Starting phenix.real_space_refine on Sat May 2 10:05:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qjj_53204/05_2026/9qjj_53204.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qjj_53204/05_2026/9qjj_53204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qjj_53204/05_2026/9qjj_53204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qjj_53204/05_2026/9qjj_53204.map" model { file = "/net/cci-nas-00/data/ceres_data/9qjj_53204/05_2026/9qjj_53204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qjj_53204/05_2026/9qjj_53204.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2882 2.51 5 N 734 2.21 5 O 845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4481 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2084 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 243} Chain: "B" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2314 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 19, 'TRANS': 268} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'NK3': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Time building chain proxies: 1.11, per 1000 atoms: 0.25 Number of scatterers: 4481 At special positions: 0 Unit cell: (79.56, 84.66, 71.4, 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 20 16.00 O 845 8.00 N 734 7.00 C 2882 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: 0.33 Conformation dependent library (CDL) restraints added in 171.8 milliseconds 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1042 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 3 sheets defined 57.3% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.176A pdb=" N VAL A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.676A pdb=" N LYS A 201 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 225 Processing helix chain 'A' and resid 228 through 244 removed outlier: 3.710A pdb=" N LEU A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 252 through 269 Processing helix chain 'A' and resid 274 through 281 Processing helix chain 'A' and resid 287 through 303 Processing helix chain 'A' and resid 310 through 320 removed outlier: 3.863A pdb=" N LEU A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.858A pdb=" N TYR A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 414 through 419 removed outlier: 6.161A pdb=" N LYS A 417 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 121 Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 170 through 175 Processing helix chain 'B' and resid 181 through 199 removed outlier: 4.265A pdb=" N ASP B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.579A pdb=" N VAL B 251 " --> pdb=" O ASP B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 267 Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.629A pdb=" N ALA B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 11 removed outlier: 6.785A pdb=" N LYS B 20 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LYS B 9 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL B 18 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP B 68 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU B 81 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU B 66 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 124 218 hydrogen bonds defined for protein. 618 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: 0.57 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 704 1.31 - 1.43: 1196 1.43 - 1.56: 2604 1.56 - 1.68: 0 1.68 - 1.81: 34 Bond restraints: 4538 Sorted by residual: bond pdb=" C09 NK3 B 301 " pdb=" C11 NK3 B 301 " ideal model delta sigma weight residual 1.434 1.509 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C07 NK3 B 301 " pdb=" N08 NK3 B 301 " ideal model delta sigma weight residual 1.420 1.474 -0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" C09 NK3 B 301 " pdb=" O10 NK3 B 301 " ideal model delta sigma weight residual 1.238 1.184 0.054 2.00e-02 2.50e+03 7.18e+00 bond pdb=" C27 NK3 B 301 " pdb=" N25 NK3 B 301 " ideal model delta sigma weight residual 1.497 1.452 0.045 2.00e-02 2.50e+03 5.17e+00 bond pdb=" C05 NK3 B 301 " pdb=" C16 NK3 B 301 " ideal model delta sigma weight residual 1.476 1.433 0.043 2.00e-02 2.50e+03 4.60e+00 ... (remaining 4533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 6080 1.77 - 3.53: 65 3.53 - 5.30: 10 5.30 - 7.06: 6 7.06 - 8.83: 1 Bond angle restraints: 6162 Sorted by residual: angle pdb=" C09 NK3 B 301 " pdb=" C11 NK3 B 301 " pdb=" S15 NK3 B 301 " ideal model delta sigma weight residual 123.31 132.14 -8.83 3.00e+00 1.11e-01 8.66e+00 angle pdb=" CG ARG B 22 " pdb=" CD ARG B 22 " pdb=" NE ARG B 22 " ideal model delta sigma weight residual 112.00 118.01 -6.01 2.20e+00 2.07e-01 7.46e+00 angle pdb=" CB ARG B 22 " pdb=" CG ARG B 22 " pdb=" CD ARG B 22 " ideal model delta sigma weight residual 111.30 116.69 -5.39 2.30e+00 1.89e-01 5.48e+00 angle pdb=" C HIS B 121 " pdb=" N ARG B 122 " pdb=" CA ARG B 122 " ideal model delta sigma weight residual 122.46 125.53 -3.07 1.41e+00 5.03e-01 4.74e+00 angle pdb=" N PRO B 253 " pdb=" CA PRO B 253 " pdb=" C PRO B 253 " ideal model delta sigma weight residual 110.70 113.18 -2.48 1.22e+00 6.72e-01 4.12e+00 ... (remaining 6157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.22: 2356 18.22 - 36.44: 279 36.44 - 54.66: 73 54.66 - 72.88: 21 72.88 - 91.10: 8 Dihedral angle restraints: 2737 sinusoidal: 1127 harmonic: 1610 Sorted by residual: dihedral pdb=" CA ASP A 177 " pdb=" CB ASP A 177 " pdb=" CG ASP A 177 " pdb=" OD1 ASP A 177 " ideal model delta sinusoidal sigma weight residual -30.00 -89.19 59.19 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA GLY B 153 " pdb=" C GLY B 153 " pdb=" N VAL B 154 " pdb=" CA VAL B 154 " ideal model delta harmonic sigma weight residual 180.00 162.95 17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ASP A 345 " pdb=" CB ASP A 345 " pdb=" CG ASP A 345 " pdb=" OD1 ASP A 345 " ideal model delta sinusoidal sigma weight residual -30.00 -87.41 57.41 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 2734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 412 0.026 - 0.053: 168 0.053 - 0.079: 72 0.079 - 0.105: 31 0.105 - 0.131: 11 Chirality restraints: 694 Sorted by residual: chirality pdb=" CA VAL B 44 " pdb=" N VAL B 44 " pdb=" C VAL B 44 " pdb=" CB VAL B 44 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA VAL B 154 " pdb=" N VAL B 154 " pdb=" C VAL B 154 " pdb=" CB VAL B 154 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE B 99 " pdb=" N ILE B 99 " pdb=" C ILE B 99 " pdb=" CB ILE B 99 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 691 not shown) Planarity restraints: 773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 22 " -0.118 9.50e-02 1.11e+02 5.36e-02 2.44e+00 pdb=" NE ARG B 22 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 22 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 22 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 22 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 345 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO A 346 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 346 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 346 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 283 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO B 284 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " -0.018 5.00e-02 4.00e+02 ... (remaining 770 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 995 2.78 - 3.31: 4203 3.31 - 3.84: 7656 3.84 - 4.37: 9553 4.37 - 4.90: 15622 Nonbonded interactions: 38029 Sorted by model distance: nonbonded pdb=" OG SER B 181 " pdb=" O HOH B 401 " model vdw 2.254 3.040 nonbonded pdb=" O HOH A 503 " pdb=" O HOH A 527 " model vdw 2.260 3.040 nonbonded pdb=" O HOH A 507 " pdb=" O HOH A 521 " model vdw 2.267 3.040 nonbonded pdb=" O HOH A 512 " pdb=" O HOH B 419 " model vdw 2.292 3.040 nonbonded pdb=" O PHE B 152 " pdb=" O HOH B 402 " model vdw 2.327 3.040 ... (remaining 38024 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: 0.220 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: 0.040 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.690 Find NCS groups from input model: 0.010 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:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 4538 Z= 0.157 Angle : 0.510 8.828 6162 Z= 0.250 Chirality : 0.039 0.131 694 Planarity : 0.004 0.054 773 Dihedral : 17.770 91.098 1695 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.44 % Allowed : 20.82 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.35), residues: 538 helix: 1.75 (0.31), residues: 273 sheet: 0.42 (0.87), residues: 30 loop : 0.61 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 22 TYR 0.007 0.001 TYR A 347 PHE 0.015 0.001 PHE B 152 TRP 0.008 0.001 TRP A 372 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4538) covalent geometry : angle 0.51001 ( 6162) hydrogen bonds : bond 0.15183 ( 218) hydrogen bonds : angle 5.38654 ( 618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.189 Fit side-chains REVERT: A 289 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7535 (tppt) outliers start: 7 outliers final: 7 residues processed: 86 average time/residue: 0.4469 time to fit residues: 39.7967 Evaluate side-chains 82 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.0670 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 229 ASN A 233 HIS A 290 GLN A 313 GLN B 60 HIS B 62 ASN B 85 GLN B 131 GLN B 265 GLN B 268 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.136225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117244 restraints weight = 5012.453| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.41 r_work: 0.3203 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4538 Z= 0.113 Angle : 0.478 6.142 6162 Z= 0.254 Chirality : 0.040 0.131 694 Planarity : 0.004 0.035 773 Dihedral : 5.995 56.978 612 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.06 % Allowed : 18.97 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.36), residues: 538 helix: 2.16 (0.32), residues: 274 sheet: 1.44 (0.98), residues: 22 loop : 0.64 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 22 TYR 0.010 0.001 TYR B 179 PHE 0.017 0.001 PHE B 152 TRP 0.007 0.001 TRP A 372 HIS 0.002 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 4538) covalent geometry : angle 0.47791 ( 6162) hydrogen bonds : bond 0.04417 ( 218) hydrogen bonds : angle 4.19495 ( 618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.105 Fit side-chains REVERT: A 289 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7496 (tppt) outliers start: 10 outliers final: 6 residues processed: 89 average time/residue: 0.4382 time to fit residues: 40.3288 Evaluate side-chains 84 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 290 GLN B 62 ASN B 131 GLN B 265 GLN B 268 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117416 restraints weight = 4962.637| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.46 r_work: 0.3187 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4538 Z= 0.120 Angle : 0.490 6.180 6162 Z= 0.257 Chirality : 0.041 0.135 694 Planarity : 0.004 0.035 773 Dihedral : 5.619 48.736 609 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.06 % Allowed : 18.97 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.37), residues: 538 helix: 2.25 (0.32), residues: 274 sheet: 1.44 (0.98), residues: 22 loop : 0.58 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 250 TYR 0.010 0.001 TYR A 347 PHE 0.019 0.001 PHE B 152 TRP 0.008 0.001 TRP A 372 HIS 0.002 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4538) covalent geometry : angle 0.49024 ( 6162) hydrogen bonds : bond 0.04154 ( 218) hydrogen bonds : angle 4.04199 ( 618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.195 Fit side-chains REVERT: A 289 LYS cc_start: 0.8018 (mtpp) cc_final: 0.7250 (mppt) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.4609 time to fit residues: 43.9818 Evaluate side-chains 82 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 8 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 265 GLN B 268 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118870 restraints weight = 4939.942| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.45 r_work: 0.3208 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4538 Z= 0.107 Angle : 0.469 6.166 6162 Z= 0.247 Chirality : 0.040 0.133 694 Planarity : 0.004 0.035 773 Dihedral : 5.388 44.174 608 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.65 % Allowed : 18.97 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.37), residues: 538 helix: 2.31 (0.32), residues: 274 sheet: 1.34 (0.97), residues: 22 loop : 0.62 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 378 TYR 0.009 0.001 TYR A 413 PHE 0.018 0.001 PHE B 152 TRP 0.008 0.001 TRP A 372 HIS 0.002 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 4538) covalent geometry : angle 0.46932 ( 6162) hydrogen bonds : bond 0.03785 ( 218) hydrogen bonds : angle 3.94664 ( 618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.184 Fit side-chains REVERT: A 289 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7238 (mppt) outliers start: 8 outliers final: 6 residues processed: 86 average time/residue: 0.4418 time to fit residues: 39.2964 Evaluate side-chains 82 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN B 85 GLN B 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.136663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116942 restraints weight = 4961.728| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.46 r_work: 0.3184 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4538 Z= 0.134 Angle : 0.501 6.196 6162 Z= 0.264 Chirality : 0.041 0.135 694 Planarity : 0.004 0.038 773 Dihedral : 5.481 43.543 608 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.06 % Allowed : 18.76 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.36), residues: 538 helix: 2.23 (0.32), residues: 274 sheet: 1.19 (0.96), residues: 22 loop : 0.55 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 378 TYR 0.012 0.001 TYR A 347 PHE 0.019 0.002 PHE B 152 TRP 0.010 0.001 TRP A 372 HIS 0.003 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 4538) covalent geometry : angle 0.50127 ( 6162) hydrogen bonds : bond 0.04253 ( 218) hydrogen bonds : angle 4.00155 ( 618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.101 Fit side-chains REVERT: A 289 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7250 (mppt) REVERT: B 131 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7118 (pm20) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 0.4189 time to fit residues: 36.7820 Evaluate side-chains 83 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN B 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.136533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117568 restraints weight = 4971.368| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.43 r_work: 0.3195 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4538 Z= 0.119 Angle : 0.486 6.182 6162 Z= 0.256 Chirality : 0.041 0.134 694 Planarity : 0.004 0.033 773 Dihedral : 5.400 41.898 608 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.86 % Allowed : 18.97 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.37), residues: 538 helix: 2.24 (0.32), residues: 274 sheet: 1.25 (0.95), residues: 22 loop : 0.53 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 250 TYR 0.010 0.001 TYR A 347 PHE 0.018 0.001 PHE B 152 TRP 0.009 0.001 TRP A 372 HIS 0.002 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4538) covalent geometry : angle 0.48572 ( 6162) hydrogen bonds : bond 0.03976 ( 218) hydrogen bonds : angle 3.95367 ( 618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.097 Fit side-chains REVERT: A 289 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7268 (mppt) outliers start: 9 outliers final: 8 residues processed: 87 average time/residue: 0.3683 time to fit residues: 33.1649 Evaluate side-chains 85 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 49 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.137603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118759 restraints weight = 4960.543| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.42 r_work: 0.3218 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4538 Z= 0.100 Angle : 0.464 6.164 6162 Z= 0.245 Chirality : 0.040 0.133 694 Planarity : 0.004 0.036 773 Dihedral : 5.253 40.395 608 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.06 % Allowed : 18.97 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.37), residues: 538 helix: 2.31 (0.32), residues: 274 sheet: 1.38 (0.95), residues: 22 loop : 0.56 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 250 TYR 0.009 0.001 TYR B 19 PHE 0.018 0.001 PHE B 152 TRP 0.008 0.001 TRP A 372 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 4538) covalent geometry : angle 0.46418 ( 6162) hydrogen bonds : bond 0.03589 ( 218) hydrogen bonds : angle 3.87319 ( 618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.097 Fit side-chains REVERT: A 289 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7346 (mppt) REVERT: B 131 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7102 (pm20) outliers start: 10 outliers final: 7 residues processed: 85 average time/residue: 0.3637 time to fit residues: 31.9815 Evaluate side-chains 85 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 50 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN B 131 GLN B 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.133537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.114601 restraints weight = 4971.793| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.42 r_work: 0.3155 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4538 Z= 0.211 Angle : 0.599 6.585 6162 Z= 0.316 Chirality : 0.045 0.146 694 Planarity : 0.005 0.034 773 Dihedral : 5.801 42.610 608 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.27 % Allowed : 18.76 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.36), residues: 538 helix: 1.94 (0.32), residues: 273 sheet: 0.79 (0.94), residues: 22 loop : 0.33 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 22 TYR 0.016 0.002 TYR A 347 PHE 0.022 0.002 PHE B 152 TRP 0.013 0.002 TRP A 372 HIS 0.005 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 4538) covalent geometry : angle 0.59889 ( 6162) hydrogen bonds : bond 0.05334 ( 218) hydrogen bonds : angle 4.23786 ( 618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.116 Fit side-chains REVERT: A 289 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7531 (tppt) outliers start: 11 outliers final: 9 residues processed: 83 average time/residue: 0.3576 time to fit residues: 30.7413 Evaluate side-chains 82 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 chunk 2 optimal weight: 0.0060 chunk 16 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118776 restraints weight = 4849.836| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.41 r_work: 0.3208 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4538 Z= 0.099 Angle : 0.478 6.139 6162 Z= 0.254 Chirality : 0.040 0.132 694 Planarity : 0.004 0.035 773 Dihedral : 5.412 40.289 608 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.47 % Allowed : 18.35 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.37), residues: 538 helix: 2.24 (0.32), residues: 272 sheet: 1.07 (0.93), residues: 22 loop : 0.48 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.011 0.001 TYR B 19 PHE 0.017 0.001 PHE B 152 TRP 0.011 0.001 TRP A 372 HIS 0.003 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 4538) covalent geometry : angle 0.47804 ( 6162) hydrogen bonds : bond 0.03562 ( 218) hydrogen bonds : angle 3.90078 ( 618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.116 Fit side-chains REVERT: A 289 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7263 (mppt) outliers start: 12 outliers final: 7 residues processed: 86 average time/residue: 0.3499 time to fit residues: 31.1721 Evaluate side-chains 80 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.118883 restraints weight = 4899.668| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.41 r_work: 0.3214 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4538 Z= 0.105 Angle : 0.482 6.172 6162 Z= 0.254 Chirality : 0.040 0.133 694 Planarity : 0.004 0.034 773 Dihedral : 5.262 38.849 608 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.65 % Allowed : 20.00 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.37), residues: 538 helix: 2.30 (0.32), residues: 273 sheet: 1.29 (0.92), residues: 22 loop : 0.49 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.010 0.001 TYR B 19 PHE 0.019 0.001 PHE B 152 TRP 0.009 0.001 TRP A 372 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 4538) covalent geometry : angle 0.48225 ( 6162) hydrogen bonds : bond 0.03661 ( 218) hydrogen bonds : angle 3.90125 ( 618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.096 Fit side-chains REVERT: A 289 LYS cc_start: 0.8030 (mtpp) cc_final: 0.7259 (mppt) outliers start: 8 outliers final: 7 residues processed: 87 average time/residue: 0.3485 time to fit residues: 31.3922 Evaluate side-chains 84 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.138338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119545 restraints weight = 4959.168| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.42 r_work: 0.3230 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4538 Z= 0.099 Angle : 0.474 6.161 6162 Z= 0.249 Chirality : 0.040 0.133 694 Planarity : 0.004 0.034 773 Dihedral : 5.116 37.457 608 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.65 % Allowed : 21.03 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.37), residues: 538 helix: 2.35 (0.32), residues: 272 sheet: 1.34 (0.91), residues: 22 loop : 0.54 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.010 0.001 TYR B 19 PHE 0.018 0.001 PHE B 152 TRP 0.008 0.001 TRP A 372 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 4538) covalent geometry : angle 0.47356 ( 6162) hydrogen bonds : bond 0.03444 ( 218) hydrogen bonds : angle 3.87015 ( 618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1244.14 seconds wall clock time: 24 minutes 48.66 seconds (1488.66 seconds total)