Starting phenix.real_space_refine on Fri Aug 22 15:51:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p6y_17511/08_2025/8p6y_17511.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p6y_17511/08_2025/8p6y_17511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p6y_17511/08_2025/8p6y_17511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p6y_17511/08_2025/8p6y_17511.map" model { file = "/net/cci-nas-00/data/ceres_data/8p6y_17511/08_2025/8p6y_17511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p6y_17511/08_2025/8p6y_17511.cif" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 32 5.16 5 C 3279 2.51 5 N 869 2.21 5 O 1082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5266 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "I" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "J" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Time building chain proxies: 1.40, per 1000 atoms: 0.27 Number of scatterers: 5266 At special positions: 0 Unit cell: (84.7875, 94.7625, 68.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 3 15.00 Mg 1 11.99 O 1082 8.00 N 869 7.00 C 3279 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: 0.34 Conformation dependent library (CDL) restraints added in 195.5 milliseconds Enol-peptide restraints added in 715.3 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, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'H' and resid 262 through 266 Processing helix chain 'H' and resid 270 through 275 Processing helix chain 'H' and resid 279 through 285 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.883A 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 removed outlier: 3.546A pdb=" N LEU I 19 " --> pdb=" O SER I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.983A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.703A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 removed outlier: 3.622A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.571A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.613A 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 Processing helix chain 'I' and resid 187 through 200 Processing helix chain 'I' and resid 201 through 206 removed outlier: 4.519A pdb=" N TYR I 204 " --> pdb=" O THR I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.743A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 240 removed outlier: 3.539A pdb=" N GLU I 240 " --> pdb=" O MET I 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 237 through 240' 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 67 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: 4.435A 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 removed outlier: 3.886A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) 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 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.824A 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 19 removed outlier: 7.149A pdb=" N LEU J 15 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ARG J 30 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.974A 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 134 274 hydrogen bonds defined for protein. 759 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: 0.62 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 1669 1.36 - 1.50: 1384 1.50 - 1.64: 2120 1.64 - 1.78: 7 1.78 - 1.91: 50 Bond restraints: 5230 Sorted by residual: bond pdb=" C6 AGS J 401 " pdb=" N6 AGS J 401 " ideal model delta sigma weight residual 1.335 1.457 -0.122 1.00e-02 1.00e+04 1.48e+02 bond pdb=" C1' AGS J 401 " pdb=" N9 AGS J 401 " ideal model delta sigma weight residual 1.459 1.319 0.140 1.40e-02 5.10e+03 1.00e+02 bond pdb=" C5 AGS J 401 " pdb=" N7 AGS J 401 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.94e+01 bond pdb=" O3B AGS J 401 " pdb=" PG AGS J 401 " ideal model delta sigma weight residual 1.559 1.656 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C4 AGS J 401 " pdb=" C5 AGS J 401 " ideal model delta sigma weight residual 1.386 1.338 0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 5225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 6949 1.77 - 3.53: 105 3.53 - 5.30: 22 5.30 - 7.06: 5 7.06 - 8.83: 4 Bond angle restraints: 7085 Sorted by residual: angle pdb=" N1 AGS J 401 " pdb=" C2 AGS J 401 " pdb=" N3 AGS J 401 " ideal model delta sigma weight residual 128.80 120.14 8.66 8.41e-01 1.41e+00 1.06e+02 angle pdb=" C5 AGS J 401 " pdb=" N7 AGS J 401 " pdb=" C8 AGS J 401 " ideal model delta sigma weight residual 103.67 107.94 -4.27 4.26e-01 5.51e+00 1.01e+02 angle pdb=" C5 AGS J 401 " pdb=" C4 AGS J 401 " pdb=" N3 AGS J 401 " ideal model delta sigma weight residual 126.80 119.81 6.99 7.41e-01 1.82e+00 8.90e+01 angle pdb=" N7 AGS J 401 " pdb=" C8 AGS J 401 " pdb=" N9 AGS J 401 " ideal model delta sigma weight residual 114.03 108.21 5.82 6.99e-01 2.05e+00 6.93e+01 angle pdb=" C4 AGS J 401 " pdb=" C5 AGS J 401 " pdb=" N7 AGS J 401 " ideal model delta sigma weight residual 110.73 108.03 2.70 4.52e-01 4.89e+00 3.57e+01 ... (remaining 7080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.94: 2818 19.94 - 39.88: 257 39.88 - 59.81: 73 59.81 - 79.75: 11 79.75 - 99.69: 8 Dihedral angle restraints: 3167 sinusoidal: 1320 harmonic: 1847 Sorted by residual: dihedral pdb=" O1B AGS J 401 " pdb=" O3B AGS J 401 " pdb=" PB AGS J 401 " pdb=" PG AGS J 401 " ideal model delta sinusoidal sigma weight residual 68.91 168.60 -99.69 1 3.00e+01 1.11e-03 1.25e+01 dihedral pdb=" CB GLU I 145 " pdb=" CG GLU I 145 " pdb=" CD GLU I 145 " pdb=" OE1 GLU I 145 " ideal model delta sinusoidal sigma weight residual 0.00 90.26 -90.26 1 3.00e+01 1.11e-03 1.07e+01 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 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.97e+00 ... (remaining 3164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 613 0.047 - 0.094: 131 0.094 - 0.142: 34 0.142 - 0.189: 1 0.189 - 0.236: 2 Chirality restraints: 781 Sorted by residual: chirality pdb=" C1' AGS J 401 " pdb=" C2' AGS J 401 " pdb=" N9 AGS J 401 " pdb=" O4' AGS J 401 " both_signs ideal model delta sigma weight residual False 2.41 2.17 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C2' AGS J 401 " pdb=" C1' AGS J 401 " pdb=" C3' AGS J 401 " pdb=" O2' AGS J 401 " both_signs ideal model delta sigma weight residual False -2.67 -2.87 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" C4' AGS J 401 " pdb=" C3' AGS J 401 " pdb=" C5' AGS J 401 " pdb=" O4' AGS J 401 " both_signs ideal model delta sigma weight residual False -2.49 -2.63 0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 778 not shown) Planarity restraints: 902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU I 66 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" CD GLU I 66 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU I 66 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU I 66 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 183 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO I 184 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO I 184 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 184 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO J 140 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.019 5.00e-02 4.00e+02 ... (remaining 899 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 186 2.70 - 3.25: 5265 3.25 - 3.80: 9244 3.80 - 4.35: 12178 4.35 - 4.90: 19355 Nonbonded interactions: 46228 Sorted by model distance: nonbonded pdb="MG MG J 402 " pdb=" O HOH J 551 " model vdw 2.148 2.170 nonbonded pdb=" O ARG I 242 " pdb=" NH1 ARG I 242 " model vdw 2.203 3.120 nonbonded pdb=" O HOH J 535 " pdb=" O HOH J 561 " model vdw 2.246 3.040 nonbonded pdb=" O HOH I 402 " pdb=" O HOH I 467 " model vdw 2.255 3.040 nonbonded pdb=" O HOH J 505 " pdb=" O HOH J 539 " model vdw 2.260 3.040 ... (remaining 46223 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: 5.610 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.570 Find NCS groups from input model: 0.030 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:8.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.005 0.140 5230 Z= 0.336 Angle : 0.600 8.826 7085 Z= 0.400 Chirality : 0.042 0.236 781 Planarity : 0.004 0.036 902 Dihedral : 17.032 99.688 1971 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 0.36 % Allowed : 15.34 % Favored : 84.30 % 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: 1.99 (0.34), residues: 618 helix: 2.21 (0.29), residues: 331 sheet: -0.61 (1.27), residues: 19 loop : 0.43 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 188 TYR 0.016 0.001 TYR I 91 PHE 0.013 0.002 PHE I 110 TRP 0.006 0.001 TRP I 11 HIS 0.009 0.001 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 5230) covalent geometry : angle 0.60019 ( 7085) hydrogen bonds : bond 0.13824 ( 274) hydrogen bonds : angle 5.80312 ( 759) *********************** 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 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.145 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 90 average time/residue: 0.7626 time to fit residues: 70.6880 Evaluate side-chains 87 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 0.0070 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.158357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.134174 restraints weight = 4529.270| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 0.82 r_work: 0.3417 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.0539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5230 Z= 0.141 Angle : 0.578 8.480 7085 Z= 0.297 Chirality : 0.042 0.148 781 Planarity : 0.005 0.034 902 Dihedral : 8.158 92.821 712 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 1.08 % Allowed : 14.08 % Favored : 84.84 % 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: 2.04 (0.34), residues: 618 helix: 2.29 (0.28), residues: 338 sheet: -0.28 (1.00), residues: 25 loop : 0.32 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 61 TYR 0.017 0.002 TYR I 91 PHE 0.013 0.002 PHE J 295 TRP 0.008 0.001 TRP J 132 HIS 0.010 0.002 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5230) covalent geometry : angle 0.57835 ( 7085) hydrogen bonds : bond 0.05612 ( 274) hydrogen bonds : angle 4.70530 ( 759) *********************** 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 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.218 Fit side-chains REVERT: I 234 GLU cc_start: 0.7273 (mm-30) cc_final: 0.7053 (mp0) outliers start: 6 outliers final: 2 residues processed: 96 average time/residue: 0.7670 time to fit residues: 75.7955 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 124 GLN J 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.156821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.132493 restraints weight = 4435.366| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 0.81 r_work: 0.3393 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5230 Z= 0.222 Angle : 0.700 8.312 7085 Z= 0.359 Chirality : 0.047 0.181 781 Planarity : 0.005 0.037 902 Dihedral : 7.888 83.661 709 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.99 % Allowed : 12.45 % Favored : 85.56 % 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: 1.65 (0.34), residues: 618 helix: 1.98 (0.27), residues: 338 sheet: -0.56 (0.98), residues: 25 loop : 0.15 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 61 TYR 0.020 0.002 TYR I 91 PHE 0.018 0.003 PHE I 13 TRP 0.012 0.002 TRP J 132 HIS 0.012 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 5230) covalent geometry : angle 0.70009 ( 7085) hydrogen bonds : bond 0.06610 ( 274) hydrogen bonds : angle 4.86642 ( 759) *********************** 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 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.204 Fit side-chains REVERT: I 18 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: I 234 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7048 (mp0) REVERT: J 52 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6761 (mmtm) outliers start: 11 outliers final: 5 residues processed: 93 average time/residue: 0.6338 time to fit residues: 60.9302 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 124 GLN J 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.156579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.132125 restraints weight = 4485.370| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 0.82 r_work: 0.3389 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5230 Z= 0.233 Angle : 0.723 8.246 7085 Z= 0.371 Chirality : 0.047 0.183 781 Planarity : 0.006 0.038 902 Dihedral : 7.851 81.879 709 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.62 % Allowed : 13.18 % Favored : 85.20 % 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: 1.50 (0.33), residues: 618 helix: 1.82 (0.27), residues: 338 sheet: -0.81 (1.18), residues: 19 loop : 0.13 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 61 TYR 0.019 0.002 TYR I 91 PHE 0.019 0.003 PHE I 13 TRP 0.013 0.002 TRP J 132 HIS 0.012 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 5230) covalent geometry : angle 0.72264 ( 7085) hydrogen bonds : bond 0.06689 ( 274) hydrogen bonds : angle 4.90023 ( 759) *********************** 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 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.231 Fit side-chains REVERT: I 234 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7080 (mp0) REVERT: J 52 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6571 (mmtm) outliers start: 9 outliers final: 6 residues processed: 91 average time/residue: 0.8470 time to fit residues: 79.4817 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 0.0170 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.158193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133812 restraints weight = 4559.200| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 0.83 r_work: 0.3409 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5230 Z= 0.143 Angle : 0.594 8.633 7085 Z= 0.303 Chirality : 0.043 0.144 781 Planarity : 0.005 0.036 902 Dihedral : 7.617 81.357 709 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 0.90 % Allowed : 14.62 % Favored : 84.48 % 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: 1.78 (0.34), residues: 618 helix: 2.13 (0.28), residues: 338 sheet: -0.41 (0.95), residues: 25 loop : 0.13 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 61 TYR 0.016 0.002 TYR I 2 PHE 0.015 0.002 PHE I 30 TRP 0.008 0.001 TRP J 132 HIS 0.010 0.002 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5230) covalent geometry : angle 0.59390 ( 7085) hydrogen bonds : bond 0.05495 ( 274) hydrogen bonds : angle 4.61406 ( 759) *********************** 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 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.293 Fit side-chains REVERT: I 18 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: I 234 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7107 (mp0) outliers start: 5 outliers final: 3 residues processed: 90 average time/residue: 0.8843 time to fit residues: 81.9517 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 6.9990 chunk 3 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 6 optimal weight: 0.0570 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.160290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136142 restraints weight = 4594.532| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 0.83 r_work: 0.3442 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5230 Z= 0.108 Angle : 0.534 9.016 7085 Z= 0.271 Chirality : 0.041 0.137 781 Planarity : 0.004 0.035 902 Dihedral : 7.358 79.346 709 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 1.26 % Allowed : 14.80 % Favored : 83.94 % 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: 2.00 (0.34), residues: 618 helix: 2.28 (0.28), residues: 344 sheet: -0.16 (0.96), residues: 25 loop : 0.20 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 188 TYR 0.014 0.001 TYR I 91 PHE 0.013 0.001 PHE I 30 TRP 0.005 0.001 TRP J 132 HIS 0.009 0.001 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 5230) covalent geometry : angle 0.53387 ( 7085) hydrogen bonds : bond 0.04577 ( 274) hydrogen bonds : angle 4.35855 ( 759) *********************** 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 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.231 Fit side-chains REVERT: I 18 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7999 (tt0) outliers start: 7 outliers final: 3 residues processed: 93 average time/residue: 0.8981 time to fit residues: 85.9335 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 124 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.155858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131449 restraints weight = 4493.380| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 0.82 r_work: 0.3381 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 5230 Z= 0.339 Angle : 0.858 9.058 7085 Z= 0.440 Chirality : 0.053 0.222 781 Planarity : 0.007 0.055 902 Dihedral : 7.872 79.258 709 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.62 % Allowed : 14.80 % Favored : 83.57 % 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: 1.38 (0.33), residues: 618 helix: 1.68 (0.27), residues: 338 sheet: -0.65 (1.18), residues: 19 loop : 0.13 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 188 TYR 0.023 0.003 TYR I 91 PHE 0.025 0.004 PHE I 13 TRP 0.014 0.003 TRP J 132 HIS 0.014 0.003 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00763 ( 5230) covalent geometry : angle 0.85763 ( 7085) hydrogen bonds : bond 0.07461 ( 274) hydrogen bonds : angle 5.06522 ( 759) *********************** 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 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.231 Fit side-chains REVERT: I 18 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: J 52 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6442 (mmtt) outliers start: 9 outliers final: 6 residues processed: 88 average time/residue: 0.8594 time to fit residues: 77.9633 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 263 LEU Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.158112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133915 restraints weight = 4460.986| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 0.82 r_work: 0.3413 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5230 Z= 0.147 Angle : 0.625 10.813 7085 Z= 0.318 Chirality : 0.043 0.143 781 Planarity : 0.005 0.036 902 Dihedral : 7.614 80.795 709 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.65 % Favored : 99.19 % Rotamer: Outliers : 0.90 % Allowed : 15.52 % Favored : 83.57 % 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: 1.75 (0.34), residues: 618 helix: 2.08 (0.28), residues: 338 sheet: -0.25 (0.98), residues: 25 loop : 0.12 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 188 TYR 0.016 0.002 TYR I 91 PHE 0.016 0.002 PHE I 30 TRP 0.008 0.001 TRP J 132 HIS 0.010 0.002 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5230) covalent geometry : angle 0.62519 ( 7085) hydrogen bonds : bond 0.05538 ( 274) hydrogen bonds : angle 4.63165 ( 759) *********************** 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 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.225 Fit side-chains REVERT: J 52 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6470 (mmtt) outliers start: 5 outliers final: 2 residues processed: 91 average time/residue: 0.8685 time to fit residues: 81.4209 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.157711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133322 restraints weight = 4537.382| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 0.83 r_work: 0.3404 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.004 0.038 5230 Z= 0.170 Angle : 0.655 9.519 7085 Z= 0.334 Chirality : 0.044 0.147 781 Planarity : 0.005 0.037 902 Dihedral : 7.622 79.760 709 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 1.08 % Allowed : 15.34 % Favored : 83.57 % 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: 1.71 (0.34), residues: 618 helix: 2.04 (0.27), residues: 338 sheet: -0.28 (0.97), residues: 25 loop : 0.13 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 61 TYR 0.017 0.002 TYR I 91 PHE 0.016 0.002 PHE I 30 TRP 0.010 0.002 TRP J 132 HIS 0.010 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5230) covalent geometry : angle 0.65498 ( 7085) hydrogen bonds : bond 0.05840 ( 274) hydrogen bonds : angle 4.67547 ( 759) *********************** 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 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.223 Fit side-chains REVERT: I 18 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: J 52 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6463 (mmtt) outliers start: 6 outliers final: 2 residues processed: 89 average time/residue: 0.8752 time to fit residues: 80.2862 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.159192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.134905 restraints weight = 4580.081| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 0.83 r_work: 0.3427 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5230 Z= 0.129 Angle : 0.591 9.769 7085 Z= 0.302 Chirality : 0.042 0.149 781 Planarity : 0.004 0.036 902 Dihedral : 7.452 79.075 709 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 0.90 % Allowed : 15.70 % Favored : 83.39 % 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: 1.83 (0.34), residues: 618 helix: 2.11 (0.28), residues: 344 sheet: -0.12 (0.94), residues: 25 loop : 0.16 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 188 TYR 0.015 0.002 TYR I 2 PHE 0.015 0.002 PHE I 30 TRP 0.006 0.001 TRP J 132 HIS 0.010 0.002 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 5230) covalent geometry : angle 0.59145 ( 7085) hydrogen bonds : bond 0.05044 ( 274) hydrogen bonds : angle 4.48801 ( 759) ********************** 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 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.150 Fit side-chains REVERT: I 18 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: J 52 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6432 (mmtt) outliers start: 5 outliers final: 2 residues processed: 87 average time/residue: 0.8553 time to fit residues: 76.6148 Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.158692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134507 restraints weight = 4590.180| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 0.83 r_work: 0.3422 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5230 Z= 0.138 Angle : 0.605 9.465 7085 Z= 0.308 Chirality : 0.042 0.142 781 Planarity : 0.005 0.036 902 Dihedral : 7.451 78.021 709 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 0.90 % Allowed : 15.52 % Favored : 83.57 % 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: 1.92 (0.34), residues: 618 helix: 2.22 (0.28), residues: 338 sheet: -0.09 (0.95), residues: 25 loop : 0.19 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 188 TYR 0.016 0.002 TYR I 2 PHE 0.015 0.002 PHE I 30 TRP 0.008 0.001 TRP J 132 HIS 0.009 0.002 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5230) covalent geometry : angle 0.60477 ( 7085) hydrogen bonds : bond 0.05247 ( 274) hydrogen bonds : angle 4.49913 ( 759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3193.51 seconds wall clock time: 55 minutes 3.53 seconds (3303.53 seconds total)