Starting phenix.real_space_refine on Thu Jul 2 04:33:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tbf_25797/07_2026/7tbf_25797.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tbf_25797/07_2026/7tbf_25797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7tbf_25797/07_2026/7tbf_25797.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tbf_25797/07_2026/7tbf_25797.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tbf_25797/07_2026/7tbf_25797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tbf_25797/07_2026/7tbf_25797.map" model { file = "/net/cci-nas-00/data/ceres_data/7tbf_25797/07_2026/7tbf_25797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tbf_25797/07_2026/7tbf_25797.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.007 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 29 5.16 5 C 4181 2.51 5 N 1114 2.21 5 O 1293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6617 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 1611 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 215, 1611 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 1641 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "D" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 973 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "E" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.37, per 1000 atoms: 0.21 Number of scatterers: 6617 At special positions: 0 Unit cell: (88.173, 104.76, 138.807, 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 29 16.00 O 1293 8.00 N 1114 7.00 C 4181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 332.1 milliseconds 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 20 sheets defined 2.7% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.529A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.524A pdb=" N SER D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.532A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.695A pdb=" N TYR H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'H' and resid 97 through 98 removed outlier: 3.954A pdb=" N SER H 100A" --> pdb=" O SER H 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 121 Processing sheet with id=AA9, first strand: chain 'H' and resid 137 through 139 Processing sheet with id=AB1, first strand: chain 'H' and resid 150 through 154 removed outlier: 3.586A pdb=" N ASN H 197 " --> pdb=" O SER H 153 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR H 205 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.760A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.760A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 19 through 22 Processing sheet with id=AB5, first strand: chain 'L' and resid 116 through 117 removed outlier: 3.566A pdb=" N SER L 176 " --> pdb=" O SER L 162 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER L 162 " --> pdb=" O SER L 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 18 through 23 removed outlier: 3.628A pdb=" N LEU D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.701A pdb=" N TYR D 59 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL D 50 " --> pdb=" O PHE D 34 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N HIS D 35 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 97 " --> pdb=" O HIS D 35 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN D 39 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 102 through 104 Processing sheet with id=AB9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'E' and resid 34 through 37 removed outlier: 6.605A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 85 through 86 145 hydrogen bonds defined for protein. 351 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: 0.75 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 1 1.20 - 1.36: 2146 1.36 - 1.52: 3616 1.52 - 1.69: 980 1.69 - 1.85: 36 Bond restraints: 6779 Sorted by residual: bond pdb=" CG PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 1.503 1.042 0.461 3.40e-02 8.65e+02 1.84e+02 bond pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 1.492 1.338 0.154 5.00e-02 4.00e+02 9.43e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.41e+00 bond pdb=" CB PRO A 337 " pdb=" CG PRO A 337 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.44e+00 ... (remaining 6774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.38: 9204 5.38 - 10.76: 13 10.76 - 16.14: 0 16.14 - 21.51: 1 21.51 - 26.89: 2 Bond angle restraints: 9220 Sorted by residual: angle pdb=" N PRO A 384 " pdb=" CD PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 103.20 76.31 26.89 1.50e+00 4.44e-01 3.21e+02 angle pdb=" CA PRO A 384 " pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 104.50 84.12 20.38 1.90e+00 2.77e-01 1.15e+02 angle pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 106.10 132.40 -26.30 3.20e+00 9.77e-02 6.76e+01 angle pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 112.00 101.89 10.11 1.40e+00 5.10e-01 5.21e+01 angle pdb=" N ASP H 144 " pdb=" CA ASP H 144 " pdb=" C ASP H 144 " ideal model delta sigma weight residual 110.91 116.10 -5.19 1.17e+00 7.31e-01 1.97e+01 ... (remaining 9215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 3537 16.05 - 32.10: 363 32.10 - 48.15: 75 48.15 - 64.20: 13 64.20 - 80.25: 7 Dihedral angle restraints: 3995 sinusoidal: 1523 harmonic: 2472 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 150.23 -57.23 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " pdb=" CB CYS E 88 " ideal model delta sinusoidal sigma weight residual 93.00 150.21 -57.21 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 36.52 56.48 1 1.00e+01 1.00e-02 4.30e+01 ... (remaining 3992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 571 0.031 - 0.062: 280 0.062 - 0.093: 99 0.093 - 0.124: 56 0.124 - 0.154: 12 Chirality restraints: 1018 Sorted by residual: chirality pdb=" CA VAL H 211 " pdb=" N VAL H 211 " pdb=" C VAL H 211 " pdb=" CB VAL H 211 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA VAL L 132 " pdb=" N VAL L 132 " pdb=" C VAL L 132 " pdb=" CB VAL L 132 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA PRO E 40 " pdb=" N PRO E 40 " pdb=" C PRO E 40 " pdb=" CB PRO E 40 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 1015 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " -0.070 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO A 384 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " -0.052 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO A 337 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 14 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO L 15 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " 0.023 5.00e-02 4.00e+02 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 62 2.63 - 3.20: 5629 3.20 - 3.77: 8740 3.77 - 4.33: 12681 4.33 - 4.90: 22334 Nonbonded interactions: 49446 Sorted by model distance: nonbonded pdb=" NE2 GLN L 124 " pdb=" O THR L 129 " model vdw 2.064 3.120 nonbonded pdb=" N THR H 135 " pdb=" O VAL H 184 " model vdw 2.224 3.120 nonbonded pdb=" OH TYR E 36 " pdb=" OE1 GLN E 89 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASP L 60 " pdb=" N ARG L 61 " model vdw 2.247 3.120 nonbonded pdb=" OD1 ASP L 167 " pdb=" N ASP L 170 " model vdw 2.297 3.120 ... (remaining 49441 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: 9.230 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.780 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.008 0.461 6791 Z= 0.269 Angle : 0.879 26.893 9246 Z= 0.470 Chirality : 0.046 0.154 1018 Planarity : 0.006 0.098 1184 Dihedral : 13.371 80.248 2391 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.47 % Allowed : 14.91 % Favored : 84.62 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.27), residues: 845 helix: -5.25 (0.24), residues: 20 sheet: -1.34 (0.30), residues: 316 loop : -3.03 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 142 TYR 0.013 0.001 TYR L 140 PHE 0.013 0.001 PHE A 347 TRP 0.007 0.001 TRP D 47 HIS 0.009 0.003 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.27 ( 6779) covalent geometry : angle 0.87473 / 0.47 ( 9220) SS BOND : bond 0.00720 / 0.34 ( 10) SS BOND : angle 1.61083 / 1.07 ( 20) hydrogen bonds : bond 0.30403 / 19.25 ( 138) hydrogen bonds : angle 9.87923 / 6.73 ( 351) link_BETA1-4 : bond 0.00975 / 0.51 ( 1) link_BETA1-4 : angle 2.72892 / 1.31 ( 3) link_NAG-ASN : bond 0.00059 / 0.03 ( 1) link_NAG-ASN : angle 2.48408 / 1.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.0950 time to fit residues: 18.6991 Evaluate side-chains 119 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN A 388 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 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 = 0.3504 r_free = 0.3504 target = 0.094012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083063 restraints weight = 15460.733| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.75 r_work: 0.3243 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6791 Z= 0.162 Angle : 0.730 9.468 9246 Z= 0.371 Chirality : 0.046 0.188 1018 Planarity : 0.005 0.043 1184 Dihedral : 5.339 25.694 934 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.78 % Favored : 86.75 % Rotamer: Outliers : 1.10 % Allowed : 10.45 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.27), residues: 845 helix: -5.24 (0.24), residues: 20 sheet: -1.06 (0.30), residues: 327 loop : -2.94 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 24 TYR 0.017 0.001 TYR A 396 PHE 0.012 0.001 PHE A 347 TRP 0.007 0.001 TRP D 47 HIS 0.006 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 6779) covalent geometry : angle 0.72681 / 0.37 ( 9220) SS BOND : bond 0.00686 / 0.31 ( 10) SS BOND : angle 1.30715 / 0.87 ( 20) hydrogen bonds : bond 0.04883 / 3.19 ( 138) hydrogen bonds : angle 6.72137 / 4.72 ( 351) link_BETA1-4 : bond 0.00591 / 0.31 ( 1) link_BETA1-4 : angle 1.61675 / 0.74 ( 3) link_NAG-ASN : bond 0.00074 / 0.04 ( 1) link_NAG-ASN : angle 2.27442 / 1.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.8197 (mmm) cc_final: 0.7921 (pmm) REVERT: H 71 ARG cc_start: 0.8848 (ttp80) cc_final: 0.8565 (ttp80) REVERT: H 72 ASP cc_start: 0.8381 (t0) cc_final: 0.7994 (t0) REVERT: L 60 ASP cc_start: 0.7889 (t0) cc_final: 0.7664 (t0) REVERT: L 103 LYS cc_start: 0.8624 (ttpp) cc_final: 0.8338 (tttm) REVERT: L 124 GLN cc_start: 0.5828 (mm-40) cc_final: 0.5380 (mm-40) outliers start: 8 outliers final: 5 residues processed: 129 average time/residue: 0.0870 time to fit residues: 14.5159 Evaluate side-chains 126 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 36 optimal weight: 0.0770 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.092559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.081360 restraints weight = 15385.425| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.80 r_work: 0.3217 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6791 Z= 0.187 Angle : 0.716 9.126 9246 Z= 0.367 Chirality : 0.046 0.154 1018 Planarity : 0.005 0.043 1184 Dihedral : 5.275 26.286 934 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.96 % Favored : 85.56 % Rotamer: Outliers : 2.61 % Allowed : 11.97 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.28), residues: 845 helix: -5.22 (0.25), residues: 20 sheet: -0.93 (0.30), residues: 326 loop : -2.90 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 142 TYR 0.018 0.001 TYR A 396 PHE 0.010 0.001 PHE H 146 TRP 0.008 0.001 TRP D 47 HIS 0.008 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 6779) covalent geometry : angle 0.71284 / 0.37 ( 9220) SS BOND : bond 0.00666 / 0.34 ( 10) SS BOND : angle 1.23385 / 0.79 ( 20) hydrogen bonds : bond 0.04413 / 2.85 ( 138) hydrogen bonds : angle 6.11923 / 4.29 ( 351) link_BETA1-4 : bond 0.00528 / 0.28 ( 1) link_BETA1-4 : angle 1.66316 / 0.78 ( 3) link_NAG-ASN : bond 0.00237 / 0.12 ( 1) link_NAG-ASN : angle 2.36208 / 1.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: H 71 ARG cc_start: 0.8857 (ttp80) cc_final: 0.8512 (ttp80) REVERT: H 72 ASP cc_start: 0.8404 (t0) cc_final: 0.8066 (t0) REVERT: L 60 ASP cc_start: 0.7978 (t0) cc_final: 0.7659 (t0) REVERT: L 103 LYS cc_start: 0.8685 (ttpp) cc_final: 0.8403 (tttm) REVERT: D 126 SER cc_start: 0.8875 (p) cc_final: 0.8674 (t) REVERT: E 82 ASP cc_start: 0.8123 (m-30) cc_final: 0.7769 (m-30) outliers start: 19 outliers final: 12 residues processed: 133 average time/residue: 0.0843 time to fit residues: 14.7940 Evaluate side-chains 121 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081744 restraints weight = 15531.800| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.79 r_work: 0.3220 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6791 Z= 0.161 Angle : 0.703 9.633 9246 Z= 0.355 Chirality : 0.045 0.152 1018 Planarity : 0.004 0.041 1184 Dihedral : 5.093 26.220 934 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.25 % Favored : 86.27 % Rotamer: Outliers : 3.03 % Allowed : 13.62 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.28), residues: 845 helix: -5.15 (0.27), residues: 20 sheet: -0.88 (0.30), residues: 331 loop : -2.82 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 142 TYR 0.018 0.001 TYR E 49 PHE 0.009 0.001 PHE H 146 TRP 0.006 0.001 TRP D 47 HIS 0.006 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 6779) covalent geometry : angle 0.70063 / 0.35 ( 9220) SS BOND : bond 0.00622 / 0.32 ( 10) SS BOND : angle 1.12895 / 0.71 ( 20) hydrogen bonds : bond 0.03810 / 2.44 ( 138) hydrogen bonds : angle 5.74869 / 4.05 ( 351) link_BETA1-4 : bond 0.00464 / 0.24 ( 1) link_BETA1-4 : angle 1.57634 / 0.74 ( 3) link_NAG-ASN : bond 0.00169 / 0.09 ( 1) link_NAG-ASN : angle 2.16119 / 1.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.8244 (mmm) cc_final: 0.8034 (pmm) REVERT: H 71 ARG cc_start: 0.8757 (ttp80) cc_final: 0.8492 (ttp80) REVERT: H 72 ASP cc_start: 0.8408 (t0) cc_final: 0.8095 (t0) REVERT: H 135 THR cc_start: 0.6616 (OUTLIER) cc_final: 0.4673 (t) REVERT: L 60 ASP cc_start: 0.7793 (t0) cc_final: 0.7402 (t0) REVERT: L 103 LYS cc_start: 0.8648 (ttpp) cc_final: 0.8375 (tttm) REVERT: D 58 GLN cc_start: 0.9205 (mp10) cc_final: 0.8942 (mp10) REVERT: D 126 SER cc_start: 0.8856 (p) cc_final: 0.8652 (t) outliers start: 22 outliers final: 16 residues processed: 124 average time/residue: 0.0868 time to fit residues: 14.2059 Evaluate side-chains 131 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 17 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 48 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.093232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.082037 restraints weight = 15507.006| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.87 r_work: 0.3229 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6791 Z= 0.144 Angle : 0.682 9.480 9246 Z= 0.345 Chirality : 0.045 0.145 1018 Planarity : 0.004 0.042 1184 Dihedral : 4.971 26.473 934 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.25 % Favored : 86.27 % Rotamer: Outliers : 3.44 % Allowed : 15.54 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.28), residues: 845 helix: -5.15 (0.27), residues: 20 sheet: -0.79 (0.30), residues: 323 loop : -2.70 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 107 TYR 0.018 0.001 TYR E 49 PHE 0.008 0.001 PHE L 118 TRP 0.006 0.001 TRP A 436 HIS 0.004 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 6779) covalent geometry : angle 0.68018 / 0.34 ( 9220) SS BOND : bond 0.00611 / 0.31 ( 10) SS BOND : angle 0.99749 / 0.62 ( 20) hydrogen bonds : bond 0.03523 / 2.26 ( 138) hydrogen bonds : angle 5.59320 / 3.94 ( 351) link_BETA1-4 : bond 0.00457 / 0.24 ( 1) link_BETA1-4 : angle 1.54393 / 0.72 ( 3) link_NAG-ASN : bond 0.00110 / 0.06 ( 1) link_NAG-ASN : angle 2.04341 / 1.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: H 71 ARG cc_start: 0.8733 (ttp80) cc_final: 0.8480 (ttp80) REVERT: H 72 ASP cc_start: 0.8383 (t0) cc_final: 0.8084 (t0) REVERT: L 60 ASP cc_start: 0.7817 (t0) cc_final: 0.7408 (t0) REVERT: L 103 LYS cc_start: 0.8686 (ttpp) cc_final: 0.8419 (tttm) REVERT: D 126 SER cc_start: 0.8860 (p) cc_final: 0.8651 (t) outliers start: 25 outliers final: 18 residues processed: 132 average time/residue: 0.0816 time to fit residues: 13.9808 Evaluate side-chains 132 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 18 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.092938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.081985 restraints weight = 15470.869| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.76 r_work: 0.3230 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6791 Z= 0.155 Angle : 0.685 9.354 9246 Z= 0.346 Chirality : 0.045 0.163 1018 Planarity : 0.004 0.042 1184 Dihedral : 4.951 26.180 934 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.25 % Favored : 86.27 % Rotamer: Outliers : 3.71 % Allowed : 16.09 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.28), residues: 845 helix: -5.16 (0.27), residues: 20 sheet: -0.70 (0.30), residues: 323 loop : -2.67 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 107 TYR 0.019 0.001 TYR E 49 PHE 0.008 0.001 PHE H 146 TRP 0.006 0.001 TRP D 47 HIS 0.005 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 6779) covalent geometry : angle 0.68300 / 0.34 ( 9220) SS BOND : bond 0.00633 / 0.31 ( 10) SS BOND : angle 1.03320 / 0.64 ( 20) hydrogen bonds : bond 0.03565 / 2.24 ( 138) hydrogen bonds : angle 5.51631 / 3.89 ( 351) link_BETA1-4 : bond 0.00485 / 0.26 ( 1) link_BETA1-4 : angle 1.56447 / 0.73 ( 3) link_NAG-ASN : bond 0.00114 / 0.06 ( 1) link_NAG-ASN : angle 2.04767 / 1.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.8214 (mmm) cc_final: 0.7865 (pmm) REVERT: H 71 ARG cc_start: 0.8719 (ttp80) cc_final: 0.8461 (ttp80) REVERT: H 72 ASP cc_start: 0.8321 (t0) cc_final: 0.8033 (t0) REVERT: H 135 THR cc_start: 0.6486 (OUTLIER) cc_final: 0.4641 (t) REVERT: L 60 ASP cc_start: 0.7793 (t0) cc_final: 0.7351 (t0) REVERT: L 103 LYS cc_start: 0.8699 (ttpp) cc_final: 0.8412 (tttm) REVERT: D 17 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.8057 (t) REVERT: D 126 SER cc_start: 0.8835 (p) cc_final: 0.8621 (t) outliers start: 27 outliers final: 22 residues processed: 131 average time/residue: 0.0875 time to fit residues: 15.1170 Evaluate side-chains 139 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.092257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.081106 restraints weight = 15490.812| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.85 r_work: 0.3216 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6791 Z= 0.175 Angle : 0.696 9.151 9246 Z= 0.353 Chirality : 0.045 0.140 1018 Planarity : 0.004 0.043 1184 Dihedral : 4.990 26.061 934 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.37 % Favored : 86.15 % Rotamer: Outliers : 4.13 % Allowed : 16.23 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.28), residues: 845 helix: -5.15 (0.27), residues: 20 sheet: -0.66 (0.30), residues: 323 loop : -2.64 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 107 TYR 0.019 0.001 TYR E 49 PHE 0.009 0.001 PHE H 122 TRP 0.006 0.001 TRP D 47 HIS 0.005 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 6779) covalent geometry : angle 0.69148 / 0.35 ( 9220) SS BOND : bond 0.00653 / 0.32 ( 10) SS BOND : angle 1.60598 / 1.01 ( 20) hydrogen bonds : bond 0.03733 / 2.38 ( 138) hydrogen bonds : angle 5.49345 / 3.88 ( 351) link_BETA1-4 : bond 0.00511 / 0.27 ( 1) link_BETA1-4 : angle 1.59665 / 0.75 ( 3) link_NAG-ASN : bond 0.00177 / 0.09 ( 1) link_NAG-ASN : angle 2.15005 / 1.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.8223 (mmm) cc_final: 0.7910 (pmm) REVERT: H 71 ARG cc_start: 0.8712 (ttp80) cc_final: 0.8460 (ttp80) REVERT: H 72 ASP cc_start: 0.8316 (t0) cc_final: 0.8045 (t0) REVERT: H 135 THR cc_start: 0.6558 (OUTLIER) cc_final: 0.4698 (t) REVERT: L 60 ASP cc_start: 0.7846 (t0) cc_final: 0.7380 (t0) REVERT: L 103 LYS cc_start: 0.8715 (ttpp) cc_final: 0.8422 (tttm) REVERT: D 126 SER cc_start: 0.8861 (p) cc_final: 0.8648 (t) outliers start: 30 outliers final: 26 residues processed: 132 average time/residue: 0.0806 time to fit residues: 14.1082 Evaluate side-chains 139 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.091452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.080376 restraints weight = 15640.950| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.79 r_work: 0.3207 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6791 Z= 0.192 Angle : 0.719 9.978 9246 Z= 0.362 Chirality : 0.045 0.138 1018 Planarity : 0.005 0.045 1184 Dihedral : 5.071 26.010 934 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.37 % Favored : 86.15 % Rotamer: Outliers : 3.85 % Allowed : 17.06 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.28), residues: 845 helix: -5.13 (0.28), residues: 20 sheet: -0.62 (0.31), residues: 323 loop : -2.63 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 107 TYR 0.020 0.001 TYR E 49 PHE 0.009 0.001 PHE L 118 TRP 0.007 0.001 TRP D 47 HIS 0.006 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 6779) covalent geometry : angle 0.71478 / 0.36 ( 9220) SS BOND : bond 0.00596 / 0.32 ( 10) SS BOND : angle 1.51458 / 0.95 ( 20) hydrogen bonds : bond 0.03837 / 2.44 ( 138) hydrogen bonds : angle 5.48357 / 3.89 ( 351) link_BETA1-4 : bond 0.00580 / 0.31 ( 1) link_BETA1-4 : angle 1.63624 / 0.77 ( 3) link_NAG-ASN : bond 0.00248 / 0.13 ( 1) link_NAG-ASN : angle 2.24216 / 1.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.8228 (mmm) cc_final: 0.7962 (pmm) REVERT: H 71 ARG cc_start: 0.8707 (ttp80) cc_final: 0.8444 (ttp80) REVERT: H 72 ASP cc_start: 0.8294 (t0) cc_final: 0.8011 (t0) REVERT: H 135 THR cc_start: 0.6604 (OUTLIER) cc_final: 0.4822 (t) REVERT: L 60 ASP cc_start: 0.7833 (t0) cc_final: 0.7404 (t0) REVERT: L 103 LYS cc_start: 0.8769 (ttpp) cc_final: 0.8463 (tttm) REVERT: D 126 SER cc_start: 0.8862 (p) cc_final: 0.8647 (t) outliers start: 28 outliers final: 26 residues processed: 130 average time/residue: 0.0839 time to fit residues: 14.3893 Evaluate side-chains 140 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 37 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 0.0870 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.091572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.080527 restraints weight = 15586.975| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.79 r_work: 0.3209 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6791 Z= 0.182 Angle : 0.717 9.026 9246 Z= 0.361 Chirality : 0.045 0.140 1018 Planarity : 0.005 0.044 1184 Dihedral : 5.053 26.148 934 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.85 % Favored : 85.68 % Rotamer: Outliers : 3.99 % Allowed : 17.06 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.28), residues: 845 helix: -5.12 (0.29), residues: 20 sheet: -0.59 (0.31), residues: 323 loop : -2.62 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 107 TYR 0.020 0.001 TYR E 49 PHE 0.009 0.001 PHE H 122 TRP 0.007 0.001 TRP D 47 HIS 0.006 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 6779) covalent geometry : angle 0.71354 / 0.36 ( 9220) SS BOND : bond 0.00584 / 0.31 ( 10) SS BOND : angle 1.45380 / 0.91 ( 20) hydrogen bonds : bond 0.03749 / 2.39 ( 138) hydrogen bonds : angle 5.45608 / 3.87 ( 351) link_BETA1-4 : bond 0.00582 / 0.31 ( 1) link_BETA1-4 : angle 1.65899 / 0.78 ( 3) link_NAG-ASN : bond 0.00202 / 0.11 ( 1) link_NAG-ASN : angle 2.19767 / 1.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.8246 (mmm) cc_final: 0.8004 (pmm) REVERT: H 71 ARG cc_start: 0.8696 (ttp80) cc_final: 0.8445 (ttp80) REVERT: H 72 ASP cc_start: 0.8288 (t0) cc_final: 0.8001 (t0) REVERT: H 135 THR cc_start: 0.6554 (OUTLIER) cc_final: 0.4826 (t) REVERT: L 60 ASP cc_start: 0.7825 (t0) cc_final: 0.7399 (t0) REVERT: L 103 LYS cc_start: 0.8766 (ttpp) cc_final: 0.8463 (tttm) REVERT: D 126 SER cc_start: 0.8852 (p) cc_final: 0.8642 (t) outliers start: 29 outliers final: 27 residues processed: 131 average time/residue: 0.0934 time to fit residues: 16.0002 Evaluate side-chains 141 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 48 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.0060 chunk 5 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 41 optimal weight: 0.0570 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.093021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081873 restraints weight = 15563.965| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.81 r_work: 0.3229 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6791 Z= 0.131 Angle : 0.702 11.832 9246 Z= 0.349 Chirality : 0.044 0.163 1018 Planarity : 0.004 0.041 1184 Dihedral : 4.858 26.476 934 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.66 % Favored : 86.86 % Rotamer: Outliers : 3.16 % Allowed : 17.74 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.29), residues: 845 helix: -5.11 (0.30), residues: 20 sheet: -0.45 (0.31), residues: 324 loop : -2.56 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 107 TYR 0.020 0.001 TYR E 49 PHE 0.007 0.001 PHE H 146 TRP 0.006 0.001 TRP A 436 HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 6779) covalent geometry : angle 0.69856 / 0.35 ( 9220) SS BOND : bond 0.00503 / 0.26 ( 10) SS BOND : angle 1.31003 / 0.80 ( 20) hydrogen bonds : bond 0.03289 / 2.13 ( 138) hydrogen bonds : angle 5.33631 / 3.77 ( 351) link_BETA1-4 : bond 0.00547 / 0.29 ( 1) link_BETA1-4 : angle 1.60821 / 0.74 ( 3) link_NAG-ASN : bond 0.00013 / 0.01 ( 1) link_NAG-ASN : angle 1.93038 / 1.08 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 2 MET cc_start: 0.8141 (mmm) cc_final: 0.7872 (pmm) REVERT: H 72 ASP cc_start: 0.8256 (t0) cc_final: 0.7991 (t0) REVERT: H 135 THR cc_start: 0.6339 (OUTLIER) cc_final: 0.4710 (t) REVERT: L 13 LEU cc_start: 0.7887 (tp) cc_final: 0.7405 (mt) REVERT: L 60 ASP cc_start: 0.7782 (t0) cc_final: 0.7379 (t0) REVERT: L 103 LYS cc_start: 0.8741 (ttpp) cc_final: 0.8444 (tttm) REVERT: D 126 SER cc_start: 0.8803 (p) cc_final: 0.8585 (t) outliers start: 23 outliers final: 18 residues processed: 128 average time/residue: 0.0815 time to fit residues: 13.6391 Evaluate side-chains 131 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 58 optimal weight: 0.0570 chunk 55 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.092970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081872 restraints weight = 15422.597| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.78 r_work: 0.3235 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6791 Z= 0.140 Angle : 0.704 10.936 9246 Z= 0.350 Chirality : 0.044 0.161 1018 Planarity : 0.004 0.042 1184 Dihedral : 4.807 26.173 934 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.61 % Favored : 85.92 % Rotamer: Outliers : 3.03 % Allowed : 18.29 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.29), residues: 845 helix: -5.10 (0.30), residues: 20 sheet: -0.42 (0.31), residues: 325 loop : -2.58 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 107 TYR 0.020 0.001 TYR E 49 PHE 0.008 0.001 PHE H 146 TRP 0.005 0.001 TRP A 436 HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 6779) covalent geometry : angle 0.70073 / 0.35 ( 9220) SS BOND : bond 0.00514 / 0.27 ( 10) SS BOND : angle 1.27161 / 0.78 ( 20) hydrogen bonds : bond 0.03321 / 2.14 ( 138) hydrogen bonds : angle 5.27887 / 3.73 ( 351) link_BETA1-4 : bond 0.00532 / 0.28 ( 1) link_BETA1-4 : angle 1.56605 / 0.72 ( 3) link_NAG-ASN : bond 0.00044 / 0.02 ( 1) link_NAG-ASN : angle 1.89756 / 1.06 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1835.24 seconds wall clock time: 32 minutes 13.07 seconds (1933.07 seconds total)