Starting phenix.real_space_refine on Tue Feb 3 15:07:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jv1_61836/02_2026/9jv1_61836.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jv1_61836/02_2026/9jv1_61836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jv1_61836/02_2026/9jv1_61836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jv1_61836/02_2026/9jv1_61836.map" model { file = "/net/cci-nas-00/data/ceres_data/9jv1_61836/02_2026/9jv1_61836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jv1_61836/02_2026/9jv1_61836.cif" } resolution = 3.1 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= -0.003 sd= 0.071 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 35 5.16 5 C 2687 2.51 5 N 652 2.21 5 O 691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4065 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4040 Classifications: {'peptide': 531} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 500} Chain breaks: 6 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.13, per 1000 atoms: 0.28 Number of scatterers: 4065 At special positions: 0 Unit cell: (94.35, 56.95, 73.1, 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 35 16.00 O 691 8.00 N 652 7.00 C 2687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 448 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 444 " - pdb=" SG CYS A 494 " distance=2.03 Simple disulfide: pdb=" SG CYS A 450 " - pdb=" SG CYS A 470 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 492 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 594 " distance=2.03 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: 0.35 Conformation dependent library (CDL) restraints added in 161.8 milliseconds 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 982 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 71.9% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 26 through 29 Processing helix chain 'A' and resid 30 through 64 removed outlier: 3.617A pdb=" N PHE A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N THR A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N THR A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 91 removed outlier: 4.673A pdb=" N ASN A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLU A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N PHE A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 96 through 115 Processing helix chain 'A' and resid 116 through 122 removed outlier: 3.717A pdb=" N PHE A 120 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.671A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 198 removed outlier: 3.557A pdb=" N PHE A 190 " --> pdb=" O PRO A 186 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 193 " --> pdb=" O PRO A 189 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 217 through 230 Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.766A pdb=" N ALA A 243 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 273 removed outlier: 4.244A pdb=" N GLY A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 261 " --> pdb=" O TRP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 277 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 314 through 324 removed outlier: 3.858A pdb=" N ARG A 321 " --> pdb=" O CYS A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 346 removed outlier: 3.548A pdb=" N VAL A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 341 " --> pdb=" O THR A 337 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 358 Processing helix chain 'A' and resid 360 through 371 Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.681A pdb=" N GLY A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 411 removed outlier: 3.970A pdb=" N THR A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.577A pdb=" N MET A 418 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 514 through 530 Processing helix chain 'A' and resid 532 through 543 removed outlier: 3.580A pdb=" N VAL A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 541 " --> pdb=" O TYR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 564 Processing helix chain 'A' and resid 566 through 577 removed outlier: 4.004A pdb=" N ALA A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 631 removed outlier: 3.620A pdb=" N GLN A 610 " --> pdb=" O TYR A 606 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 621 " --> pdb=" O GLY A 617 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 466 removed outlier: 4.614A pdb=" N ILE A 488 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N CYS A 492 " --> pdb=" O CYS A 474 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N CYS A 474 " --> pdb=" O CYS A 492 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 580 through 583 removed outlier: 6.649A pdb=" N CYS A 580 " --> pdb=" O TYR A 597 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR A 597 " --> pdb=" O CYS A 580 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG A 582 " --> pdb=" O ALA A 595 " (cutoff:3.500A) 248 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: 0.64 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 711 1.33 - 1.45: 1068 1.45 - 1.57: 2340 1.57 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 4168 Sorted by residual: bond pdb=" C1 P2E A 701 " pdb=" O2 P2E A 701 " ideal model delta sigma weight residual 1.250 1.312 -0.062 2.00e-02 2.50e+03 9.59e+00 bond pdb=" C1 P2E A 701 " pdb=" C2 P2E A 701 " ideal model delta sigma weight residual 1.539 1.500 0.039 2.00e-02 2.50e+03 3.88e+00 bond pdb=" C1 P2E A 701 " pdb=" O1 P2E A 701 " ideal model delta sigma weight residual 1.247 1.210 0.037 2.00e-02 2.50e+03 3.47e+00 bond pdb=" C19 P2E A 701 " pdb=" C20 P2E A 701 " ideal model delta sigma weight residual 1.522 1.490 0.032 2.00e-02 2.50e+03 2.55e+00 bond pdb=" C18 P2E A 701 " pdb=" C19 P2E A 701 " ideal model delta sigma weight residual 1.524 1.494 0.030 2.00e-02 2.50e+03 2.32e+00 ... (remaining 4163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 5464 1.15 - 2.30: 130 2.30 - 3.46: 43 3.46 - 4.61: 10 4.61 - 5.76: 17 Bond angle restraints: 5664 Sorted by residual: angle pdb=" N ARG A 97 " pdb=" CA ARG A 97 " pdb=" C ARG A 97 " ideal model delta sigma weight residual 109.81 114.12 -4.31 2.21e+00 2.05e-01 3.80e+00 angle pdb=" C2 P2E A 701 " pdb=" C1 P2E A 701 " pdb=" O1 P2E A 701 " ideal model delta sigma weight residual 117.90 123.66 -5.76 3.00e+00 1.11e-01 3.69e+00 angle pdb=" C ALA A 426 " pdb=" N GLU A 427 " pdb=" CA GLU A 427 " ideal model delta sigma weight residual 121.54 125.18 -3.64 1.91e+00 2.74e-01 3.63e+00 angle pdb=" C10 P2E A 701 " pdb=" C11 P2E A 701 " pdb=" C12 P2E A 701 " ideal model delta sigma weight residual 103.54 98.15 5.39 3.00e+00 1.11e-01 3.23e+00 angle pdb=" N MET A 409 " pdb=" CA MET A 409 " pdb=" C MET A 409 " ideal model delta sigma weight residual 114.75 112.49 2.26 1.26e+00 6.30e-01 3.21e+00 ... (remaining 5659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 2215 16.75 - 33.50: 208 33.50 - 50.25: 37 50.25 - 67.01: 9 67.01 - 83.76: 2 Dihedral angle restraints: 2471 sinusoidal: 946 harmonic: 1525 Sorted by residual: dihedral pdb=" CB CYS A 143 " pdb=" SG CYS A 143 " pdb=" SG CYS A 448 " pdb=" CB CYS A 448 " ideal model delta sinusoidal sigma weight residual 93.00 132.02 -39.02 1 1.00e+01 1.00e-02 2.14e+01 dihedral pdb=" CB CYS A 420 " pdb=" SG CYS A 420 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual -86.00 -51.10 -34.90 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CB CYS A 459 " pdb=" SG CYS A 459 " pdb=" SG CYS A 507 " pdb=" CB CYS A 507 " ideal model delta sinusoidal sigma weight residual 93.00 127.82 -34.82 1 1.00e+01 1.00e-02 1.72e+01 ... (remaining 2468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 532 0.052 - 0.105: 114 0.105 - 0.157: 12 0.157 - 0.210: 2 0.210 - 0.262: 2 Chirality restraints: 662 Sorted by residual: chirality pdb=" C15 P2E A 701 " pdb=" C14 P2E A 701 " pdb=" C16 P2E A 701 " pdb=" O5 P2E A 701 " both_signs ideal model delta sigma weight residual False 2.23 2.49 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C8 P2E A 701 " pdb=" C12 P2E A 701 " pdb=" C7 P2E A 701 " pdb=" C9 P2E A 701 " both_signs ideal model delta sigma weight residual False -2.53 -2.76 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C11 P2E A 701 " pdb=" C10 P2E A 701 " pdb=" C12 P2E A 701 " pdb=" O4 P2E A 701 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 659 not shown) Planarity restraints: 700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 P2E A 701 " 0.083 2.00e-02 2.50e+03 1.67e-01 2.80e+02 pdb=" C5 P2E A 701 " -0.218 2.00e-02 2.50e+03 pdb=" C6 P2E A 701 " 0.223 2.00e-02 2.50e+03 pdb=" C7 P2E A 701 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 P2E A 701 " -0.081 2.00e-02 2.50e+03 8.36e-02 6.99e+01 pdb=" C13 P2E A 701 " 0.074 2.00e-02 2.50e+03 pdb=" C14 P2E A 701 " 0.093 2.00e-02 2.50e+03 pdb=" C15 P2E A 701 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 413 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO A 414 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 414 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 414 " -0.019 5.00e-02 4.00e+02 ... (remaining 697 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 515 2.75 - 3.29: 3850 3.29 - 3.82: 6349 3.82 - 4.36: 7316 4.36 - 4.90: 13167 Nonbonded interactions: 31197 Sorted by model distance: nonbonded pdb=" OD2 ASP A 461 " pdb=" OG SER A 499 " model vdw 2.212 3.040 nonbonded pdb=" O ILE A 73 " pdb=" NE2 GLN A 177 " model vdw 2.305 3.120 nonbonded pdb=" O PRO A 398 " pdb=" OG1 THR A 402 " model vdw 2.333 3.040 nonbonded pdb=" O SER A 449 " pdb=" OG SER A 449 " model vdw 2.338 3.040 nonbonded pdb=" OD1 ASN A 350 " pdb=" N LYS A 351 " model vdw 2.380 3.120 ... (remaining 31192 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: 2.330 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.170 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4175 Z= 0.168 Angle : 0.576 5.760 5678 Z= 0.270 Chirality : 0.046 0.262 662 Planarity : 0.008 0.167 700 Dihedral : 13.371 83.757 1468 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.58 (0.38), residues: 517 helix: 0.96 (0.30), residues: 330 sheet: -1.26 (2.22), residues: 5 loop : -0.50 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 94 TYR 0.012 0.001 TYR A 194 PHE 0.010 0.001 PHE A 52 TRP 0.003 0.001 TRP A 257 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 4168) covalent geometry : angle 0.57642 ( 5664) SS BOND : bond 0.00132 ( 7) SS BOND : angle 0.41153 ( 14) hydrogen bonds : bond 0.23475 ( 248) hydrogen bonds : angle 7.16701 ( 723) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.162 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0615 time to fit residues: 4.6843 Evaluate side-chains 50 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.0170 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 534 ASN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.142634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114630 restraints weight = 4653.524| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.58 r_work: 0.3014 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4175 Z= 0.128 Angle : 0.549 5.428 5678 Z= 0.273 Chirality : 0.041 0.132 662 Planarity : 0.004 0.027 700 Dihedral : 5.879 57.614 593 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.15 % Allowed : 5.28 % Favored : 93.58 % 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: 1.27 (0.38), residues: 517 helix: 1.60 (0.30), residues: 341 sheet: -0.56 (2.72), residues: 5 loop : -0.63 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 561 TYR 0.009 0.001 TYR A 194 PHE 0.014 0.001 PHE A 348 TRP 0.004 0.001 TRP A 170 HIS 0.002 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 4168) covalent geometry : angle 0.54935 ( 5664) SS BOND : bond 0.00133 ( 7) SS BOND : angle 0.38417 ( 14) hydrogen bonds : bond 0.05458 ( 248) hydrogen bonds : angle 4.59821 ( 723) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.153 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 0.0855 time to fit residues: 5.8801 Evaluate side-chains 52 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 391 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113196 restraints weight = 4601.281| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.58 r_work: 0.3033 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4175 Z= 0.123 Angle : 0.528 5.365 5678 Z= 0.258 Chirality : 0.041 0.142 662 Planarity : 0.004 0.029 700 Dihedral : 5.606 55.621 593 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.15 % Allowed : 6.88 % Favored : 91.97 % 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 (0.38), residues: 517 helix: 1.87 (0.29), residues: 341 sheet: -0.62 (2.73), residues: 5 loop : -0.66 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 582 TYR 0.010 0.001 TYR A 194 PHE 0.012 0.001 PHE A 348 TRP 0.005 0.001 TRP A 170 HIS 0.001 0.000 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4168) covalent geometry : angle 0.52875 ( 5664) SS BOND : bond 0.00125 ( 7) SS BOND : angle 0.35719 ( 14) hydrogen bonds : bond 0.04989 ( 248) hydrogen bonds : angle 4.22793 ( 723) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.093 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.0685 time to fit residues: 4.5093 Evaluate side-chains 50 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 391 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.133973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.101845 restraints weight = 4725.944| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.78 r_work: 0.2962 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4175 Z= 0.133 Angle : 0.539 5.340 5678 Z= 0.264 Chirality : 0.041 0.139 662 Planarity : 0.004 0.029 700 Dihedral : 5.466 52.985 593 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.92 % Allowed : 8.26 % Favored : 90.83 % 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: 1.57 (0.38), residues: 517 helix: 1.88 (0.29), residues: 342 sheet: -0.61 (2.83), residues: 5 loop : -0.63 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 582 TYR 0.011 0.001 TYR A 194 PHE 0.010 0.001 PHE A 348 TRP 0.004 0.001 TRP A 170 HIS 0.002 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4168) covalent geometry : angle 0.53921 ( 5664) SS BOND : bond 0.00150 ( 7) SS BOND : angle 0.34618 ( 14) hydrogen bonds : bond 0.05067 ( 248) hydrogen bonds : angle 4.14547 ( 723) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.164 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.0830 time to fit residues: 5.3330 Evaluate side-chains 50 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 391 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 0.0040 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.142702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.114780 restraints weight = 4643.357| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.59 r_work: 0.3012 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4175 Z= 0.116 Angle : 0.516 5.311 5678 Z= 0.252 Chirality : 0.040 0.135 662 Planarity : 0.004 0.029 700 Dihedral : 5.238 50.583 593 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.92 % Allowed : 8.72 % Favored : 90.37 % 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: 1.79 (0.38), residues: 517 helix: 2.07 (0.29), residues: 341 sheet: -0.45 (2.93), residues: 5 loop : -0.59 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 582 TYR 0.010 0.001 TYR A 194 PHE 0.011 0.001 PHE A 348 TRP 0.004 0.001 TRP A 170 HIS 0.001 0.000 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4168) covalent geometry : angle 0.51597 ( 5664) SS BOND : bond 0.00121 ( 7) SS BOND : angle 0.30093 ( 14) hydrogen bonds : bond 0.04526 ( 248) hydrogen bonds : angle 3.91478 ( 723) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.158 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.0663 time to fit residues: 4.1804 Evaluate side-chains 50 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 391 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.136123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.104059 restraints weight = 4772.083| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.76 r_work: 0.2998 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4175 Z= 0.109 Angle : 0.507 5.307 5678 Z= 0.247 Chirality : 0.040 0.136 662 Planarity : 0.003 0.029 700 Dihedral : 5.023 48.311 593 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.69 % Allowed : 9.17 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.38), residues: 517 helix: 2.22 (0.29), residues: 340 sheet: -0.39 (2.94), residues: 5 loop : -0.60 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 582 TYR 0.009 0.001 TYR A 194 PHE 0.018 0.001 PHE A 348 TRP 0.005 0.001 TRP A 170 HIS 0.001 0.000 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4168) covalent geometry : angle 0.50791 ( 5664) SS BOND : bond 0.00110 ( 7) SS BOND : angle 0.28181 ( 14) hydrogen bonds : bond 0.04263 ( 248) hydrogen bonds : angle 3.74937 ( 723) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.148 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 53 average time/residue: 0.0634 time to fit residues: 4.2546 Evaluate side-chains 51 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 391 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.134460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.101993 restraints weight = 4786.138| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.80 r_work: 0.2969 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4175 Z= 0.129 Angle : 0.527 5.372 5678 Z= 0.257 Chirality : 0.041 0.136 662 Planarity : 0.004 0.029 700 Dihedral : 5.019 46.768 593 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.15 % Allowed : 9.40 % Favored : 89.45 % 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: 1.83 (0.38), residues: 517 helix: 2.14 (0.29), residues: 341 sheet: -0.66 (2.73), residues: 5 loop : -0.67 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 582 TYR 0.011 0.001 TYR A 194 PHE 0.024 0.001 PHE A 348 TRP 0.004 0.001 TRP A 170 HIS 0.002 0.000 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4168) covalent geometry : angle 0.52781 ( 5664) SS BOND : bond 0.00145 ( 7) SS BOND : angle 0.31308 ( 14) hydrogen bonds : bond 0.04771 ( 248) hydrogen bonds : angle 3.79539 ( 723) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.155 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 0.0799 time to fit residues: 5.5724 Evaluate side-chains 52 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 37 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.141071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112940 restraints weight = 4630.800| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.61 r_work: 0.3006 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4175 Z= 0.135 Angle : 0.540 5.373 5678 Z= 0.264 Chirality : 0.042 0.135 662 Planarity : 0.004 0.028 700 Dihedral : 5.020 45.759 593 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.15 % Allowed : 10.09 % Favored : 88.76 % 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: 1.79 (0.38), residues: 517 helix: 2.11 (0.29), residues: 341 sheet: -0.67 (2.73), residues: 5 loop : -0.69 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 582 TYR 0.011 0.001 TYR A 194 PHE 0.031 0.001 PHE A 348 TRP 0.004 0.001 TRP A 170 HIS 0.002 0.000 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4168) covalent geometry : angle 0.53996 ( 5664) SS BOND : bond 0.00151 ( 7) SS BOND : angle 0.31673 ( 14) hydrogen bonds : bond 0.04949 ( 248) hydrogen bonds : angle 3.80861 ( 723) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.162 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 0.0787 time to fit residues: 5.3644 Evaluate side-chains 53 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 36 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 45 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 610 GLN A 631 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112951 restraints weight = 4690.471| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.64 r_work: 0.3059 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4175 Z= 0.107 Angle : 0.510 5.307 5678 Z= 0.250 Chirality : 0.040 0.134 662 Planarity : 0.004 0.028 700 Dihedral : 4.836 44.684 593 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.92 % Allowed : 10.55 % Favored : 88.53 % 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: 1.94 (0.38), residues: 517 helix: 2.25 (0.29), residues: 340 sheet: -0.81 (2.58), residues: 5 loop : -0.66 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 582 TYR 0.008 0.001 TYR A 194 PHE 0.032 0.001 PHE A 348 TRP 0.004 0.001 TRP A 253 HIS 0.001 0.000 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 4168) covalent geometry : angle 0.51015 ( 5664) SS BOND : bond 0.00165 ( 7) SS BOND : angle 0.51961 ( 14) hydrogen bonds : bond 0.04112 ( 248) hydrogen bonds : angle 3.67637 ( 723) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.153 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 56 average time/residue: 0.0769 time to fit residues: 5.4456 Evaluate side-chains 54 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 48 optimal weight: 0.1980 chunk 31 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.140570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.111204 restraints weight = 4662.456| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.70 r_work: 0.3048 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4175 Z= 0.119 Angle : 0.524 5.348 5678 Z= 0.258 Chirality : 0.041 0.138 662 Planarity : 0.003 0.028 700 Dihedral : 4.837 44.147 593 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.69 % Allowed : 10.55 % Favored : 88.76 % 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: 1.87 (0.38), residues: 517 helix: 2.19 (0.29), residues: 341 sheet: -1.00 (2.56), residues: 5 loop : -0.68 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 582 TYR 0.010 0.001 TYR A 194 PHE 0.006 0.001 PHE A 52 TRP 0.005 0.001 TRP A 170 HIS 0.001 0.000 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 4168) covalent geometry : angle 0.52416 ( 5664) SS BOND : bond 0.00159 ( 7) SS BOND : angle 0.49933 ( 14) hydrogen bonds : bond 0.04462 ( 248) hydrogen bonds : angle 3.69756 ( 723) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.096 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 55 average time/residue: 0.0544 time to fit residues: 3.7716 Evaluate side-chains 55 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 17 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.111194 restraints weight = 4678.675| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.69 r_work: 0.3041 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4175 Z= 0.108 Angle : 0.510 5.312 5678 Z= 0.250 Chirality : 0.040 0.136 662 Planarity : 0.003 0.028 700 Dihedral : 4.742 43.448 593 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.92 % Allowed : 9.86 % Favored : 89.22 % 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: 2.00 (0.38), residues: 517 helix: 2.31 (0.29), residues: 340 sheet: -0.99 (2.55), residues: 5 loop : -0.65 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 582 TYR 0.009 0.001 TYR A 194 PHE 0.006 0.001 PHE A 52 TRP 0.004 0.001 TRP A 253 HIS 0.001 0.000 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4168) covalent geometry : angle 0.51033 ( 5664) SS BOND : bond 0.00126 ( 7) SS BOND : angle 0.42610 ( 14) hydrogen bonds : bond 0.04100 ( 248) hydrogen bonds : angle 3.61761 ( 723) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1167.34 seconds wall clock time: 20 minutes 36.75 seconds (1236.75 seconds total)