Starting phenix.real_space_refine on Wed Sep 17 08:52:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xum_38677/09_2025/8xum_38677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xum_38677/09_2025/8xum_38677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xum_38677/09_2025/8xum_38677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xum_38677/09_2025/8xum_38677.map" model { file = "/net/cci-nas-00/data/ceres_data/8xum_38677/09_2025/8xum_38677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xum_38677/09_2025/8xum_38677.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.019 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 52 5.16 5 C 4729 2.51 5 N 1234 2.21 5 O 1344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7359 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 834 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 106} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 5728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5728 Classifications: {'peptide': 738} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 36, 'TRANS': 701} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 797 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 2.06, per 1000 atoms: 0.28 Number of scatterers: 7359 At special positions: 0 Unit cell: (109.242, 153.153, 78.183, 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 52 16.00 O 1344 8.00 N 1234 7.00 C 4729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS C 447 " - pdb=" SG CYS C 520 " distance=2.03 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 44 " distance=2.03 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 693 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 46 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 141 " 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: 0.59 Conformation dependent library (CDL) restraints added in 551.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1782 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 13 sheets defined 27.2% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.834A pdb=" N LEU A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.601A pdb=" N LYS A 246 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 248 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 471 through 476 Processing helix chain 'A' and resid 538 through 565 Processing helix chain 'A' and resid 571 through 601 Processing helix chain 'A' and resid 604 through 607 Processing helix chain 'A' and resid 608 through 614 removed outlier: 3.519A pdb=" N THR A 614 " --> pdb=" O ILE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 649 removed outlier: 3.854A pdb=" N LYS A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 683 Proline residue: A 680 - end of helix removed outlier: 3.740A pdb=" N HIS A 683 " --> pdb=" O PHE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 732 removed outlier: 3.520A pdb=" N THR A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 769 removed outlier: 3.506A pdb=" N VAL A 749 " --> pdb=" O MET A 745 " (cutoff:3.500A) Proline residue: A 762 - end of helix Processing helix chain 'A' and resid 770 through 772 No H-bonds generated for 'chain 'A' and resid 770 through 772' Processing helix chain 'A' and resid 778 through 790 Processing helix chain 'A' and resid 791 through 804 Proline residue: A 798 - end of helix Processing helix chain 'A' and resid 805 through 821 removed outlier: 3.675A pdb=" N LYS A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 442 through 448 removed outlier: 3.527A pdb=" N LEU C 445 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 482 through 484 removed outlier: 6.766A pdb=" N TRP C 461 " --> pdb=" O VAL C 473 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N THR C 475 " --> pdb=" O MET C 459 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET C 459 " --> pdb=" O THR C 475 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 482 through 484 removed outlier: 6.766A pdb=" N TRP C 461 " --> pdb=" O VAL C 473 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N THR C 475 " --> pdb=" O MET C 459 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET C 459 " --> pdb=" O THR C 475 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA5, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA6, first strand: chain 'A' and resid 192 through 193 removed outlier: 3.564A pdb=" N ILE A 193 " --> pdb=" O SER A 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 263 through 264 Processing sheet with id=AA8, first strand: chain 'A' and resid 303 through 305 Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 350 removed outlier: 6.852A pdb=" N LEU A 349 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 371 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 43 through 47 removed outlier: 7.551A pdb=" N CYS B 43 " --> pdb=" O CYS B 55 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N CYS B 55 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 69 through 75 removed outlier: 5.729A pdb=" N LEU B 63 " --> pdb=" O CYS B 93 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N ARG B 95 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 15.136A pdb=" N ARG B 65 " --> pdb=" O ARG B 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 101 through 103 removed outlier: 6.675A pdb=" N LYS B 112 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 118 through 120 269 hydrogen bonds defined for protein. 771 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: 1.23 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1179 1.30 - 1.43: 2001 1.43 - 1.56: 4277 1.56 - 1.69: 8 1.69 - 1.82: 66 Bond restraints: 7531 Sorted by residual: bond pdb=" CA ASN A 115 " pdb=" C ASN A 115 " ideal model delta sigma weight residual 1.523 1.620 -0.097 1.34e-02 5.57e+03 5.25e+01 bond pdb=" N PRO A 798 " pdb=" CD PRO A 798 " ideal model delta sigma weight residual 1.473 1.375 0.098 1.40e-02 5.10e+03 4.91e+01 bond pdb=" C VAL A 749 " pdb=" O VAL A 749 " ideal model delta sigma weight residual 1.237 1.165 0.072 1.19e-02 7.06e+03 3.64e+01 bond pdb=" N PRO A 178 " pdb=" CD PRO A 178 " ideal model delta sigma weight residual 1.473 1.390 0.083 1.40e-02 5.10e+03 3.50e+01 bond pdb=" C MET A 587 " pdb=" O MET A 587 " ideal model delta sigma weight residual 1.236 1.172 0.065 1.15e-02 7.56e+03 3.18e+01 ... (remaining 7526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 9824 2.97 - 5.95: 317 5.95 - 8.92: 60 8.92 - 11.89: 15 11.89 - 14.87: 5 Bond angle restraints: 10221 Sorted by residual: angle pdb=" CA LYS C 500 " pdb=" C LYS C 500 " pdb=" O LYS C 500 " ideal model delta sigma weight residual 121.20 109.32 11.88 1.04e+00 9.25e-01 1.31e+02 angle pdb=" N ARG B 64 " pdb=" CA ARG B 64 " pdb=" C ARG B 64 " ideal model delta sigma weight residual 109.40 124.27 -14.87 1.63e+00 3.76e-01 8.32e+01 angle pdb=" N LEU B 59 " pdb=" CA LEU B 59 " pdb=" C LEU B 59 " ideal model delta sigma weight residual 110.35 121.75 -11.40 1.36e+00 5.41e-01 7.02e+01 angle pdb=" N CYS B 96 " pdb=" CA CYS B 96 " pdb=" C CYS B 96 " ideal model delta sigma weight residual 108.67 96.18 12.49 1.55e+00 4.16e-01 6.50e+01 angle pdb=" N GLY A 46 " pdb=" CA GLY A 46 " pdb=" C GLY A 46 " ideal model delta sigma weight residual 115.36 125.77 -10.41 1.33e+00 5.65e-01 6.13e+01 ... (remaining 10216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3881 17.99 - 35.98: 468 35.98 - 53.97: 107 53.97 - 71.96: 29 71.96 - 89.95: 11 Dihedral angle restraints: 4496 sinusoidal: 1745 harmonic: 2751 Sorted by residual: dihedral pdb=" CB CYS B 78 " pdb=" SG CYS B 78 " pdb=" SG CYS B 93 " pdb=" CB CYS B 93 " ideal model delta sinusoidal sigma weight residual 93.00 178.81 -85.81 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS B 55 " pdb=" SG CYS B 55 " pdb=" SG CYS B 74 " pdb=" CB CYS B 74 " ideal model delta sinusoidal sigma weight residual 93.00 178.74 -85.74 1 1.00e+01 1.00e-02 8.89e+01 dihedral pdb=" CB CYS B 113 " pdb=" SG CYS B 113 " pdb=" SG CYS B 124 " pdb=" CB CYS B 124 " ideal model delta sinusoidal sigma weight residual 93.00 175.74 -82.74 1 1.00e+01 1.00e-02 8.39e+01 ... (remaining 4493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1107 0.145 - 0.289: 56 0.289 - 0.434: 5 0.434 - 0.579: 1 0.579 - 0.723: 1 Chirality restraints: 1170 Sorted by residual: chirality pdb=" CA ASN A 115 " pdb=" N ASN A 115 " pdb=" C ASN A 115 " pdb=" CB ASN A 115 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ASN A 116 " pdb=" N ASN A 116 " pdb=" C ASN A 116 " pdb=" CB ASN A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CA LEU B 59 " pdb=" N LEU B 59 " pdb=" C LEU B 59 " pdb=" CB LEU B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.84e+00 ... (remaining 1167 not shown) Planarity restraints: 1302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 136 " 0.973 9.50e-02 1.11e+02 4.36e-01 1.15e+02 pdb=" NE ARG A 136 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 136 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 136 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 136 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 525 " -0.620 9.50e-02 1.11e+02 2.78e-01 4.70e+01 pdb=" NE ARG C 525 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG C 525 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 525 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 525 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 102 " -0.024 2.00e-02 2.50e+03 4.94e-02 2.44e+01 pdb=" C ASP B 102 " 0.085 2.00e-02 2.50e+03 pdb=" O ASP B 102 " -0.031 2.00e-02 2.50e+03 pdb=" N SER B 103 " -0.030 2.00e-02 2.50e+03 ... (remaining 1299 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2688 2.85 - 3.37: 6924 3.37 - 3.88: 12224 3.88 - 4.39: 13824 4.39 - 4.90: 23542 Nonbonded interactions: 59202 Sorted by model distance: nonbonded pdb=" N ASN A 259 " pdb=" OD1 ASN A 283 " model vdw 2.342 3.120 nonbonded pdb=" OG1 THR A 417 " pdb=" OD1 ASN A 418 " model vdw 2.349 3.040 nonbonded pdb=" O MET A 782 " pdb=" OG1 THR A 786 " model vdw 2.353 3.040 nonbonded pdb=" O ASP C 497 " pdb=" OD1 ASP C 497 " model vdw 2.358 3.040 nonbonded pdb=" O LYS A 382 " pdb=" OG1 THR A 385 " model vdw 2.373 3.040 ... (remaining 59197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.420 Find NCS groups from input model: 0.040 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:10.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.006 0.098 7542 Z= 0.424 Angle : 1.223 14.868 10243 Z= 0.797 Chirality : 0.074 0.723 1170 Planarity : 0.016 0.436 1302 Dihedral : 16.899 89.946 2681 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.26 % Favored : 95.42 % Rotamer: Outliers : 3.20 % Allowed : 27.59 % Favored : 69.21 % Cbeta Deviations : 0.67 % 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 aren not related in a simple way. whole: -0.29 (0.28), residues: 939 helix: 2.10 (0.34), residues: 234 sheet: -1.54 (0.41), residues: 157 loop : -0.80 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 444 TYR 0.014 0.002 TYR B 71 PHE 0.028 0.002 PHE A 679 TRP 0.009 0.001 TRP A 160 HIS 0.006 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00616 ( 7531) covalent geometry : angle 1.22366 (10221) SS BOND : bond 0.00177 ( 11) SS BOND : angle 0.52319 ( 22) hydrogen bonds : bond 0.14751 ( 258) hydrogen bonds : angle 6.45332 ( 771) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: C 459 MET cc_start: 0.6992 (mtp) cc_final: 0.6425 (mtm) REVERT: C 464 GLN cc_start: 0.8318 (tt0) cc_final: 0.7786 (tt0) REVERT: C 514 ASP cc_start: 0.9091 (m-30) cc_final: 0.8099 (m-30) REVERT: C 537 PHE cc_start: 0.9069 (m-80) cc_final: 0.8469 (m-80) REVERT: A 61 GLN cc_start: 0.8320 (mt0) cc_final: 0.8024 (pt0) REVERT: A 120 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8455 (p) REVERT: A 191 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8266 (t) REVERT: A 642 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8643 (tm-30) REVERT: A 671 LEU cc_start: 0.9212 (mm) cc_final: 0.8863 (pp) REVERT: A 729 TYR cc_start: 0.8293 (t80) cc_final: 0.8005 (m-10) REVERT: A 799 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9049 (p) REVERT: B 118 TYR cc_start: 0.6880 (m-10) cc_final: 0.6624 (m-10) REVERT: B 123 ARG cc_start: 0.8778 (mmm160) cc_final: 0.8521 (mmm160) outliers start: 26 outliers final: 5 residues processed: 134 average time/residue: 0.4996 time to fit residues: 71.2952 Evaluate side-chains 113 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 799 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0270 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN A 92 ASN A 115 ASN A 211 ASN A 424 ASN A 439 GLN A 756 ASN A 797 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.106149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.074255 restraints weight = 16460.249| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.77 r_work: 0.2980 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7542 Z= 0.110 Angle : 0.636 10.790 10243 Z= 0.308 Chirality : 0.043 0.236 1170 Planarity : 0.004 0.051 1302 Dihedral : 5.325 66.700 1019 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.77 % Favored : 97.12 % Rotamer: Outliers : 3.57 % Allowed : 28.20 % Favored : 68.23 % 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 aren not related in a simple way. whole: 0.12 (0.28), residues: 939 helix: 2.39 (0.34), residues: 240 sheet: -1.20 (0.42), residues: 153 loop : -0.58 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 97 TYR 0.020 0.001 TYR B 71 PHE 0.013 0.001 PHE A 808 TRP 0.006 0.001 TRP C 534 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7531) covalent geometry : angle 0.63633 (10221) SS BOND : bond 0.00110 ( 11) SS BOND : angle 0.58706 ( 22) hydrogen bonds : bond 0.04214 ( 258) hydrogen bonds : angle 4.57499 ( 771) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 464 GLN cc_start: 0.8727 (tt0) cc_final: 0.7682 (tp40) REVERT: C 518 TYR cc_start: 0.8407 (m-80) cc_final: 0.8148 (m-80) REVERT: C 537 PHE cc_start: 0.9061 (m-80) cc_final: 0.8411 (m-80) REVERT: A 211 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8869 (m-40) REVERT: A 671 LEU cc_start: 0.9111 (mm) cc_final: 0.8718 (pp) REVERT: A 678 CYS cc_start: 0.9371 (t) cc_final: 0.9047 (m) REVERT: A 686 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6641 (pm20) REVERT: B 64 ARG cc_start: 0.7973 (ppp80) cc_final: 0.7449 (ptm-80) REVERT: B 97 ARG cc_start: 0.8570 (mmm160) cc_final: 0.8347 (mmm160) REVERT: B 108 ASP cc_start: 0.8516 (m-30) cc_final: 0.8202 (m-30) outliers start: 29 outliers final: 9 residues processed: 129 average time/residue: 0.4588 time to fit residues: 63.4516 Evaluate side-chains 112 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain B residue 73 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 0.0010 chunk 83 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 GLN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN B 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.105665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.073673 restraints weight = 16274.409| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.75 r_work: 0.2970 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7542 Z= 0.117 Angle : 0.626 11.565 10243 Z= 0.298 Chirality : 0.043 0.212 1170 Planarity : 0.003 0.050 1302 Dihedral : 4.984 66.063 1011 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.98 % Favored : 96.91 % Rotamer: Outliers : 3.57 % Allowed : 29.19 % Favored : 67.24 % 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 aren not related in a simple way. whole: 0.22 (0.28), residues: 939 helix: 2.44 (0.33), residues: 240 sheet: -1.01 (0.43), residues: 153 loop : -0.55 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 817 TYR 0.015 0.001 TYR B 71 PHE 0.014 0.001 PHE A 808 TRP 0.011 0.001 TRP C 461 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7531) covalent geometry : angle 0.62611 (10221) SS BOND : bond 0.00106 ( 11) SS BOND : angle 0.45587 ( 22) hydrogen bonds : bond 0.03913 ( 258) hydrogen bonds : angle 4.38967 ( 771) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: C 464 GLN cc_start: 0.8674 (tt0) cc_final: 0.7639 (tp-100) REVERT: C 478 LEU cc_start: 0.8566 (pp) cc_final: 0.8353 (pp) REVERT: C 496 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7752 (mt0) REVERT: C 513 GLU cc_start: 0.9498 (tm-30) cc_final: 0.9162 (pp20) REVERT: C 514 ASP cc_start: 0.9182 (m-30) cc_final: 0.8418 (m-30) REVERT: A 199 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.8928 (m) REVERT: A 671 LEU cc_start: 0.9086 (mm) cc_final: 0.8711 (pp) REVERT: A 678 CYS cc_start: 0.9381 (t) cc_final: 0.9085 (m) REVERT: A 799 VAL cc_start: 0.9284 (t) cc_final: 0.9050 (p) REVERT: B 48 LYS cc_start: 0.9214 (tppt) cc_final: 0.8999 (mmpt) REVERT: B 70 GLN cc_start: 0.8626 (pt0) cc_final: 0.7997 (pp30) REVERT: B 97 ARG cc_start: 0.8607 (mmm160) cc_final: 0.8325 (mmm160) REVERT: B 108 ASP cc_start: 0.8515 (m-30) cc_final: 0.8099 (m-30) REVERT: B 123 ARG cc_start: 0.8514 (mmp-170) cc_final: 0.8184 (mmm160) outliers start: 29 outliers final: 10 residues processed: 123 average time/residue: 0.4467 time to fit residues: 58.7116 Evaluate side-chains 109 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 103 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 424 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.104973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.072717 restraints weight = 16555.726| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.76 r_work: 0.2952 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7542 Z= 0.134 Angle : 0.617 12.638 10243 Z= 0.297 Chirality : 0.043 0.202 1170 Planarity : 0.003 0.051 1302 Dihedral : 4.969 66.241 1011 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.62 % Favored : 96.27 % Rotamer: Outliers : 5.17 % Allowed : 26.60 % Favored : 68.23 % 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 aren not related in a simple way. whole: 0.21 (0.28), residues: 939 helix: 2.55 (0.34), residues: 235 sheet: -0.96 (0.44), residues: 154 loop : -0.59 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 64 TYR 0.014 0.001 TYR B 71 PHE 0.014 0.001 PHE A 808 TRP 0.008 0.001 TRP C 461 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7531) covalent geometry : angle 0.61724 (10221) SS BOND : bond 0.00130 ( 11) SS BOND : angle 0.53709 ( 22) hydrogen bonds : bond 0.03937 ( 258) hydrogen bonds : angle 4.30621 ( 771) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 450 SER cc_start: 0.7781 (OUTLIER) cc_final: 0.7503 (p) REVERT: C 459 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.5797 (mpt) REVERT: C 464 GLN cc_start: 0.8671 (tt0) cc_final: 0.7608 (tp-100) REVERT: C 513 GLU cc_start: 0.9528 (tm-30) cc_final: 0.9161 (pp20) REVERT: C 514 ASP cc_start: 0.9184 (m-30) cc_final: 0.8343 (m-30) REVERT: A 199 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.8934 (m) REVERT: A 232 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8257 (t70) REVERT: A 272 ASN cc_start: 0.9299 (OUTLIER) cc_final: 0.8999 (p0) REVERT: A 678 CYS cc_start: 0.9397 (t) cc_final: 0.9110 (m) REVERT: A 720 LEU cc_start: 0.9468 (mm) cc_final: 0.9182 (mp) REVERT: A 799 VAL cc_start: 0.9251 (t) cc_final: 0.9032 (p) REVERT: B 70 GLN cc_start: 0.8719 (pt0) cc_final: 0.8056 (pp30) REVERT: B 85 HIS cc_start: 0.7886 (t-90) cc_final: 0.7660 (t70) REVERT: B 108 ASP cc_start: 0.8546 (m-30) cc_final: 0.8140 (m-30) REVERT: B 118 TYR cc_start: 0.6508 (m-10) cc_final: 0.6303 (m-10) outliers start: 42 outliers final: 16 residues processed: 138 average time/residue: 0.4113 time to fit residues: 60.9934 Evaluate side-chains 122 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 113 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 25 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 chunk 90 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN B 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.105658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.073655 restraints weight = 16304.628| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.67 r_work: 0.2957 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7542 Z= 0.115 Angle : 0.639 14.179 10243 Z= 0.301 Chirality : 0.043 0.199 1170 Planarity : 0.003 0.051 1302 Dihedral : 4.430 66.050 1007 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.98 % Favored : 96.91 % Rotamer: Outliers : 5.17 % Allowed : 27.22 % Favored : 67.61 % 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 aren not related in a simple way. whole: 0.31 (0.28), residues: 939 helix: 2.68 (0.34), residues: 233 sheet: -0.84 (0.43), residues: 157 loop : -0.56 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 817 TYR 0.018 0.001 TYR B 71 PHE 0.014 0.001 PHE A 808 TRP 0.007 0.001 TRP C 461 HIS 0.004 0.000 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7531) covalent geometry : angle 0.63826 (10221) SS BOND : bond 0.00350 ( 11) SS BOND : angle 0.88572 ( 22) hydrogen bonds : bond 0.03796 ( 258) hydrogen bonds : angle 4.22973 ( 771) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 450 SER cc_start: 0.7721 (OUTLIER) cc_final: 0.7447 (p) REVERT: C 459 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.5806 (mpt) REVERT: C 464 GLN cc_start: 0.8713 (tt0) cc_final: 0.7573 (tp-100) REVERT: C 496 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7838 (mt0) REVERT: C 501 ASN cc_start: 0.9078 (p0) cc_final: 0.8128 (t0) REVERT: C 511 LYS cc_start: 0.8715 (ptmm) cc_final: 0.8434 (ptmm) REVERT: A 199 THR cc_start: 0.9356 (OUTLIER) cc_final: 0.8893 (m) REVERT: A 232 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8055 (t70) REVERT: A 272 ASN cc_start: 0.9308 (OUTLIER) cc_final: 0.8998 (p0) REVERT: A 575 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8282 (tm) REVERT: A 678 CYS cc_start: 0.9349 (t) cc_final: 0.9056 (m) REVERT: A 720 LEU cc_start: 0.9498 (mm) cc_final: 0.9193 (mp) REVERT: B 70 GLN cc_start: 0.8736 (pt0) cc_final: 0.8078 (pp30) REVERT: B 71 TYR cc_start: 0.9127 (p90) cc_final: 0.8927 (p90) REVERT: B 97 ARG cc_start: 0.8720 (mmm160) cc_final: 0.8274 (mmm160) REVERT: B 108 ASP cc_start: 0.8599 (m-30) cc_final: 0.8126 (m-30) REVERT: B 114 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7316 (tppp) REVERT: B 125 PHE cc_start: 0.6025 (OUTLIER) cc_final: 0.5508 (p90) outliers start: 42 outliers final: 17 residues processed: 135 average time/residue: 0.4066 time to fit residues: 59.2176 Evaluate side-chains 125 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 113 CYS Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 125 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 32 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.0570 chunk 5 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN A 115 ASN A 424 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.105447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.073603 restraints weight = 16431.235| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.68 r_work: 0.2952 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7542 Z= 0.121 Angle : 0.651 14.416 10243 Z= 0.307 Chirality : 0.043 0.206 1170 Planarity : 0.003 0.051 1302 Dihedral : 4.425 66.208 1007 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.30 % Favored : 96.59 % Rotamer: Outliers : 5.30 % Allowed : 28.08 % Favored : 66.63 % 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 aren not related in a simple way. whole: 0.25 (0.28), residues: 939 helix: 2.57 (0.34), residues: 234 sheet: -0.76 (0.45), residues: 153 loop : -0.63 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 123 TYR 0.019 0.001 TYR B 71 PHE 0.013 0.001 PHE A 808 TRP 0.007 0.001 TRP A 160 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7531) covalent geometry : angle 0.65089 (10221) SS BOND : bond 0.00232 ( 11) SS BOND : angle 0.72596 ( 22) hydrogen bonds : bond 0.03706 ( 258) hydrogen bonds : angle 4.20363 ( 771) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: C 450 SER cc_start: 0.7826 (OUTLIER) cc_final: 0.7575 (p) REVERT: C 459 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.5775 (mpt) REVERT: C 464 GLN cc_start: 0.8684 (tt0) cc_final: 0.7520 (tp-100) REVERT: C 501 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8151 (t0) REVERT: C 511 LYS cc_start: 0.8691 (ptmm) cc_final: 0.7872 (ptmm) REVERT: C 514 ASP cc_start: 0.9211 (m-30) cc_final: 0.8491 (m-30) REVERT: A 199 THR cc_start: 0.9356 (OUTLIER) cc_final: 0.8893 (m) REVERT: A 232 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8086 (t70) REVERT: A 272 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.8964 (p0) REVERT: A 435 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8378 (m110) REVERT: A 575 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8320 (tm) REVERT: A 678 CYS cc_start: 0.9353 (t) cc_final: 0.9021 (m) REVERT: A 720 LEU cc_start: 0.9516 (mm) cc_final: 0.9212 (mp) REVERT: B 70 GLN cc_start: 0.8758 (pt0) cc_final: 0.8158 (pp30) REVERT: B 97 ARG cc_start: 0.8745 (mmm160) cc_final: 0.8228 (mmm160) REVERT: B 108 ASP cc_start: 0.8659 (m-30) cc_final: 0.8235 (m-30) REVERT: B 114 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7303 (tppp) REVERT: B 123 ARG cc_start: 0.8563 (mmm160) cc_final: 0.8287 (mmm160) REVERT: B 125 PHE cc_start: 0.6008 (OUTLIER) cc_final: 0.5497 (p90) outliers start: 43 outliers final: 17 residues processed: 131 average time/residue: 0.4154 time to fit residues: 58.7174 Evaluate side-chains 128 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 CYS Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 125 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 7 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 72 optimal weight: 0.0070 chunk 47 optimal weight: 0.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 GLN A 424 ASN B 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.104213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.072189 restraints weight = 16500.040| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.68 r_work: 0.2925 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7542 Z= 0.154 Angle : 0.678 13.611 10243 Z= 0.322 Chirality : 0.046 0.404 1170 Planarity : 0.004 0.051 1302 Dihedral : 4.505 66.508 1007 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.51 % Favored : 96.38 % Rotamer: Outliers : 4.80 % Allowed : 28.20 % Favored : 67.00 % 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 aren not related in a simple way. whole: 0.23 (0.28), residues: 939 helix: 2.44 (0.34), residues: 233 sheet: -0.74 (0.44), residues: 156 loop : -0.58 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 123 TYR 0.021 0.001 TYR B 71 PHE 0.014 0.001 PHE A 808 TRP 0.008 0.001 TRP A 160 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 7531) covalent geometry : angle 0.67762 (10221) SS BOND : bond 0.00219 ( 11) SS BOND : angle 0.64603 ( 22) hydrogen bonds : bond 0.03981 ( 258) hydrogen bonds : angle 4.21405 ( 771) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 450 SER cc_start: 0.7756 (OUTLIER) cc_final: 0.7507 (p) REVERT: C 459 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.5771 (mpt) REVERT: C 464 GLN cc_start: 0.8662 (tt0) cc_final: 0.7485 (tp-100) REVERT: C 501 ASN cc_start: 0.9134 (p0) cc_final: 0.8241 (t0) REVERT: A 115 ASN cc_start: 0.9156 (OUTLIER) cc_final: 0.8955 (t0) REVERT: A 199 THR cc_start: 0.9369 (OUTLIER) cc_final: 0.8912 (m) REVERT: A 232 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8108 (t70) REVERT: A 272 ASN cc_start: 0.9339 (OUTLIER) cc_final: 0.9044 (p0) REVERT: A 435 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8394 (m110) REVERT: A 575 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8367 (tm) REVERT: A 678 CYS cc_start: 0.9351 (t) cc_final: 0.9000 (m) REVERT: A 720 LEU cc_start: 0.9506 (mm) cc_final: 0.9195 (mp) REVERT: A 799 VAL cc_start: 0.9211 (t) cc_final: 0.8976 (p) REVERT: B 70 GLN cc_start: 0.8765 (pt0) cc_final: 0.8162 (pp30) REVERT: B 97 ARG cc_start: 0.8780 (mmm160) cc_final: 0.8244 (mmm160) REVERT: B 98 ILE cc_start: 0.9053 (tp) cc_final: 0.8764 (tp) REVERT: B 108 ASP cc_start: 0.8723 (m-30) cc_final: 0.8274 (m-30) REVERT: B 123 ARG cc_start: 0.8482 (mmm160) cc_final: 0.8151 (mmm160) outliers start: 39 outliers final: 16 residues processed: 129 average time/residue: 0.4325 time to fit residues: 59.9696 Evaluate side-chains 126 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN A 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.103620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.071410 restraints weight = 16622.962| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.69 r_work: 0.2911 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7542 Z= 0.168 Angle : 0.707 13.817 10243 Z= 0.335 Chirality : 0.046 0.371 1170 Planarity : 0.004 0.054 1302 Dihedral : 4.634 66.820 1007 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.83 % Favored : 96.06 % Rotamer: Outliers : 4.43 % Allowed : 29.56 % Favored : 66.01 % 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 aren not related in a simple way. whole: 0.16 (0.28), residues: 939 helix: 2.39 (0.35), residues: 233 sheet: -0.77 (0.44), residues: 151 loop : -0.64 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 64 TYR 0.021 0.001 TYR B 71 PHE 0.015 0.001 PHE A 808 TRP 0.009 0.001 TRP A 160 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7531) covalent geometry : angle 0.70705 (10221) SS BOND : bond 0.00213 ( 11) SS BOND : angle 0.65212 ( 22) hydrogen bonds : bond 0.04116 ( 258) hydrogen bonds : angle 4.24404 ( 771) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: C 450 SER cc_start: 0.7671 (OUTLIER) cc_final: 0.7439 (p) REVERT: C 459 MET cc_start: 0.6505 (OUTLIER) cc_final: 0.5799 (mpt) REVERT: C 464 GLN cc_start: 0.8704 (tt0) cc_final: 0.7524 (tp-100) REVERT: C 501 ASN cc_start: 0.9246 (p0) cc_final: 0.8268 (t0) REVERT: C 511 LYS cc_start: 0.8827 (ptmm) cc_final: 0.8162 (ptmm) REVERT: C 514 ASP cc_start: 0.9250 (m-30) cc_final: 0.8644 (m-30) REVERT: A 199 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.8932 (m) REVERT: A 232 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8074 (t70) REVERT: A 272 ASN cc_start: 0.9338 (OUTLIER) cc_final: 0.9052 (p0) REVERT: A 575 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8407 (tm) REVERT: A 720 LEU cc_start: 0.9501 (mm) cc_final: 0.9215 (mp) REVERT: B 70 GLN cc_start: 0.8836 (pt0) cc_final: 0.8204 (pp30) REVERT: B 98 ILE cc_start: 0.9101 (tp) cc_final: 0.8811 (tp) REVERT: B 108 ASP cc_start: 0.8746 (m-30) cc_final: 0.8298 (m-30) REVERT: B 123 ARG cc_start: 0.8551 (mmm160) cc_final: 0.8232 (mmm160) outliers start: 36 outliers final: 15 residues processed: 124 average time/residue: 0.4197 time to fit residues: 56.0722 Evaluate side-chains 119 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.5980 chunk 1 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 GLN C 501 ASN A 424 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.103936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.072031 restraints weight = 16266.083| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.65 r_work: 0.2925 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7542 Z= 0.149 Angle : 0.736 14.542 10243 Z= 0.342 Chirality : 0.046 0.345 1170 Planarity : 0.004 0.062 1302 Dihedral : 4.611 67.191 1007 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.30 % Favored : 96.59 % Rotamer: Outliers : 3.57 % Allowed : 30.79 % Favored : 65.64 % 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 aren not related in a simple way. whole: 0.09 (0.28), residues: 939 helix: 2.32 (0.35), residues: 233 sheet: -0.77 (0.44), residues: 150 loop : -0.69 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 491 TYR 0.028 0.001 TYR B 71 PHE 0.016 0.001 PHE A 808 TRP 0.008 0.001 TRP A 160 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7531) covalent geometry : angle 0.73633 (10221) SS BOND : bond 0.00190 ( 11) SS BOND : angle 0.65531 ( 22) hydrogen bonds : bond 0.04043 ( 258) hydrogen bonds : angle 4.23721 ( 771) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: C 450 SER cc_start: 0.7715 (OUTLIER) cc_final: 0.7491 (p) REVERT: C 459 MET cc_start: 0.6450 (OUTLIER) cc_final: 0.5713 (mpt) REVERT: C 464 GLN cc_start: 0.8721 (tt0) cc_final: 0.7539 (tp-100) REVERT: C 511 LYS cc_start: 0.8676 (ptmm) cc_final: 0.8000 (ptmm) REVERT: C 513 GLU cc_start: 0.9349 (pp20) cc_final: 0.9135 (pp20) REVERT: C 514 ASP cc_start: 0.9213 (m-30) cc_final: 0.8600 (m-30) REVERT: A 199 THR cc_start: 0.9374 (OUTLIER) cc_final: 0.8922 (m) REVERT: A 232 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8148 (t70) REVERT: A 272 ASN cc_start: 0.9338 (OUTLIER) cc_final: 0.9053 (p0) REVERT: A 575 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8416 (tm) REVERT: A 686 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6363 (pm20) REVERT: A 720 LEU cc_start: 0.9534 (mm) cc_final: 0.9262 (mp) REVERT: B 70 GLN cc_start: 0.8840 (pt0) cc_final: 0.8194 (pp30) REVERT: B 98 ILE cc_start: 0.9041 (tp) cc_final: 0.8732 (tp) REVERT: B 108 ASP cc_start: 0.8743 (m-30) cc_final: 0.8281 (m-30) REVERT: B 117 PHE cc_start: 0.9054 (m-80) cc_final: 0.8812 (m-80) REVERT: B 123 ARG cc_start: 0.8564 (mmm160) cc_final: 0.8218 (mmm160) REVERT: B 139 MET cc_start: 0.7299 (tpt) cc_final: 0.7098 (tpt) outliers start: 29 outliers final: 13 residues processed: 120 average time/residue: 0.4209 time to fit residues: 54.3073 Evaluate side-chains 116 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 6 optimal weight: 6.9990 chunk 77 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 GLN C 501 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.103259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.071239 restraints weight = 16550.175| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.68 r_work: 0.2908 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7542 Z= 0.173 Angle : 0.745 14.666 10243 Z= 0.349 Chirality : 0.047 0.336 1170 Planarity : 0.004 0.070 1302 Dihedral : 4.673 67.238 1007 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.42 % Rotamer: Outliers : 3.33 % Allowed : 31.28 % Favored : 65.39 % 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 aren not related in a simple way. whole: 0.05 (0.28), residues: 939 helix: 2.23 (0.35), residues: 233 sheet: -0.78 (0.43), residues: 152 loop : -0.69 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 64 TYR 0.027 0.002 TYR B 71 PHE 0.016 0.001 PHE A 754 TRP 0.009 0.001 TRP A 160 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 7531) covalent geometry : angle 0.74556 (10221) SS BOND : bond 0.00207 ( 11) SS BOND : angle 0.69516 ( 22) hydrogen bonds : bond 0.04245 ( 258) hydrogen bonds : angle 4.30848 ( 771) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 450 SER cc_start: 0.7777 (OUTLIER) cc_final: 0.7520 (p) REVERT: C 459 MET cc_start: 0.6452 (OUTLIER) cc_final: 0.5727 (mpt) REVERT: C 511 LYS cc_start: 0.8546 (ptmm) cc_final: 0.7823 (ptmm) REVERT: C 513 GLU cc_start: 0.9318 (pp20) cc_final: 0.9108 (pp20) REVERT: C 514 ASP cc_start: 0.9197 (m-30) cc_final: 0.8529 (m-30) REVERT: C 532 LEU cc_start: 0.7851 (tp) cc_final: 0.7647 (tm) REVERT: A 199 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.8932 (m) REVERT: A 232 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8050 (t70) REVERT: A 272 ASN cc_start: 0.9375 (OUTLIER) cc_final: 0.9092 (p0) REVERT: A 575 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8476 (tm) REVERT: A 686 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6405 (pm20) REVERT: A 720 LEU cc_start: 0.9529 (mm) cc_final: 0.9247 (mp) REVERT: B 70 GLN cc_start: 0.8904 (pt0) cc_final: 0.8230 (pp30) REVERT: B 98 ILE cc_start: 0.9018 (tp) cc_final: 0.8730 (tp) REVERT: B 108 ASP cc_start: 0.8754 (m-30) cc_final: 0.8305 (m-30) REVERT: B 123 ARG cc_start: 0.8578 (mmm160) cc_final: 0.8111 (mmm160) outliers start: 27 outliers final: 14 residues processed: 116 average time/residue: 0.4394 time to fit residues: 54.6313 Evaluate side-chains 115 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 GLN C 501 ASN A 424 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.103162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.070037 restraints weight = 16379.076| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.75 r_work: 0.2882 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7542 Z= 0.207 Angle : 0.760 14.557 10243 Z= 0.360 Chirality : 0.048 0.321 1170 Planarity : 0.004 0.066 1302 Dihedral : 4.817 67.248 1007 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.69 % Favored : 95.21 % Rotamer: Outliers : 3.33 % Allowed : 31.40 % Favored : 65.27 % 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 aren not related in a simple way. whole: -0.01 (0.28), residues: 939 helix: 2.20 (0.35), residues: 233 sheet: -0.82 (0.43), residues: 152 loop : -0.74 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 64 TYR 0.025 0.002 TYR B 71 PHE 0.017 0.001 PHE A 808 TRP 0.011 0.001 TRP A 160 HIS 0.005 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 7531) covalent geometry : angle 0.76004 (10221) SS BOND : bond 0.00252 ( 11) SS BOND : angle 0.85809 ( 22) hydrogen bonds : bond 0.04482 ( 258) hydrogen bonds : angle 4.34574 ( 771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2739.76 seconds wall clock time: 47 minutes 27.68 seconds (2847.68 seconds total)