Starting phenix.real_space_refine on Wed Sep 17 06:17:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jio_61512/09_2025/9jio_61512.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jio_61512/09_2025/9jio_61512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jio_61512/09_2025/9jio_61512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jio_61512/09_2025/9jio_61512.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jio_61512/09_2025/9jio_61512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jio_61512/09_2025/9jio_61512.map" } resolution = 2.87 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= 0.017 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 24 5.16 5 C 3684 2.51 5 N 970 2.21 5 O 1130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 5808 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1101 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "B" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1101 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "H" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 999 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 804 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "E" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 999 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "F" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 804 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASP L 50 " occ=0.85 ... (6 atoms not shown) pdb=" OD2 ASP L 50 " occ=0.85 residue: pdb=" N ASP F 50 " occ=0.85 ... (6 atoms not shown) pdb=" OD2 ASP F 50 " occ=0.85 Time building chain proxies: 1.58, per 1000 atoms: 0.27 Number of scatterers: 5808 At special positions: 0 Unit cell: (68.25, 98.15, 80.6, 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 24 16.00 O 1130 8.00 N 970 7.00 C 3684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 106 " - pdb=" SG CYS H 110 " distance=1.71 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 106 " - pdb=" SG CYS E 110 " distance=1.71 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " 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: 0.45 Conformation dependent library (CDL) restraints added in 238.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 17 sheets defined 4.2% alpha, 39.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.589A pdb=" N LEU A 514 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 514 removed outlier: 3.607A pdb=" N LEU B 514 " --> pdb=" O ALA B 511 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 111 removed outlier: 3.906A pdb=" N GLU H 109 " --> pdb=" O CYS H 106 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS H 110 " --> pdb=" O GLY H 107 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE H 111 " --> pdb=" O ASP H 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 111' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.633A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 111 removed outlier: 3.906A pdb=" N GLU E 109 " --> pdb=" O CYS E 106 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS E 110 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE E 111 " --> pdb=" O ASP E 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 106 through 111' Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.634A pdb=" N ILE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA2, first strand: chain 'A' and resid 497 through 502 removed outlier: 4.494A pdb=" N SER A 497 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL A 593 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 598 " --> pdb=" O SER A 546 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 497 through 502 removed outlier: 4.494A pdb=" N SER A 497 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 579 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 531 Processing sheet with id=AA5, first strand: chain 'B' and resid 464 through 465 Processing sheet with id=AA6, first strand: chain 'B' and resid 497 through 502 removed outlier: 4.455A pdb=" N SER B 497 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 570 " --> pdb=" O ALA B 580 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 497 through 502 removed outlier: 4.455A pdb=" N SER B 497 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL B 593 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 598 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.501A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.534A pdb=" N ALA H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.572A pdb=" N CYS H 96 " --> pdb=" O TRP H 120 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N TRP H 120 " --> pdb=" O CYS H 96 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.884A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.846A pdb=" N TYR L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.501A pdb=" N VAL E 18 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.534A pdb=" N ALA E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.572A pdb=" N CYS E 96 " --> pdb=" O TRP E 120 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N TRP E 120 " --> pdb=" O CYS E 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.883A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 19 through 24 removed outlier: 3.846A pdb=" N TYR F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 938 1.31 - 1.44: 1709 1.44 - 1.56: 3267 1.56 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 5950 Sorted by residual: bond pdb=" N PRO H 112 " pdb=" CD PRO H 112 " ideal model delta sigma weight residual 1.473 1.541 -0.068 1.40e-02 5.10e+03 2.36e+01 bond pdb=" N PRO E 112 " pdb=" CD PRO E 112 " ideal model delta sigma weight residual 1.473 1.541 -0.068 1.40e-02 5.10e+03 2.36e+01 bond pdb=" CA THR A 505 " pdb=" C THR A 505 " ideal model delta sigma weight residual 1.522 1.458 0.064 1.32e-02 5.74e+03 2.33e+01 bond pdb=" C VAL A 503 " pdb=" O VAL A 503 " ideal model delta sigma weight residual 1.237 1.185 0.053 1.32e-02 5.74e+03 1.60e+01 bond pdb=" CA ALA A 504 " pdb=" CB ALA A 504 " ideal model delta sigma weight residual 1.532 1.480 0.052 1.57e-02 4.06e+03 1.10e+01 ... (remaining 5945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 8013 2.19 - 4.39: 100 4.39 - 6.58: 5 6.58 - 8.78: 2 8.78 - 10.97: 2 Bond angle restraints: 8122 Sorted by residual: angle pdb=" N THR A 505 " pdb=" CA THR A 505 " pdb=" C THR A 505 " ideal model delta sigma weight residual 113.50 106.38 7.12 1.23e+00 6.61e-01 3.35e+01 angle pdb=" C THR A 505 " pdb=" N GLY A 506 " pdb=" CA GLY A 506 " ideal model delta sigma weight residual 121.93 114.25 7.68 1.94e+00 2.66e-01 1.57e+01 angle pdb=" C PHE E 111 " pdb=" N PRO E 112 " pdb=" CD PRO E 112 " ideal model delta sigma weight residual 125.00 114.03 10.97 4.10e+00 5.95e-02 7.16e+00 angle pdb=" C PHE H 111 " pdb=" N PRO H 112 " pdb=" CD PRO H 112 " ideal model delta sigma weight residual 125.00 114.07 10.93 4.10e+00 5.95e-02 7.10e+00 angle pdb=" O ASN A 502 " pdb=" C ASN A 502 " pdb=" N VAL A 503 " ideal model delta sigma weight residual 122.93 119.80 3.13 1.23e+00 6.61e-01 6.47e+00 ... (remaining 8117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3024 17.89 - 35.78: 346 35.78 - 53.68: 93 53.68 - 71.57: 15 71.57 - 89.46: 10 Dihedral angle restraints: 3488 sinusoidal: 1306 harmonic: 2182 Sorted by residual: dihedral pdb=" CA PHE H 111 " pdb=" C PHE H 111 " pdb=" N PRO H 112 " pdb=" CA PRO H 112 " ideal model delta harmonic sigma weight residual 180.00 131.03 48.97 0 5.00e+00 4.00e-02 9.59e+01 dihedral pdb=" CA PHE E 111 " pdb=" C PHE E 111 " pdb=" N PRO E 112 " pdb=" CA PRO E 112 " ideal model delta harmonic sigma weight residual 180.00 131.03 48.97 0 5.00e+00 4.00e-02 9.59e+01 dihedral pdb=" CA ASP H 118 " pdb=" C ASP H 118 " pdb=" N PRO H 119 " pdb=" CA PRO H 119 " ideal model delta harmonic sigma weight residual -180.00 -149.16 -30.84 0 5.00e+00 4.00e-02 3.80e+01 ... (remaining 3485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 640 0.037 - 0.075: 170 0.075 - 0.112: 97 0.112 - 0.150: 10 0.150 - 0.187: 1 Chirality restraints: 918 Sorted by residual: chirality pdb=" CA HIS H 31 " pdb=" N HIS H 31 " pdb=" C HIS H 31 " pdb=" CB HIS H 31 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.76e-01 chirality pdb=" CA PRO H 119 " pdb=" N PRO H 119 " pdb=" C PRO H 119 " pdb=" CB PRO H 119 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CB VAL A 503 " pdb=" CA VAL A 503 " pdb=" CG1 VAL A 503 " pdb=" CG2 VAL A 503 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 915 not shown) Planarity restraints: 1036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 67 " 0.547 9.50e-02 1.11e+02 2.45e-01 3.67e+01 pdb=" NE ARG H 67 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG H 67 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG H 67 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 67 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 67 " 0.546 9.50e-02 1.11e+02 2.45e-01 3.67e+01 pdb=" NE ARG E 67 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG E 67 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG E 67 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 67 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 111 " -0.095 5.00e-02 4.00e+02 1.44e-01 3.33e+01 pdb=" N PRO E 112 " 0.249 5.00e-02 4.00e+02 pdb=" CA PRO E 112 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO E 112 " -0.072 5.00e-02 4.00e+02 ... (remaining 1033 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1730 2.81 - 3.34: 4839 3.34 - 3.86: 9659 3.86 - 4.38: 11826 4.38 - 4.90: 20312 Nonbonded interactions: 48366 Sorted by model distance: nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.292 3.040 nonbonded pdb=" O ASP F 82 " pdb=" OH TYR F 86 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR A 493 " pdb=" O GLY A 589 " model vdw 2.298 3.040 nonbonded pdb=" OG1 THR F 34 " pdb=" O ILE F 48 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR L 34 " pdb=" O ILE L 48 " model vdw 2.341 3.040 ... (remaining 48361 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'L' } 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=0.85 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: 5.670 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.360 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 : 0.007 0.321 5956 Z= 0.360 Angle : 1.116 57.388 8134 Z= 0.550 Chirality : 0.043 0.187 918 Planarity : 0.014 0.245 1036 Dihedral : 16.806 89.461 2086 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.95 % Allowed : 27.22 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: -1.82 (0.32), residues: 748 helix: None (None), residues: 0 sheet: -0.88 (0.28), residues: 376 loop : -1.48 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 72 TYR 0.022 0.001 TYR B 559 PHE 0.006 0.001 PHE A 462 TRP 0.008 0.001 TRP H 120 HIS 0.002 0.001 HIS H 31 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5950) covalent geometry : angle 0.59468 ( 8122) SS BOND : bond 0.18491 ( 6) SS BOND : angle 24.59730 ( 12) hydrogen bonds : bond 0.25976 ( 182) hydrogen bonds : angle 10.74119 ( 495) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 473 LEU cc_start: 0.8345 (mp) cc_final: 0.8137 (mp) REVERT: B 520 THR cc_start: 0.8212 (p) cc_final: 0.7827 (t) REVERT: B 587 SER cc_start: 0.8190 (p) cc_final: 0.7972 (m) REVERT: H 4 LEU cc_start: 0.6357 (mt) cc_final: 0.6137 (mt) REVERT: L 86 TYR cc_start: 0.8443 (m-80) cc_final: 0.8165 (m-80) REVERT: E 116 TRP cc_start: 0.7582 (p90) cc_final: 0.7344 (p90) REVERT: F 4 MET cc_start: 0.7180 (ttm) cc_final: 0.6967 (ttp) REVERT: F 102 THR cc_start: 0.7746 (t) cc_final: 0.6956 (m) outliers start: 6 outliers final: 1 residues processed: 119 average time/residue: 0.2871 time to fit residues: 37.3322 Evaluate side-chains 112 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 93 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.0050 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN F 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.146700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.135002 restraints weight = 7392.546| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.66 r_work: 0.3703 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5956 Z= 0.122 Angle : 0.566 7.481 8134 Z= 0.294 Chirality : 0.044 0.153 918 Planarity : 0.007 0.096 1036 Dihedral : 5.682 45.458 830 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.43 % Allowed : 25.63 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: -1.55 (0.31), residues: 748 helix: None (None), residues: 0 sheet: -0.43 (0.28), residues: 378 loop : -1.65 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 72 TYR 0.016 0.001 TYR A 561 PHE 0.011 0.001 PHE H 64 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5950) covalent geometry : angle 0.56594 ( 8122) SS BOND : bond 0.00678 ( 6) SS BOND : angle 0.75757 ( 12) hydrogen bonds : bond 0.04152 ( 182) hydrogen bonds : angle 6.62398 ( 495) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.232 Fit side-chains REVERT: B 473 LEU cc_start: 0.8314 (mp) cc_final: 0.8109 (mp) REVERT: B 542 ARG cc_start: 0.8222 (mtt-85) cc_final: 0.8016 (mtt-85) REVERT: H 2 VAL cc_start: 0.7843 (m) cc_final: 0.7608 (t) REVERT: L 86 TYR cc_start: 0.8486 (m-80) cc_final: 0.8251 (m-80) REVERT: L 102 THR cc_start: 0.8039 (t) cc_final: 0.7299 (m) REVERT: E 118 ASP cc_start: 0.6510 (OUTLIER) cc_final: 0.6298 (m-30) REVERT: F 55 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: F 102 THR cc_start: 0.7886 (t) cc_final: 0.7136 (m) outliers start: 28 outliers final: 13 residues processed: 120 average time/residue: 0.3103 time to fit residues: 40.3714 Evaluate side-chains 113 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain E residue 31 HIS Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain F residue 55 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 28 ASN L 93 ASN E 31 HIS F 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.142081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.130517 restraints weight = 7309.355| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.61 r_work: 0.3638 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5956 Z= 0.225 Angle : 0.671 8.051 8134 Z= 0.348 Chirality : 0.046 0.162 918 Planarity : 0.007 0.090 1036 Dihedral : 6.374 50.998 830 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 6.33 % Allowed : 24.05 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 15.00 % 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: -1.42 (0.32), residues: 748 helix: None (None), residues: 0 sheet: -0.12 (0.29), residues: 342 loop : -1.72 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 542 TYR 0.026 0.002 TYR B 561 PHE 0.013 0.002 PHE B 536 TRP 0.016 0.002 TRP H 47 HIS 0.010 0.002 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 5950) covalent geometry : angle 0.66914 ( 8122) SS BOND : bond 0.00436 ( 6) SS BOND : angle 1.41270 ( 12) hydrogen bonds : bond 0.04209 ( 182) hydrogen bonds : angle 6.21259 ( 495) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.184 Fit side-chains REVERT: H 2 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7760 (t) REVERT: H 39 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.6819 (tt0) REVERT: L 102 THR cc_start: 0.8141 (t) cc_final: 0.7392 (m) REVERT: F 102 THR cc_start: 0.8008 (t) cc_final: 0.7348 (m) outliers start: 40 outliers final: 21 residues processed: 125 average time/residue: 0.2856 time to fit residues: 38.9460 Evaluate side-chains 126 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 27 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 0.5980 chunk 51 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 56 optimal weight: 0.0070 chunk 52 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 39 optimal weight: 0.3980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 31 HIS F 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.144971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.133396 restraints weight = 7423.731| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.64 r_work: 0.3685 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5956 Z= 0.130 Angle : 0.574 7.541 8134 Z= 0.297 Chirality : 0.044 0.184 918 Planarity : 0.006 0.074 1036 Dihedral : 5.873 45.480 828 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.85 % Allowed : 24.84 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: -1.29 (0.32), residues: 748 helix: None (None), residues: 0 sheet: -0.03 (0.28), residues: 366 loop : -1.73 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.018 0.002 TYR E 105 PHE 0.008 0.001 PHE B 536 TRP 0.015 0.001 TRP H 47 HIS 0.006 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 5950) covalent geometry : angle 0.57311 ( 8122) SS BOND : bond 0.00278 ( 6) SS BOND : angle 1.11328 ( 12) hydrogen bonds : bond 0.03324 ( 182) hydrogen bonds : angle 5.62661 ( 495) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: H 2 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7721 (t) REVERT: H 39 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.6774 (tt0) REVERT: L 102 THR cc_start: 0.8093 (t) cc_final: 0.7351 (m) REVERT: E 5 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7472 (m) REVERT: E 118 ASP cc_start: 0.6518 (OUTLIER) cc_final: 0.6307 (m-30) REVERT: F 55 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: F 102 THR cc_start: 0.7967 (t) cc_final: 0.7263 (m) outliers start: 37 outliers final: 25 residues processed: 120 average time/residue: 0.3247 time to fit residues: 42.2387 Evaluate side-chains 125 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain F residue 93 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.140821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.129300 restraints weight = 7519.220| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.62 r_work: 0.3618 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 5956 Z= 0.277 Angle : 0.711 8.926 8134 Z= 0.368 Chirality : 0.048 0.185 918 Planarity : 0.007 0.081 1036 Dihedral : 6.560 51.436 828 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 6.96 % Allowed : 23.42 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 15.00 % 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: -1.38 (0.32), residues: 748 helix: None (None), residues: 0 sheet: -0.17 (0.29), residues: 344 loop : -1.62 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 542 TYR 0.026 0.003 TYR B 561 PHE 0.018 0.002 PHE E 111 TRP 0.025 0.003 TRP H 47 HIS 0.011 0.002 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00638 ( 5950) covalent geometry : angle 0.70951 ( 8122) SS BOND : bond 0.00439 ( 6) SS BOND : angle 1.48376 ( 12) hydrogen bonds : bond 0.04090 ( 182) hydrogen bonds : angle 5.99291 ( 495) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: H 39 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.6862 (tt0) REVERT: L 102 THR cc_start: 0.8236 (t) cc_final: 0.7542 (m) REVERT: E 39 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.6824 (tt0) REVERT: E 118 ASP cc_start: 0.6708 (OUTLIER) cc_final: 0.6486 (m-30) REVERT: F 55 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: F 102 THR cc_start: 0.8088 (t) cc_final: 0.7459 (m) outliers start: 44 outliers final: 29 residues processed: 130 average time/residue: 0.3395 time to fit residues: 47.7046 Evaluate side-chains 133 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain F residue 93 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 31 HIS F 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.141273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129833 restraints weight = 7424.639| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.60 r_work: 0.3633 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5956 Z= 0.250 Angle : 0.687 9.031 8134 Z= 0.357 Chirality : 0.046 0.215 918 Planarity : 0.007 0.073 1036 Dihedral : 6.571 50.007 828 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 7.44 % Allowed : 23.42 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: -1.48 (0.32), residues: 748 helix: None (None), residues: 0 sheet: -0.28 (0.29), residues: 332 loop : -1.61 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 460 TYR 0.023 0.002 TYR B 561 PHE 0.014 0.002 PHE E 111 TRP 0.024 0.003 TRP H 47 HIS 0.011 0.002 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00576 ( 5950) covalent geometry : angle 0.68377 ( 8122) SS BOND : bond 0.00362 ( 6) SS BOND : angle 1.75436 ( 12) hydrogen bonds : bond 0.03949 ( 182) hydrogen bonds : angle 5.96589 ( 495) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: H 39 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.6951 (tt0) REVERT: L 102 THR cc_start: 0.8253 (t) cc_final: 0.7602 (m) REVERT: E 39 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.6885 (tt0) REVERT: E 118 ASP cc_start: 0.6776 (OUTLIER) cc_final: 0.6556 (m-30) REVERT: F 55 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: F 102 THR cc_start: 0.8059 (t) cc_final: 0.7486 (m) outliers start: 47 outliers final: 31 residues processed: 135 average time/residue: 0.3601 time to fit residues: 52.2217 Evaluate side-chains 136 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain F residue 93 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.142874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.131424 restraints weight = 7450.432| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.61 r_work: 0.3661 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5956 Z= 0.181 Angle : 0.640 8.416 8134 Z= 0.329 Chirality : 0.045 0.236 918 Planarity : 0.006 0.074 1036 Dihedral : 6.306 49.449 828 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 7.12 % Allowed : 24.05 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: -1.31 (0.32), residues: 748 helix: None (None), residues: 0 sheet: -0.10 (0.29), residues: 340 loop : -1.59 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 542 TYR 0.038 0.002 TYR B 561 PHE 0.011 0.002 PHE A 536 TRP 0.016 0.002 TRP E 47 HIS 0.009 0.002 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 5950) covalent geometry : angle 0.63810 ( 8122) SS BOND : bond 0.00367 ( 6) SS BOND : angle 1.50803 ( 12) hydrogen bonds : bond 0.03565 ( 182) hydrogen bonds : angle 5.69689 ( 495) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: H 38 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7408 (ptm160) REVERT: H 39 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.6895 (tt0) REVERT: L 102 THR cc_start: 0.8231 (t) cc_final: 0.7575 (m) REVERT: E 39 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.6868 (tt0) REVERT: E 118 ASP cc_start: 0.6742 (OUTLIER) cc_final: 0.6527 (m-30) REVERT: F 4 MET cc_start: 0.7197 (ttm) cc_final: 0.6978 (ttp) REVERT: F 55 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: F 102 THR cc_start: 0.8034 (t) cc_final: 0.7434 (m) outliers start: 45 outliers final: 31 residues processed: 132 average time/residue: 0.3375 time to fit residues: 48.0383 Evaluate side-chains 135 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain F residue 93 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 6 optimal weight: 0.0030 chunk 40 optimal weight: 0.0470 chunk 55 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 overall best weight: 0.2688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN E 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.145544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.134105 restraints weight = 7405.476| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.62 r_work: 0.3682 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5956 Z= 0.120 Angle : 0.591 8.177 8134 Z= 0.299 Chirality : 0.044 0.245 918 Planarity : 0.006 0.070 1036 Dihedral : 5.897 47.528 828 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 5.54 % Allowed : 25.63 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: -1.24 (0.32), residues: 748 helix: None (None), residues: 0 sheet: -0.07 (0.28), residues: 360 loop : -1.58 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.025 0.002 TYR B 561 PHE 0.010 0.001 PHE A 536 TRP 0.013 0.001 TRP H 47 HIS 0.007 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 5950) covalent geometry : angle 0.58983 ( 8122) SS BOND : bond 0.00325 ( 6) SS BOND : angle 1.27273 ( 12) hydrogen bonds : bond 0.03195 ( 182) hydrogen bonds : angle 5.30416 ( 495) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: H 2 VAL cc_start: 0.7972 (m) cc_final: 0.7738 (t) REVERT: H 39 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.6880 (tt0) REVERT: H 78 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7715 (p) REVERT: L 102 THR cc_start: 0.8153 (t) cc_final: 0.7454 (m) REVERT: E 39 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.6860 (tt0) REVERT: E 109 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7117 (tp30) REVERT: F 55 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: F 102 THR cc_start: 0.7968 (t) cc_final: 0.7320 (m) outliers start: 35 outliers final: 23 residues processed: 114 average time/residue: 0.3574 time to fit residues: 43.7663 Evaluate side-chains 117 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain F residue 93 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.0570 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 482 GLN L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.143896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132462 restraints weight = 7492.479| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.61 r_work: 0.3668 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5956 Z= 0.171 Angle : 0.630 9.002 8134 Z= 0.321 Chirality : 0.045 0.249 918 Planarity : 0.006 0.074 1036 Dihedral : 6.124 50.061 828 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 5.54 % Allowed : 25.63 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: -1.18 (0.32), residues: 748 helix: None (None), residues: 0 sheet: 0.02 (0.29), residues: 344 loop : -1.53 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 542 TYR 0.032 0.002 TYR B 561 PHE 0.013 0.002 PHE A 536 TRP 0.015 0.002 TRP H 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 5950) covalent geometry : angle 0.62773 ( 8122) SS BOND : bond 0.00366 ( 6) SS BOND : angle 1.46428 ( 12) hydrogen bonds : bond 0.03444 ( 182) hydrogen bonds : angle 5.45034 ( 495) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: H 2 VAL cc_start: 0.8002 (m) cc_final: 0.7783 (t) REVERT: H 39 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.6922 (tt0) REVERT: L 102 THR cc_start: 0.8181 (t) cc_final: 0.7502 (m) REVERT: E 39 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.6894 (tt0) REVERT: F 55 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: F 102 THR cc_start: 0.8021 (t) cc_final: 0.7391 (m) outliers start: 35 outliers final: 26 residues processed: 117 average time/residue: 0.3383 time to fit residues: 42.7284 Evaluate side-chains 123 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain F residue 93 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.144148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.132675 restraints weight = 7527.072| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.62 r_work: 0.3671 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5956 Z= 0.163 Angle : 0.637 9.684 8134 Z= 0.322 Chirality : 0.045 0.251 918 Planarity : 0.006 0.071 1036 Dihedral : 6.089 49.066 828 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 5.70 % Allowed : 25.63 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: -1.13 (0.32), residues: 748 helix: None (None), residues: 0 sheet: 0.06 (0.29), residues: 342 loop : -1.50 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 542 TYR 0.029 0.002 TYR B 561 PHE 0.012 0.001 PHE A 536 TRP 0.015 0.002 TRP H 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 5950) covalent geometry : angle 0.63206 ( 8122) SS BOND : bond 0.00361 ( 6) SS BOND : angle 2.08358 ( 12) hydrogen bonds : bond 0.03422 ( 182) hydrogen bonds : angle 5.44127 ( 495) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: H 2 VAL cc_start: 0.8014 (m) cc_final: 0.7802 (t) REVERT: H 39 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.6955 (tt0) REVERT: H 78 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7724 (p) REVERT: L 102 THR cc_start: 0.8172 (t) cc_final: 0.7484 (m) REVERT: E 39 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.6889 (tt0) REVERT: F 55 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: F 102 THR cc_start: 0.8002 (t) cc_final: 0.7383 (m) outliers start: 36 outliers final: 29 residues processed: 112 average time/residue: 0.3762 time to fit residues: 45.2118 Evaluate side-chains 124 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain F residue 93 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 4 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 0.0970 chunk 22 optimal weight: 0.1980 chunk 19 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.144188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.132820 restraints weight = 7356.300| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.60 r_work: 0.3675 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5956 Z= 0.164 Angle : 0.642 9.800 8134 Z= 0.324 Chirality : 0.045 0.246 918 Planarity : 0.006 0.073 1036 Dihedral : 6.094 49.596 828 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.85 % Allowed : 25.95 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: -1.12 (0.32), residues: 748 helix: None (None), residues: 0 sheet: 0.06 (0.29), residues: 342 loop : -1.48 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 542 TYR 0.029 0.002 TYR B 561 PHE 0.012 0.001 PHE A 536 TRP 0.015 0.002 TRP H 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 5950) covalent geometry : angle 0.63799 ( 8122) SS BOND : bond 0.00354 ( 6) SS BOND : angle 1.99259 ( 12) hydrogen bonds : bond 0.03442 ( 182) hydrogen bonds : angle 5.44870 ( 495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2255.92 seconds wall clock time: 39 minutes 23.03 seconds (2363.03 seconds total)