Starting phenix.real_space_refine on Wed Mar 12 06:01:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xum_38677/03_2025/8xum_38677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xum_38677/03_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_38677/03_2025/8xum_38677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xum_38677/03_2025/8xum_38677.map" model { file = "/net/cci-nas-00/data/ceres_data/8xum_38677/03_2025/8xum_38677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xum_38677/03_2025/8xum_38677.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 4.67, per 1000 atoms: 0.63 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: 1.70 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.85 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: 2.12 Time building geometry restraints manager: 2.05 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: 0.870 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.040 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.560 ------------------------------------------------------------------------------- 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 7531 Z= 0.416 Angle : 1.224 14.868 10221 Z= 0.798 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP A 160 HIS 0.006 0.001 HIS A 98 PHE 0.028 0.002 PHE A 679 TYR 0.014 0.002 TYR B 71 ARG 0.010 0.001 ARG C 444 *********************** 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 : 0.835 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: 0.8098 (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: 0.9784 time to fit residues: 140.6643 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 : 0.816 ------------------------------------------------------------------------------- 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 79 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN A 584 ASN A 756 ASN A 797 ASN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.101637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.069336 restraints weight = 16351.659| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.70 r_work: 0.2877 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 7531 Z= 0.415 Angle : 0.698 10.587 10221 Z= 0.349 Chirality : 0.047 0.241 1170 Planarity : 0.004 0.052 1302 Dihedral : 5.866 66.224 1019 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.22 % Favored : 94.68 % Rotamer: Outliers : 5.05 % Allowed : 27.83 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.28), residues: 939 helix: 2.07 (0.34), residues: 244 sheet: -1.30 (0.41), residues: 156 loop : -0.64 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 160 HIS 0.005 0.001 HIS A 257 PHE 0.017 0.002 PHE A 808 TYR 0.016 0.002 TYR B 71 ARG 0.008 0.001 ARG B 97 *********************** 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 151 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 445 LEU cc_start: 0.8444 (mm) cc_final: 0.7907 (mm) REVERT: C 450 SER cc_start: 0.7841 (OUTLIER) cc_final: 0.7520 (p) REVERT: C 459 MET cc_start: 0.6961 (mtp) cc_final: 0.6592 (mtm) REVERT: C 511 LYS cc_start: 0.8583 (ptmm) cc_final: 0.7134 (ptmm) REVERT: C 514 ASP cc_start: 0.9213 (m-30) cc_final: 0.8408 (m-30) REVERT: C 537 PHE cc_start: 0.9082 (m-80) cc_final: 0.8434 (m-80) REVERT: A 199 THR cc_start: 0.9437 (OUTLIER) cc_final: 0.9004 (m) REVERT: A 663 ARG cc_start: 0.5146 (OUTLIER) cc_final: 0.4906 (tpt170) REVERT: A 671 LEU cc_start: 0.9157 (mm) cc_final: 0.8812 (pp) REVERT: A 678 CYS cc_start: 0.9421 (t) cc_final: 0.9125 (m) REVERT: A 686 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6790 (pm20) REVERT: A 720 LEU cc_start: 0.9269 (mp) cc_final: 0.8997 (mp) REVERT: A 799 VAL cc_start: 0.9265 (t) cc_final: 0.8984 (p) REVERT: B 70 GLN cc_start: 0.8574 (pt0) cc_final: 0.7957 (pp30) REVERT: B 108 ASP cc_start: 0.8613 (m-30) cc_final: 0.8330 (m-30) outliers start: 41 outliers final: 14 residues processed: 136 average time/residue: 0.8680 time to fit residues: 127.1776 Evaluate side-chains 118 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 450 SER 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 192 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 663 ARG Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 103 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 61 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 0.0020 chunk 25 optimal weight: 2.9990 chunk 80 optimal weight: 0.0470 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 0.5288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN ** A 439 GLN ** 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 = 0.3723 r_free = 0.3723 target = 0.104891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.072869 restraints weight = 16398.264| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.74 r_work: 0.2949 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7531 Z= 0.169 Angle : 0.625 11.267 10221 Z= 0.300 Chirality : 0.043 0.206 1170 Planarity : 0.003 0.052 1302 Dihedral : 5.205 65.703 1011 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.77 % Favored : 97.12 % Rotamer: Outliers : 4.68 % Allowed : 29.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.28), residues: 939 helix: 2.47 (0.34), residues: 240 sheet: -1.11 (0.43), residues: 153 loop : -0.56 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 461 HIS 0.004 0.001 HIS A 257 PHE 0.016 0.001 PHE A 808 TYR 0.015 0.001 TYR B 71 ARG 0.006 0.000 ARG A 817 *********************** 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 151 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: C 458 CYS cc_start: 0.8121 (p) cc_final: 0.7357 (t) REVERT: C 464 GLN cc_start: 0.8700 (tt0) cc_final: 0.7727 (tp-100) REVERT: C 476 VAL cc_start: 0.7240 (m) cc_final: 0.6665 (m) REVERT: C 511 LYS cc_start: 0.8834 (ptmm) cc_final: 0.8020 (ptmm) REVERT: C 514 ASP cc_start: 0.9157 (m-30) cc_final: 0.8411 (m-30) REVERT: C 518 TYR cc_start: 0.8326 (m-80) cc_final: 0.7863 (m-80) REVERT: C 537 PHE cc_start: 0.9016 (m-80) cc_final: 0.8026 (m-80) REVERT: A 232 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8179 (t70) REVERT: A 272 ASN cc_start: 0.9287 (OUTLIER) cc_final: 0.8994 (p0) REVERT: A 671 LEU cc_start: 0.9091 (mm) cc_final: 0.8720 (pp) REVERT: A 678 CYS cc_start: 0.9384 (t) cc_final: 0.9073 (m) REVERT: A 686 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6665 (pm20) REVERT: B 64 ARG cc_start: 0.8036 (ppp80) cc_final: 0.7511 (ptm-80) REVERT: B 70 GLN cc_start: 0.8597 (pt0) cc_final: 0.7982 (pp30) REVERT: B 97 ARG cc_start: 0.8624 (mmm160) cc_final: 0.8145 (mmm160) REVERT: B 100 ASN cc_start: 0.7698 (t0) cc_final: 0.7284 (t0) REVERT: B 108 ASP cc_start: 0.8596 (m-30) cc_final: 0.8179 (m-30) outliers start: 38 outliers final: 15 residues processed: 136 average time/residue: 0.8142 time to fit residues: 119.8139 Evaluate side-chains 122 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 45 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 345 MET 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 686 GLU 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 20 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.102652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.070426 restraints weight = 16424.734| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.71 r_work: 0.2900 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7531 Z= 0.305 Angle : 0.655 11.955 10221 Z= 0.318 Chirality : 0.045 0.208 1170 Planarity : 0.004 0.051 1302 Dihedral : 5.287 66.115 1011 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.99 % Rotamer: Outliers : 5.54 % Allowed : 29.56 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.28), residues: 939 helix: 2.54 (0.34), residues: 232 sheet: -0.97 (0.43), residues: 154 loop : -0.65 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 160 HIS 0.005 0.001 HIS A 257 PHE 0.017 0.001 PHE A 808 TYR 0.013 0.001 TYR A 725 ARG 0.006 0.000 ARG B 123 *********************** 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 151 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 106 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: C 458 CYS cc_start: 0.8279 (p) cc_final: 0.7442 (t) REVERT: C 464 GLN cc_start: 0.8717 (tt0) cc_final: 0.7640 (tp-100) REVERT: C 476 VAL cc_start: 0.7730 (m) cc_final: 0.7189 (m) REVERT: C 511 LYS cc_start: 0.8796 (ptmm) cc_final: 0.8043 (ptmm) REVERT: C 513 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9212 (tm-30) REVERT: C 514 ASP cc_start: 0.9142 (m-30) cc_final: 0.8388 (m-30) REVERT: A 199 THR cc_start: 0.9408 (OUTLIER) cc_final: 0.8958 (m) REVERT: A 232 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8212 (t70) REVERT: A 272 ASN cc_start: 0.9381 (OUTLIER) cc_final: 0.9105 (p0) REVERT: A 575 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8485 (tm) REVERT: A 663 ARG cc_start: 0.5188 (OUTLIER) cc_final: 0.4946 (tpt170) REVERT: A 671 LEU cc_start: 0.9125 (mm) cc_final: 0.8782 (pp) REVERT: A 678 CYS cc_start: 0.9428 (t) cc_final: 0.9139 (m) REVERT: A 686 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6725 (pm20) REVERT: B 70 GLN cc_start: 0.8639 (pt0) cc_final: 0.8030 (pp30) REVERT: B 97 ARG cc_start: 0.8627 (mmm160) cc_final: 0.8149 (mmm160) REVERT: B 100 ASN cc_start: 0.7607 (t0) cc_final: 0.7362 (t0) REVERT: B 108 ASP cc_start: 0.8621 (m-30) cc_final: 0.8282 (m-30) outliers start: 45 outliers final: 22 residues processed: 136 average time/residue: 0.8332 time to fit residues: 122.5639 Evaluate side-chains 132 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 45 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 345 MET 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 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 663 ARG Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 686 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 11 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 GLN 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 = 0.3670 r_free = 0.3670 target = 0.102139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.068814 restraints weight = 16247.953| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.78 r_work: 0.2861 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7531 Z= 0.370 Angle : 0.703 12.986 10221 Z= 0.337 Chirality : 0.046 0.205 1170 Planarity : 0.004 0.053 1302 Dihedral : 5.423 65.865 1011 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % Rotamer: Outliers : 6.40 % Allowed : 28.94 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.28), residues: 939 helix: 2.35 (0.34), residues: 238 sheet: -1.04 (0.42), residues: 154 loop : -0.67 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 160 HIS 0.005 0.001 HIS A 257 PHE 0.017 0.001 PHE A 808 TYR 0.017 0.002 TYR B 71 ARG 0.007 0.001 ARG B 123 *********************** 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 156 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 104 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: C 450 SER cc_start: 0.7846 (OUTLIER) cc_final: 0.7542 (p) REVERT: C 464 GLN cc_start: 0.8745 (tt0) cc_final: 0.7564 (tp-100) REVERT: C 518 TYR cc_start: 0.8363 (m-80) cc_final: 0.7888 (m-80) REVERT: A 199 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.8945 (m) REVERT: A 232 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8138 (t70) REVERT: A 272 ASN cc_start: 0.9383 (OUTLIER) cc_final: 0.9098 (p0) REVERT: A 575 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8569 (tm) REVERT: A 663 ARG cc_start: 0.5020 (OUTLIER) cc_final: 0.4803 (tpt170) REVERT: A 671 LEU cc_start: 0.9068 (mm) cc_final: 0.8748 (pp) REVERT: A 678 CYS cc_start: 0.9415 (t) cc_final: 0.9144 (m) REVERT: A 686 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6785 (pm20) REVERT: B 70 GLN cc_start: 0.8653 (pt0) cc_final: 0.8065 (pp30) REVERT: B 97 ARG cc_start: 0.8592 (mmm160) cc_final: 0.8074 (mmm160) REVERT: B 100 ASN cc_start: 0.7733 (t0) cc_final: 0.7390 (t0) REVERT: B 108 ASP cc_start: 0.8738 (m-30) cc_final: 0.8353 (m-30) REVERT: B 125 PHE cc_start: 0.6061 (OUTLIER) cc_final: 0.5715 (p90) outliers start: 52 outliers final: 26 residues processed: 139 average time/residue: 0.8126 time to fit residues: 122.3118 Evaluate side-chains 133 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 450 SER 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 216 SER Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 421 VAL 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 557 LEU 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 663 ARG Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 113 CYS 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 93 optimal weight: 2.9990 chunk 83 optimal weight: 0.0970 chunk 56 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 0.0010 chunk 79 optimal weight: 7.9990 chunk 57 optimal weight: 0.0870 overall best weight: 0.5564 ------------------------------------------------------------------------------- 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 ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 797 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.104225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.072380 restraints weight = 16159.055| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.64 r_work: 0.2930 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7531 Z= 0.181 Angle : 0.672 14.644 10221 Z= 0.316 Chirality : 0.043 0.198 1170 Planarity : 0.004 0.051 1302 Dihedral : 4.619 65.465 1007 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.41 % Favored : 96.49 % Rotamer: Outliers : 4.80 % Allowed : 30.05 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.28), residues: 939 helix: 2.61 (0.34), residues: 233 sheet: -0.84 (0.44), residues: 150 loop : -0.68 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 160 HIS 0.004 0.001 HIS A 257 PHE 0.016 0.001 PHE A 808 TYR 0.019 0.001 TYR B 71 ARG 0.008 0.000 ARG B 123 *********************** 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 146 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 450 SER cc_start: 0.7912 (OUTLIER) cc_final: 0.7680 (p) REVERT: C 464 GLN cc_start: 0.8689 (tt0) cc_final: 0.7574 (tp-100) REVERT: C 511 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8588 (ptmm) REVERT: C 518 TYR cc_start: 0.8390 (m-80) cc_final: 0.7960 (m-80) REVERT: A 199 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.8901 (m) REVERT: A 232 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8041 (t70) REVERT: A 272 ASN cc_start: 0.9319 (OUTLIER) cc_final: 0.9005 (p0) REVERT: A 575 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8382 (tm) REVERT: A 678 CYS cc_start: 0.9406 (t) cc_final: 0.9126 (m) REVERT: A 686 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6671 (pm20) REVERT: B 70 GLN cc_start: 0.8708 (pt0) cc_final: 0.8080 (pp30) REVERT: B 97 ARG cc_start: 0.8502 (mmm160) cc_final: 0.8041 (mmm160) REVERT: B 100 ASN cc_start: 0.8041 (t0) cc_final: 0.7714 (t0) REVERT: B 108 ASP cc_start: 0.8672 (m-30) cc_final: 0.8272 (m-30) REVERT: B 125 PHE cc_start: 0.5876 (OUTLIER) cc_final: 0.5587 (p90) outliers start: 39 outliers final: 16 residues processed: 132 average time/residue: 0.8752 time to fit residues: 124.8321 Evaluate side-chains 122 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 511 LYS Chi-restraints excluded: chain C residue 544 THR 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 285 LEU 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 668 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 73 GLU 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 85 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 55 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.105656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.073188 restraints weight = 16329.672| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.78 r_work: 0.2936 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7531 Z= 0.186 Angle : 0.697 13.690 10221 Z= 0.324 Chirality : 0.045 0.403 1170 Planarity : 0.004 0.052 1302 Dihedral : 4.538 66.035 1007 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.70 % Rotamer: Outliers : 4.80 % Allowed : 29.68 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.28), residues: 939 helix: 2.49 (0.35), residues: 233 sheet: -0.73 (0.44), residues: 150 loop : -0.66 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 160 HIS 0.004 0.000 HIS A 257 PHE 0.015 0.001 PHE A 808 TYR 0.020 0.001 TYR B 71 ARG 0.014 0.001 ARG B 123 *********************** 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 144 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: C 450 SER cc_start: 0.7730 (OUTLIER) cc_final: 0.7478 (p) REVERT: C 464 GLN cc_start: 0.8671 (tt0) cc_final: 0.7544 (tp-100) REVERT: C 513 GLU cc_start: 0.9413 (pp20) cc_final: 0.9097 (pp20) REVERT: C 514 ASP cc_start: 0.9261 (m-30) cc_final: 0.8400 (m-30) REVERT: A 199 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.8875 (m) REVERT: A 232 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8014 (t70) REVERT: A 272 ASN cc_start: 0.9315 (OUTLIER) cc_final: 0.9003 (p0) REVERT: A 435 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8405 (m110) REVERT: A 575 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8253 (tm) REVERT: A 678 CYS cc_start: 0.9392 (t) cc_final: 0.9109 (m) REVERT: B 56 GLN cc_start: 0.7818 (pm20) cc_final: 0.7049 (pm20) REVERT: B 70 GLN cc_start: 0.8756 (pt0) cc_final: 0.8105 (pp30) REVERT: B 85 HIS cc_start: 0.7833 (t-90) cc_final: 0.7611 (t70) REVERT: B 100 ASN cc_start: 0.8110 (t0) cc_final: 0.7771 (t0) REVERT: B 108 ASP cc_start: 0.8693 (m-30) cc_final: 0.8296 (m-30) REVERT: B 125 PHE cc_start: 0.5777 (OUTLIER) cc_final: 0.5561 (p90) outliers start: 39 outliers final: 15 residues processed: 131 average time/residue: 0.8502 time to fit residues: 120.2153 Evaluate side-chains 125 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain A residue 45 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 725 TYR Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 125 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN ** A 439 GLN ** 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 = 0.3726 r_free = 0.3726 target = 0.105176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.073315 restraints weight = 16442.147| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.67 r_work: 0.2949 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7531 Z= 0.195 Angle : 0.708 14.016 10221 Z= 0.327 Chirality : 0.045 0.380 1170 Planarity : 0.004 0.062 1302 Dihedral : 4.526 66.377 1007 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.41 % Favored : 96.49 % Rotamer: Outliers : 4.19 % Allowed : 30.79 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.28), residues: 939 helix: 2.38 (0.35), residues: 233 sheet: -0.68 (0.45), residues: 150 loop : -0.63 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 160 HIS 0.004 0.000 HIS A 257 PHE 0.015 0.001 PHE A 808 TYR 0.022 0.001 TYR B 71 ARG 0.016 0.001 ARG B 123 *********************** 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 141 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: C 459 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.5857 (mpt) REVERT: C 464 GLN cc_start: 0.8662 (tt0) cc_final: 0.7561 (tp-100) REVERT: C 486 ASP cc_start: 0.9301 (m-30) cc_final: 0.8752 (p0) REVERT: C 511 LYS cc_start: 0.8989 (ptmm) cc_final: 0.8189 (ptmm) REVERT: C 514 ASP cc_start: 0.9284 (m-30) cc_final: 0.8549 (m-30) REVERT: A 199 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.8871 (m) REVERT: A 232 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8157 (t70) REVERT: A 272 ASN cc_start: 0.9299 (OUTLIER) cc_final: 0.8992 (p0) REVERT: A 435 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8428 (m110) REVERT: A 575 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8249 (tm) REVERT: A 678 CYS cc_start: 0.9233 (t) cc_final: 0.9020 (m) REVERT: B 56 GLN cc_start: 0.8010 (pm20) cc_final: 0.7248 (pm20) REVERT: B 70 GLN cc_start: 0.8790 (pt0) cc_final: 0.8149 (pp30) REVERT: B 100 ASN cc_start: 0.8209 (t0) cc_final: 0.7731 (t0) REVERT: B 108 ASP cc_start: 0.8676 (m-30) cc_final: 0.8279 (m-30) REVERT: B 125 PHE cc_start: 0.5909 (OUTLIER) cc_final: 0.5668 (p90) outliers start: 34 outliers final: 17 residues processed: 126 average time/residue: 0.9137 time to fit residues: 124.0887 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 : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain A residue 45 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 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 802 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 125 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 69 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 GLN A 115 ASN A 211 ASN A 424 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.105085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.073252 restraints weight = 16630.249| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.69 r_work: 0.2948 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7531 Z= 0.200 Angle : 0.735 14.516 10221 Z= 0.337 Chirality : 0.046 0.356 1170 Planarity : 0.004 0.074 1302 Dihedral : 4.508 66.494 1007 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.09 % Favored : 96.81 % Rotamer: Outliers : 3.94 % Allowed : 31.53 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.28), residues: 939 helix: 2.33 (0.35), residues: 233 sheet: -0.62 (0.44), residues: 152 loop : -0.63 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 160 HIS 0.004 0.001 HIS A 257 PHE 0.015 0.001 PHE A 754 TYR 0.025 0.001 TYR B 71 ARG 0.018 0.001 ARG B 123 *********************** 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 135 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.844 Fit side-chains REVERT: C 450 SER cc_start: 0.7689 (OUTLIER) cc_final: 0.7445 (p) REVERT: C 464 GLN cc_start: 0.8672 (tt0) cc_final: 0.7590 (tp-100) REVERT: C 486 ASP cc_start: 0.9308 (m-30) cc_final: 0.8764 (p0) REVERT: C 511 LYS cc_start: 0.8816 (ptmm) cc_final: 0.8001 (ptmm) REVERT: C 513 GLU cc_start: 0.9294 (pp20) cc_final: 0.9045 (pp20) REVERT: C 514 ASP cc_start: 0.9271 (m-30) cc_final: 0.8502 (m-30) REVERT: A 199 THR cc_start: 0.9341 (OUTLIER) cc_final: 0.8867 (m) REVERT: A 211 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8721 (m-40) REVERT: A 232 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8053 (t70) REVERT: A 272 ASN cc_start: 0.9301 (OUTLIER) cc_final: 0.8992 (p0) REVERT: A 332 ILE cc_start: 0.9031 (pt) cc_final: 0.8804 (mt) REVERT: A 435 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8456 (m110) REVERT: A 575 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8253 (tm) REVERT: A 678 CYS cc_start: 0.9227 (t) cc_final: 0.8973 (m) REVERT: B 56 GLN cc_start: 0.8052 (pm20) cc_final: 0.7278 (pm20) REVERT: B 70 GLN cc_start: 0.8869 (pt0) cc_final: 0.8192 (pp30) REVERT: B 97 ARG cc_start: 0.8567 (mmm160) cc_final: 0.8037 (mmm160) REVERT: B 100 ASN cc_start: 0.8237 (t0) cc_final: 0.8014 (t0) REVERT: B 108 ASP cc_start: 0.8649 (m-30) cc_final: 0.8262 (m-30) REVERT: B 125 PHE cc_start: 0.5916 (OUTLIER) cc_final: 0.5687 (p90) outliers start: 32 outliers final: 17 residues processed: 122 average time/residue: 0.8853 time to fit residues: 116.2483 Evaluate side-chains 126 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 458 VAL 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 688 SER Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 125 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 chunk 54 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 20 optimal weight: 0.0020 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN A 424 ASN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.105501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.073687 restraints weight = 16472.418| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.68 r_work: 0.2956 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7531 Z= 0.195 Angle : 0.756 14.884 10221 Z= 0.346 Chirality : 0.046 0.343 1170 Planarity : 0.005 0.086 1302 Dihedral : 4.514 66.461 1007 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.30 % Favored : 96.59 % Rotamer: Outliers : 3.57 % Allowed : 31.90 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.28), residues: 939 helix: 2.27 (0.35), residues: 233 sheet: -0.64 (0.44), residues: 152 loop : -0.65 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 461 HIS 0.009 0.001 HIS A 210 PHE 0.017 0.001 PHE A 754 TYR 0.028 0.001 TYR B 71 ARG 0.019 0.001 ARG B 123 ********************** 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 139 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.776 Fit side-chains REVERT: C 450 SER cc_start: 0.7761 (OUTLIER) cc_final: 0.7516 (p) REVERT: C 459 MET cc_start: 0.6765 (mtp) cc_final: 0.6284 (mtm) REVERT: C 464 GLN cc_start: 0.8668 (tt0) cc_final: 0.7568 (tp-100) REVERT: C 486 ASP cc_start: 0.9307 (m-30) cc_final: 0.8766 (p0) REVERT: C 513 GLU cc_start: 0.9292 (pp20) cc_final: 0.8983 (pp20) REVERT: C 514 ASP cc_start: 0.9288 (m-30) cc_final: 0.8467 (m-30) REVERT: A 199 THR cc_start: 0.9335 (OUTLIER) cc_final: 0.8859 (m) REVERT: A 211 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8789 (m-40) REVERT: A 232 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8147 (t70) REVERT: A 272 ASN cc_start: 0.9309 (OUTLIER) cc_final: 0.8997 (p0) REVERT: A 332 ILE cc_start: 0.9026 (pt) cc_final: 0.8799 (mt) REVERT: A 435 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8485 (m110) REVERT: A 575 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8237 (tm) REVERT: A 678 CYS cc_start: 0.9244 (t) cc_final: 0.8986 (m) REVERT: B 56 GLN cc_start: 0.8067 (pm20) cc_final: 0.7660 (pm20) REVERT: B 70 GLN cc_start: 0.8890 (pt0) cc_final: 0.8183 (pp30) REVERT: B 71 TYR cc_start: 0.9255 (p90) cc_final: 0.8967 (p90) REVERT: B 97 ARG cc_start: 0.8589 (mmm160) cc_final: 0.8135 (mmm160) REVERT: B 100 ASN cc_start: 0.8177 (t0) cc_final: 0.7804 (t0) REVERT: B 108 ASP cc_start: 0.8640 (m-30) cc_final: 0.8287 (p0) REVERT: B 125 PHE cc_start: 0.5900 (OUTLIER) cc_final: 0.5652 (p90) REVERT: B 139 MET cc_start: 0.7110 (tpt) cc_final: 0.6853 (tpt) outliers start: 29 outliers final: 15 residues processed: 128 average time/residue: 0.8497 time to fit residues: 117.5259 Evaluate side-chains 123 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 458 VAL 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 688 SER Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 125 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 75 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 80 optimal weight: 0.0670 chunk 90 optimal weight: 0.9990 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 22 optimal weight: 0.3980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 496 GLN A 115 ASN ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.105462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.073778 restraints weight = 16335.804| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.67 r_work: 0.2957 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 7531 Z= 0.253 Angle : 1.054 59.199 10221 Z= 0.574 Chirality : 0.047 0.318 1170 Planarity : 0.005 0.101 1302 Dihedral : 4.528 66.443 1007 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.09 % Favored : 96.81 % Rotamer: Outliers : 3.33 % Allowed : 32.14 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.28), residues: 939 helix: 2.24 (0.35), residues: 233 sheet: -0.63 (0.44), residues: 152 loop : -0.67 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 461 HIS 0.013 0.001 HIS A 210 PHE 0.014 0.001 PHE A 808 TYR 0.025 0.001 TYR B 71 ARG 0.006 0.000 ARG B 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5324.51 seconds wall clock time: 91 minutes 38.59 seconds (5498.59 seconds total)