 59.201 709 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.89 % Allowed : 16.79 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.34), residues: 618 helix: 1.68 (0.27), residues: 348 sheet: 1.11 (1.39), residues: 15 loop : 0.20 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 23 TYR 0.020 0.002 TYR I 2 PHE 0.017 0.002 PHE J 91 TRP 0.012 0.002 TRP J 132 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 5227) covalent geometry : angle 0.58815 ( 7075) hydrogen bonds : bond 0.05104 ( 271) hydrogen bonds : angle 4.67764 ( 765) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.227 Fit side-chains REVERT: I 63 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7292 (mmm160) REVERT: I 85 MET cc_start: 0.7825 (tpp) cc_final: 0.7507 (tpp) outliers start: 16 outliers final: 11 residues processed: 101 average time/residue: 0.7528 time to fit residues: 78.6828 Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 44 ASP Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.178757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.155789 restraints weight = 4732.365| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.00 r_work: 0.3786 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5227 Z= 0.128 Angle : 0.526 5.679 7075 Z= 0.269 Chirality : 0.040 0.132 777 Planarity : 0.004 0.034 903 Dihedral : 5.051 59.753 709 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 3.43 % Allowed : 17.15 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.34), residues: 618 helix: 1.92 (0.28), residues: 351 sheet: 1.00 (1.31), residues: 15 loop : 0.31 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 295 TYR 0.016 0.002 TYR I 2 PHE 0.014 0.002 PHE I 110 TRP 0.011 0.002 TRP I 11 HIS 0.003 0.001 HIS I 100 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5227) covalent geometry : angle 0.52577 ( 7075) hydrogen bonds : bond 0.04444 ( 271) hydrogen bonds : angle 4.44821 ( 765) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.221 Fit side-chains REVERT: I 63 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7309 (mmm160) REVERT: I 85 MET cc_start: 0.7831 (tpp) cc_final: 0.7530 (tpp) outliers start: 19 outliers final: 10 residues processed: 102 average time/residue: 0.7683 time to fit residues: 80.9298 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.178038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.155068 restraints weight = 4694.772| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.00 r_work: 0.3776 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5227 Z= 0.149 Angle : 0.554 6.159 7075 Z= 0.283 Chirality : 0.041 0.132 777 Planarity : 0.004 0.034 903 Dihedral : 5.028 59.421 708 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.89 % Allowed : 18.05 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.34), residues: 618 helix: 1.91 (0.28), residues: 348 sheet: 0.91 (1.29), residues: 15 loop : 0.29 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 23 TYR 0.018 0.002 TYR I 2 PHE 0.016 0.002 PHE J 91 TRP 0.010 0.002 TRP I 11 HIS 0.004 0.001 HIS I 100 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5227) covalent geometry : angle 0.55424 ( 7075) hydrogen bonds : bond 0.04692 ( 271) hydrogen bonds : angle 4.50170 ( 765) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.233 Fit side-chains REVERT: I 63 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7311 (mmm160) outliers start: 16 outliers final: 11 residues processed: 97 average time/residue: 0.7576 time to fit residues: 75.9642 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 0.0170 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.180086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.157332 restraints weight = 4721.716| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.00 r_work: 0.3805 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5227 Z= 0.112 Angle : 0.515 7.353 7075 Z= 0.260 Chirality : 0.040 0.128 777 Planarity : 0.004 0.035 903 Dihedral : 4.821 59.694 708 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.17 % Allowed : 18.95 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.35), residues: 618 helix: 2.13 (0.28), residues: 348 sheet: 0.32 (1.22), residues: 16 loop : 0.39 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 295 TYR 0.015 0.001 TYR J 27 PHE 0.015 0.002 PHE I 110 TRP 0.010 0.001 TRP I 11 HIS 0.003 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 5227) covalent geometry : angle 0.51489 ( 7075) hydrogen bonds : bond 0.04115 ( 271) hydrogen bonds : angle 4.31543 ( 765) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.224 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 97 average time/residue: 0.7347 time to fit residues: 73.7145 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 32 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.176929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.154159 restraints weight = 4690.259| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 0.98 r_work: 0.3765 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5227 Z= 0.209 Angle : 0.626 7.963 7075 Z= 0.321 Chirality : 0.044 0.134 777 Planarity : 0.005 0.035 903 Dihedral : 5.198 58.425 708 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.71 % Allowed : 18.41 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.34), residues: 618 helix: 1.69 (0.27), residues: 348 sheet: 0.97 (1.32), residues: 15 loop : 0.22 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 23 TYR 0.022 0.002 TYR I 2 PHE 0.020 0.003 PHE J 91 TRP 0.009 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 5227) covalent geometry : angle 0.62576 ( 7075) hydrogen bonds : bond 0.05232 ( 271) hydrogen bonds : angle 4.64039 ( 765) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.143 Fit side-chains REVERT: I 63 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7289 (mmm160) REVERT: I 85 MET cc_start: 0.7776 (tpp) cc_final: 0.7534 (tpp) outliers start: 15 outliers final: 12 residues processed: 97 average time/residue: 0.7104 time to fit residues: 71.1474 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.177895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.155250 restraints weight = 4692.019| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 0.99 r_work: 0.3780 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5227 Z= 0.151 Angle : 0.574 9.158 7075 Z= 0.291 Chirality : 0.041 0.133 777 Planarity : 0.004 0.034 903 Dihedral : 5.036 59.681 708 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.99 % Allowed : 19.68 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.34), residues: 618 helix: 1.85 (0.28), residues: 348 sheet: 0.89 (1.31), residues: 15 loop : 0.25 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 23 TYR 0.017 0.002 TYR I 2 PHE 0.015 0.002 PHE J 91 TRP 0.011 0.002 TRP I 11 HIS 0.004 0.001 HIS I 100 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 5227) covalent geometry : angle 0.57408 ( 7075) hydrogen bonds : bond 0.04671 ( 271) hydrogen bonds : angle 4.51025 ( 765) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.234 Fit side-chains REVERT: I 85 MET cc_start: 0.7771 (tpp) cc_final: 0.7527 (tpp) outliers start: 11 outliers final: 9 residues processed: 93 average time/residue: 0.7964 time to fit residues: 76.3536 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 36 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.179285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.156540 restraints weight = 4690.027| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.00 r_work: 0.3796 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5227 Z= 0.127 Angle : 0.551 9.564 7075 Z= 0.278 Chirality : 0.041 0.131 777 Planarity : 0.004 0.034 903 Dihedral : 4.931 59.881 708 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.81 % Allowed : 19.68 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.34), residues: 618 helix: 2.02 (0.28), residues: 348 sheet: 0.91 (1.28), residues: 15 loop : 0.31 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 295 TYR 0.016 0.002 TYR I 2 PHE 0.014 0.002 PHE I 110 TRP 0.012 0.002 TRP I 11 HIS 0.003 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5227) covalent geometry : angle 0.55114 ( 7075) hydrogen bonds : bond 0.04341 ( 271) hydrogen bonds : angle 4.39644 ( 765) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.223 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 89 average time/residue: 0.7935 time to fit residues: 72.9181 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.178598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.155632 restraints weight = 4738.999| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.01 r_work: 0.3782 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5227 Z= 0.146 Angle : 0.573 9.287 7075 Z= 0.289 Chirality : 0.041 0.132 777 Planarity : 0.004 0.034 903 Dihedral : 4.989 59.531 708 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.35 % Allowed : 19.31 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.34), residues: 618 helix: 1.93 (0.28), residues: 348 sheet: 0.90 (1.29), residues: 15 loop : 0.28 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 23 TYR 0.017 0.002 TYR I 2 PHE 0.015 0.002 PHE J 91 TRP 0.011 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5227) covalent geometry : angle 0.57348 ( 7075) hydrogen bonds : bond 0.04579 ( 271) hydrogen bonds : angle 4.45912 ( 765) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2954.23 seconds wall clock time: 51 minutes 1.76 seconds (3061.76 seconds total)