Starting phenix.real_space_refine on Thu Oct 22 18:20:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wix_66010/10_2026/9wix_66010.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wix_66010/10_2026/9wix_66010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wix_66010/10_2026/9wix_66010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wix_66010/10_2026/9wix_66010.map" model { file = "/net/cci-nas-00/data/ceres_data/9wix_66010/10_2026/9wix_66010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wix_66010/10_2026/9wix_66010.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 2234 2.51 5 N 542 2.21 5 O 572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3374 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3255 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 19, 'TRANS': 424} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 2, 'ASN:plan1': 4, 'PHE:plan': 3, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 85 Chain: "A" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 119 Unusual residues: {'NAG': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.00, per 1000 atoms: 0.30 Number of scatterers: 3374 At special positions: 0 Unit cell: (59.184, 67.404, 83.022, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 572 8.00 N 542 7.00 C 2234 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 119 " Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 111.1 milliseconds 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 798 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 84.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 86 through 117 removed outlier: 4.035A pdb=" N LEU A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 111 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 158 removed outlier: 3.664A pdb=" N GLY A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N PHE A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 168 through 185 removed outlier: 3.732A pdb=" N MET A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 194 removed outlier: 4.169A pdb=" N ARG A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 210 removed outlier: 3.656A pdb=" N VAL A 198 " --> pdb=" O HIS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 224 removed outlier: 4.084A pdb=" N LYS A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 228 through 257 removed outlier: 4.003A pdb=" N GLY A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Proline residue: A 249 - end of helix Processing helix chain 'A' and resid 259 through 282 removed outlier: 4.288A pdb=" N VAL A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 280 " --> pdb=" O MET A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.677A pdb=" N GLY A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'A' and resid 326 through 346 removed outlier: 3.760A pdb=" N TYR A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 358 removed outlier: 3.510A pdb=" N GLU A 355 " --> pdb=" O PRO A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 393 removed outlier: 4.404A pdb=" N MET A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 377 " --> pdb=" O HIS A 373 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 397 through 422 Processing helix chain 'A' and resid 425 through 448 removed outlier: 3.580A pdb=" N ILE A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 455 removed outlier: 3.721A pdb=" N ASP A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 485 Proline residue: A 478 - end of helix Processing helix chain 'A' and resid 489 through 514 Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.105A pdb=" N ASP A 524 " --> pdb=" O ASP A 521 " (cutoff:3.500A) 242 hydrogen bonds defined for protein. 723 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: 0.52 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 519 1.32 - 1.44: 991 1.44 - 1.57: 1926 1.57 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 3477 Sorted by residual: bond pdb=" CAX Y01 A 604 " pdb=" OAH Y01 A 604 " ideal model delta sigma weight residual 1.248 1.313 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" CAX Y01 A 602 " pdb=" OAF Y01 A 602 " ideal model delta sigma weight residual 1.247 1.308 -0.061 2.00e-02 2.50e+03 9.39e+00 bond pdb=" CAX Y01 A 603 " pdb=" OAH Y01 A 603 " ideal model delta sigma weight residual 1.248 1.306 -0.058 2.00e-02 2.50e+03 8.45e+00 bond pdb=" CAN Y01 A 603 " pdb=" CBA Y01 A 603 " ideal model delta sigma weight residual 1.530 1.487 0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" CAL Y01 A 602 " pdb=" CAX Y01 A 602 " ideal model delta sigma weight residual 1.540 1.500 0.040 2.00e-02 2.50e+03 3.94e+00 ... (remaining 3472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 4609 1.64 - 3.28: 126 3.28 - 4.93: 23 4.93 - 6.57: 4 6.57 - 8.21: 2 Bond angle restraints: 4764 Sorted by residual: angle pdb=" N ALA A 515 " pdb=" CA ALA A 515 " pdb=" C ALA A 515 " ideal model delta sigma weight residual 110.80 102.59 8.21 2.13e+00 2.20e-01 1.49e+01 angle pdb=" N ILE A 258 " pdb=" CA ILE A 258 " pdb=" C ILE A 258 " ideal model delta sigma weight residual 110.62 114.55 -3.93 1.02e+00 9.61e-01 1.49e+01 angle pdb=" C GLY A 218 " pdb=" N MET A 219 " pdb=" CA MET A 219 " ideal model delta sigma weight residual 120.44 124.47 -4.03 1.36e+00 5.41e-01 8.76e+00 angle pdb=" C ALA A 370 " pdb=" N VAL A 371 " pdb=" CA VAL A 371 " ideal model delta sigma weight residual 120.33 122.55 -2.22 8.00e-01 1.56e+00 7.67e+00 angle pdb=" CAL Y01 A 602 " pdb=" CAX Y01 A 602 " pdb=" OAH Y01 A 602 " ideal model delta sigma weight residual 115.62 123.26 -7.64 3.00e+00 1.11e-01 6.49e+00 ... (remaining 4759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.88: 2011 24.88 - 49.76: 93 49.76 - 74.63: 15 74.63 - 99.51: 2 99.51 - 124.39: 3 Dihedral angle restraints: 2124 sinusoidal: 865 harmonic: 1259 Sorted by residual: dihedral pdb=" CAT Y01 A 603 " pdb=" CAR Y01 A 603 " pdb=" CBC Y01 A 603 " pdb=" OAW Y01 A 603 " ideal model delta sinusoidal sigma weight residual 178.96 54.57 124.39 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" CAT Y01 A 603 " pdb=" CAR Y01 A 603 " pdb=" CBC Y01 A 603 " pdb=" CAV Y01 A 603 " ideal model delta sinusoidal sigma weight residual 58.10 -64.04 122.14 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" CBC Y01 A 603 " pdb=" CAR Y01 A 603 " pdb=" CAT Y01 A 603 " pdb=" CBH Y01 A 603 " ideal model delta sinusoidal sigma weight residual -57.13 63.25 -120.38 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 2121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 315 0.035 - 0.070: 172 0.070 - 0.105: 50 0.105 - 0.140: 7 0.140 - 0.175: 2 Chirality restraints: 546 Sorted by residual: chirality pdb=" CA ALA A 515 " pdb=" N ALA A 515 " pdb=" C ALA A 515 " pdb=" CB ALA A 515 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" CA TYR A 257 " pdb=" N TYR A 257 " pdb=" C TYR A 257 " pdb=" CB TYR A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CBC Y01 A 602 " pdb=" CAR Y01 A 602 " pdb=" CAV Y01 A 602 " pdb=" OAW Y01 A 602 " both_signs ideal model delta sigma weight residual False -2.54 -2.68 0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 543 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 350 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO A 351 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 351 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 351 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 477 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 478 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 478 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 478 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 138 " -0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 139 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " -0.019 5.00e-02 4.00e+02 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 796 2.79 - 3.31: 3463 3.31 - 3.84: 5604 3.84 - 4.37: 6412 4.37 - 4.90: 11215 Nonbonded interactions: 27490 Sorted by model distance: nonbonded pdb=" OH TYR A 89 " pdb=" OE2 GLU A 228 " model vdw 2.257 3.040 nonbonded pdb=" OG SER A 102 " pdb=" OE1 GLU A 209 " model vdw 2.332 3.040 nonbonded pdb=" OD1 ASN A 119 " pdb=" N2 NAG A 601 " model vdw 2.355 3.120 nonbonded pdb=" OG1 THR A 180 " pdb=" OE2 GLU A 209 " model vdw 2.371 3.040 nonbonded pdb=" O PHE A 324 " pdb=" OH TYR A 330 " model vdw 2.378 3.040 ... (remaining 27485 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.580 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: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 5.070 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 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 0.065 3478 Z= 0.235 Angle : 0.696 8.209 4767 Z= 0.382 Chirality : 0.044 0.175 546 Planarity : 0.005 0.051 581 Dihedral : 15.073 124.389 1326 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.41), residues: 442 helix: 1.08 (0.29), residues: 335 sheet: -1.80 (1.58), residues: 12 loop : -0.71 (0.66), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.018 0.001 TYR A 195 PHE 0.013 0.001 PHE A 323 TRP 0.008 0.001 TRP A 278 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.23 ( 3477) covalent geometry : angle 0.69007 / 0.38 ( 4764) hydrogen bonds : bond 0.11576 / 6.95 ( 242) hydrogen bonds : angle 5.72284 / 4.36 ( 723) link_NAG-ASN : bond 0.01078 / 0.57 ( 1) link_NAG-ASN : angle 3.72663 / 1.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.123 Fit side-chains REVERT: A 115 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7296 (tm-30) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0584 time to fit residues: 5.8958 Evaluate side-chains 72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37] chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS A 504 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.163180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.117692 restraints weight = 3733.986| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.12 r_work: 0.3100 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3478 Z= 0.154 Angle : 0.557 5.152 4767 Z= 0.286 Chirality : 0.043 0.120 546 Planarity : 0.005 0.046 581 Dihedral : 10.678 99.853 710 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.29 % Allowed : 10.68 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.41), residues: 442 helix: 1.37 (0.29), residues: 333 sheet: -1.86 (1.52), residues: 12 loop : -0.28 (0.67), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 88 TYR 0.009 0.001 TYR A 344 PHE 0.015 0.001 PHE A 514 TRP 0.012 0.001 TRP A 278 HIS 0.002 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 3477) covalent geometry : angle 0.54819 / 0.28 ( 4764) hydrogen bonds : bond 0.03892 / 2.57 ( 242) hydrogen bonds : angle 4.52873 / 3.44 ( 723) link_NAG-ASN : bond 0.00976 / 0.51 ( 1) link_NAG-ASN : angle 3.94310 / 2.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.113 Fit side-chains REVERT: A 115 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8245 (tm-30) REVERT: A 413 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7363 (tm-30) REVERT: A 417 LEU cc_start: 0.8409 (mt) cc_final: 0.8130 (mt) outliers start: 4 outliers final: 3 residues processed: 76 average time/residue: 0.0517 time to fit residues: 5.0029 Evaluate side-chains 72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 404 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [42, 37, 32, 21, 38, 6, 36, 15, 1, 2, 19] chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.161127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115612 restraints weight = 3810.106| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.12 r_work: 0.3113 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3478 Z= 0.158 Angle : 0.544 7.260 4767 Z= 0.276 Chirality : 0.043 0.124 546 Planarity : 0.004 0.043 581 Dihedral : 9.689 87.149 710 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.94 % Allowed : 13.27 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.41), residues: 442 helix: 1.48 (0.29), residues: 333 sheet: -1.87 (1.45), residues: 12 loop : -0.32 (0.66), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.018 0.001 TYR A 195 PHE 0.010 0.001 PHE A 514 TRP 0.012 0.001 TRP A 278 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 3477) covalent geometry : angle 0.53961 / 0.28 ( 4764) hydrogen bonds : bond 0.03783 / 2.47 ( 242) hydrogen bonds : angle 4.42899 / 3.36 ( 723) link_NAG-ASN : bond 0.00690 / 0.36 ( 1) link_NAG-ASN : angle 2.75110 / 1.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.112 Fit side-chains REVERT: A 413 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7363 (tm-30) REVERT: A 417 LEU cc_start: 0.8502 (mt) cc_final: 0.8121 (mt) outliers start: 6 outliers final: 1 residues processed: 78 average time/residue: 0.0578 time to fit residues: 5.7239 Evaluate side-chains 74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [43, 25, 33, 30, 10, 9, 0, 29, 4, 26, 40] chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 30.0000 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.160861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115112 restraints weight = 3778.412| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.12 r_work: 0.3081 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3478 Z= 0.158 Angle : 0.552 8.747 4767 Z= 0.276 Chirality : 0.042 0.123 546 Planarity : 0.004 0.041 581 Dihedral : 8.272 59.259 710 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.65 % Allowed : 15.86 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.40), residues: 442 helix: 1.52 (0.28), residues: 334 sheet: -1.89 (1.38), residues: 12 loop : -0.29 (0.66), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 88 TYR 0.016 0.001 TYR A 195 PHE 0.009 0.001 PHE A 323 TRP 0.011 0.001 TRP A 278 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 3477) covalent geometry : angle 0.54975 / 0.28 ( 4764) hydrogen bonds : bond 0.03626 / 2.38 ( 242) hydrogen bonds : angle 4.35761 / 3.31 ( 723) link_NAG-ASN : bond 0.00544 / 0.29 ( 1) link_NAG-ASN : angle 2.13950 / 1.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.116 Fit side-chains REVERT: A 413 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7337 (tm-30) REVERT: A 417 LEU cc_start: 0.8540 (mt) cc_final: 0.8138 (mt) outliers start: 2 outliers final: 2 residues processed: 75 average time/residue: 0.0510 time to fit residues: 4.8880 Evaluate side-chains 74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 245 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [1, 26, 39, 23, 29, 11, 37, 18, 12, 35, 42] chunk 1 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.0870 chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.163158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.117395 restraints weight = 3754.057| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.15 r_work: 0.3005 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3478 Z= 0.122 Angle : 0.514 5.846 4767 Z= 0.259 Chirality : 0.041 0.132 546 Planarity : 0.004 0.040 581 Dihedral : 7.392 56.006 710 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.32 % Allowed : 18.12 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.41), residues: 442 helix: 1.63 (0.28), residues: 336 sheet: -1.81 (1.39), residues: 12 loop : -0.21 (0.66), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.018 0.001 TYR A 195 PHE 0.009 0.001 PHE A 514 TRP 0.010 0.001 TRP A 278 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3477) covalent geometry : angle 0.51213 / 0.26 ( 4764) hydrogen bonds : bond 0.03265 / 2.11 ( 242) hydrogen bonds : angle 4.19723 / 3.21 ( 723) link_NAG-ASN : bond 0.00509 / 0.27 ( 1) link_NAG-ASN : angle 1.76326 / 0.99 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.088 Fit side-chains REVERT: A 413 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7350 (tm-30) outliers start: 1 outliers final: 1 residues processed: 75 average time/residue: 0.0568 time to fit residues: 5.4083 Evaluate side-chains 72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [0, 19, 12, 32, 41, 5, 38, 15, 22, 14, 11] chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.0070 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.162314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.117399 restraints weight = 3775.557| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.08 r_work: 0.3147 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3478 Z= 0.131 Angle : 0.521 5.091 4767 Z= 0.264 Chirality : 0.042 0.139 546 Planarity : 0.004 0.038 581 Dihedral : 7.258 55.855 710 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.62 % Allowed : 17.15 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.40), residues: 442 helix: 1.48 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -0.57 (0.62), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 192 TYR 0.017 0.001 TYR A 195 PHE 0.007 0.001 PHE A 149 TRP 0.010 0.001 TRP A 278 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 3477) covalent geometry : angle 0.51923 / 0.26 ( 4764) hydrogen bonds : bond 0.03388 / 2.20 ( 242) hydrogen bonds : angle 4.23127 / 3.23 ( 723) link_NAG-ASN : bond 0.00460 / 0.24 ( 1) link_NAG-ASN : angle 1.61248 / 0.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.078 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 78 average time/residue: 0.0570 time to fit residues: 5.6823 Evaluate side-chains 74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 245 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [10, 25, 4, 17, 14, 9, 42, 13, 29, 11, 31] chunk 10 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.0050 chunk 9 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.165374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.120997 restraints weight = 3786.260| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.11 r_work: 0.3139 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3478 Z= 0.111 Angle : 0.513 4.995 4767 Z= 0.263 Chirality : 0.041 0.141 546 Planarity : 0.004 0.037 581 Dihedral : 7.147 57.111 710 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.62 % Allowed : 18.45 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.41), residues: 442 helix: 1.55 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -0.46 (0.63), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.018 0.001 TYR A 195 PHE 0.007 0.001 PHE A 103 TRP 0.009 0.001 TRP A 278 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 3477) covalent geometry : angle 0.51215 / 0.26 ( 4764) hydrogen bonds : bond 0.03122 / 2.01 ( 242) hydrogen bonds : angle 4.09554 / 3.14 ( 723) link_NAG-ASN : bond 0.00451 / 0.24 ( 1) link_NAG-ASN : angle 1.45240 / 0.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.079 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 75 average time/residue: 0.0510 time to fit residues: 4.9034 Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 447 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [23, 40, 28, 35, 38, 41, 15, 39, 1, 27, 16] chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.159718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.114948 restraints weight = 3907.051| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.11 r_work: 0.3086 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3478 Z= 0.186 Angle : 0.559 5.296 4767 Z= 0.289 Chirality : 0.043 0.146 546 Planarity : 0.004 0.036 581 Dihedral : 7.121 56.404 710 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.29 % Allowed : 20.06 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.40), residues: 442 helix: 1.44 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -0.54 (0.61), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 231 TYR 0.017 0.001 TYR A 195 PHE 0.010 0.001 PHE A 150 TRP 0.011 0.001 TRP A 278 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 ( 3477) covalent geometry : angle 0.55768 / 0.29 ( 4764) hydrogen bonds : bond 0.03730 / 2.45 ( 242) hydrogen bonds : angle 4.32278 / 3.28 ( 723) link_NAG-ASN : bond 0.00435 / 0.23 ( 1) link_NAG-ASN : angle 1.35899 / 0.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.086 Fit side-chains REVERT: A 97 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8466 (mt) outliers start: 4 outliers final: 1 residues processed: 74 average time/residue: 0.0534 time to fit residues: 5.0526 Evaluate side-chains 73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 245 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [41, 10, 31, 18, 43, 37, 38, 40, 22, 19, 30] chunk 41 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.160327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116096 restraints weight = 3792.284| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.07 r_work: 0.3098 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3478 Z= 0.161 Angle : 0.556 5.289 4767 Z= 0.287 Chirality : 0.042 0.142 546 Planarity : 0.004 0.036 581 Dihedral : 7.148 57.482 710 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.62 % Allowed : 20.39 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.40), residues: 442 helix: 1.42 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -0.51 (0.61), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 297 TYR 0.018 0.001 TYR A 195 PHE 0.008 0.001 PHE A 149 TRP 0.010 0.001 TRP A 278 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 3477) covalent geometry : angle 0.55514 / 0.29 ( 4764) hydrogen bonds : bond 0.03589 / 2.34 ( 242) hydrogen bonds : angle 4.29837 / 3.27 ( 723) link_NAG-ASN : bond 0.00445 / 0.23 ( 1) link_NAG-ASN : angle 1.21449 / 0.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.128 Fit side-chains REVERT: A 297 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7667 (ttm110) outliers start: 5 outliers final: 2 residues processed: 71 average time/residue: 0.0555 time to fit residues: 5.0453 Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 245 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [28, 40, 33, 31, 29, 2, 43, 41, 27, 37, 13] chunk 28 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 0.1980 chunk 29 optimal weight: 0.0270 chunk 2 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.162684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.118755 restraints weight = 3806.919| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.08 r_work: 0.3166 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3478 Z= 0.128 Angle : 0.538 5.673 4767 Z= 0.277 Chirality : 0.041 0.144 546 Planarity : 0.004 0.037 581 Dihedral : 7.098 59.613 710 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.97 % Allowed : 21.36 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.40), residues: 442 helix: 1.47 (0.28), residues: 342 sheet: None (None), residues: 0 loop : -0.39 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 297 TYR 0.018 0.001 TYR A 195 PHE 0.008 0.001 PHE A 103 TRP 0.009 0.001 TRP A 278 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 3477) covalent geometry : angle 0.53687 / 0.28 ( 4764) hydrogen bonds : bond 0.03316 / 2.15 ( 242) hydrogen bonds : angle 4.19095 / 3.20 ( 723) link_NAG-ASN : bond 0.00470 / 0.25 ( 1) link_NAG-ASN : angle 1.18152 / 0.68 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.124 Fit side-chains REVERT: A 297 ARG cc_start: 0.7950 (ttm110) cc_final: 0.7673 (ttm110) outliers start: 3 outliers final: 2 residues processed: 73 average time/residue: 0.0582 time to fit residues: 5.4070 Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 245 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [7, 14, 34, 27, 10, 20, 2, 30, 31, 38, 42] chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.162662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.117446 restraints weight = 3814.149| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.13 r_work: 0.2971 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3478 Z= 0.135 Angle : 0.545 5.752 4767 Z= 0.282 Chirality : 0.042 0.140 546 Planarity : 0.004 0.036 581 Dihedral : 7.035 59.852 710 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.29 % Allowed : 21.04 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.40), residues: 442 helix: 1.47 (0.28), residues: 342 sheet: None (None), residues: 0 loop : -0.32 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 297 TYR 0.017 0.001 TYR A 195 PHE 0.008 0.001 PHE A 439 TRP 0.009 0.001 TRP A 278 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 3477) covalent geometry : angle 0.54432 / 0.28 ( 4764) hydrogen bonds : bond 0.03368 / 2.19 ( 242) hydrogen bonds : angle 4.19725 / 3.21 ( 723) link_NAG-ASN : bond 0.00472 / 0.25 ( 1) link_NAG-ASN : angle 1.19227 / 0.68 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1022.44 seconds wall clock time: 18 minutes 12.38 seconds (1092.38 seconds total)