Starting phenix.real_space_refine on Thu Jul 2 01:04:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mlz_23914/07_2026/7mlz_23914.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mlz_23914/07_2026/7mlz_23914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mlz_23914/07_2026/7mlz_23914.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mlz_23914/07_2026/7mlz_23914.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mlz_23914/07_2026/7mlz_23914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mlz_23914/07_2026/7mlz_23914.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mlz_23914/07_2026/7mlz_23914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mlz_23914/07_2026/7mlz_23914.map" } resolution = 3.71 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= 0.006 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 22 5.16 5 C 3073 2.51 5 N 809 2.21 5 O 960 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: 4864 Number of models: 1 Model: "" Number of chains: 4 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': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.20, per 1000 atoms: 0.25 Number of scatterers: 4864 At special positions: 0 Unit cell: (86.427, 61.983, 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 22 16.00 O 960 8.00 N 809 7.00 C 3073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 181.4 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 14 sheets defined 5.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.049A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.706A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.674A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.968A pdb=" N THR H 77 " --> pdb=" O SER H 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.598A pdb=" N LEU L 125 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.689A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA3, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.599A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.896A pdb=" N LYS H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AA6, first strand: chain 'H' and resid 33 through 38 removed outlier: 6.146A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL H 52 " --> pdb=" O ASN H 56 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN H 56 " --> pdb=" O VAL H 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 93 through 94 Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 124 removed outlier: 4.262A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER H 177 " --> pdb=" O ALA H 168 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA H 168 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER H 179 " --> pdb=" O PHE H 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 198 through 200 removed outlier: 3.504A pdb=" N THR H 205 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.825A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AB3, first strand: chain 'L' and resid 33 through 37 removed outlier: 4.059A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 117 through 118 removed outlier: 3.538A pdb=" N THR L 178 " --> pdb=" O GLN L 160 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN L 160 " --> pdb=" O THR L 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 146 through 147 removed outlier: 3.520A pdb=" N GLU L 195 " --> pdb=" O GLN L 147 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 171 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: 0.48 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1544 1.35 - 1.48: 1377 1.48 - 1.60: 2037 1.60 - 1.73: 0 1.73 - 1.85: 26 Bond restraints: 4984 Sorted by residual: bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.46e+00 bond pdb=" C1 MAN B 4 " pdb=" C2 MAN B 4 " ideal model delta sigma weight residual 1.526 1.569 -0.043 2.00e-02 2.50e+03 4.73e+00 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.560 -0.041 2.00e-02 2.50e+03 4.30e+00 bond pdb=" C1 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.399 1.432 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C GLN A 498 " pdb=" N PRO A 499 " ideal model delta sigma weight residual 1.334 1.346 -0.013 8.40e-03 1.42e+04 2.34e+00 ... (remaining 4979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 6440 1.62 - 3.25: 262 3.25 - 4.87: 59 4.87 - 6.49: 15 6.49 - 8.12: 6 Bond angle restraints: 6782 Sorted by residual: angle pdb=" C THR H 191 " pdb=" N GLN H 192 " pdb=" CA GLN H 192 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.33e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 122.52 -8.12 2.30e+00 1.89e-01 1.25e+01 angle pdb=" C PHE A 347 " pdb=" N ALA A 348 " pdb=" CA ALA A 348 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 angle pdb=" C SER L 30 " pdb=" N SER L 31 " pdb=" CA SER L 31 " ideal model delta sigma weight residual 121.54 127.13 -5.59 1.91e+00 2.74e-01 8.56e+00 angle pdb=" CA GLY H 55 " pdb=" C GLY H 55 " pdb=" N ASN H 56 " ideal model delta sigma weight residual 117.06 114.03 3.03 1.08e+00 8.57e-01 7.89e+00 ... (remaining 6777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 2655 17.66 - 35.31: 239 35.31 - 52.97: 26 52.97 - 70.63: 6 70.63 - 88.29: 5 Dihedral angle restraints: 2931 sinusoidal: 1126 harmonic: 1805 Sorted by residual: dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual 93.00 179.47 -86.47 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 15.07 77.93 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 32.88 60.12 1 1.00e+01 1.00e-02 4.82e+01 ... (remaining 2928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 568 0.051 - 0.101: 154 0.101 - 0.152: 35 0.152 - 0.203: 4 0.203 - 0.254: 2 Chirality restraints: 763 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE L 48 " pdb=" CA ILE L 48 " pdb=" CG1 ILE L 48 " pdb=" CG2 ILE L 48 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LYS H 201 " pdb=" N LYS H 201 " pdb=" C LYS H 201 " pdb=" CB LYS H 201 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.34e-01 ... (remaining 760 not shown) Planarity restraints: 868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 112 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO L 113 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO L 113 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 113 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 429 " 0.014 2.00e-02 2.50e+03 1.53e-02 4.12e+00 pdb=" CG PHE A 429 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 429 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 429 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 429 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 429 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 429 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 411 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.62e+00 pdb=" N PRO A 412 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " -0.027 5.00e-02 4.00e+02 ... (remaining 865 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 212 2.70 - 3.25: 5009 3.25 - 3.80: 7178 3.80 - 4.35: 9034 4.35 - 4.90: 14971 Nonbonded interactions: 36404 Sorted by model distance: nonbonded pdb=" OG1 THR H 28 " pdb=" O CYS H 97 " model vdw 2.150 3.040 nonbonded pdb=" OG1 THR L 20 " pdb=" O LEU L 73 " model vdw 2.196 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.201 3.040 nonbonded pdb=" O ARG L 61 " pdb=" OG SER L 76 " model vdw 2.204 3.040 nonbonded pdb=" NH2 ARG A 357 " pdb=" OH TYR A 396 " model vdw 2.236 3.120 ... (remaining 36399 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 group one per residue 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: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.770 Find NCS groups from input model: 0.030 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4998 Z= 0.191 Angle : 0.843 11.298 6815 Z= 0.426 Chirality : 0.050 0.254 763 Planarity : 0.005 0.052 867 Dihedral : 12.961 88.285 1752 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 17.37 % Favored : 82.47 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.08 (0.31), residues: 616 helix: -4.58 (0.49), residues: 20 sheet: -2.30 (0.39), residues: 167 loop : -2.99 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 38 TYR 0.029 0.002 TYR L 49 PHE 0.036 0.002 PHE A 429 TRP 0.022 0.002 TRP H 47 HIS 0.004 0.001 HIS H 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 ( 4984) covalent geometry : angle 0.82130 / 0.42 ( 6782) SS BOND : bond 0.00691 / 0.35 ( 9) SS BOND : angle 1.84933 / 0.88 ( 18) hydrogen bonds : bond 0.28352 / 18.83 ( 68) hydrogen bonds : angle 12.41165 / 8.74 ( 171) link_ALPHA1-3 : bond 0.00684 / 0.36 ( 1) link_ALPHA1-3 : angle 1.08998 / 0.52 ( 3) link_ALPHA1-6 : bond 0.00424 / 0.22 ( 1) link_ALPHA1-6 : angle 1.56509 / 0.71 ( 3) link_BETA1-4 : bond 0.00838 / 0.44 ( 2) link_BETA1-4 : angle 2.22433 / 1.19 ( 6) link_NAG-ASN : bond 0.00775 / 0.41 ( 1) link_NAG-ASN : angle 7.33545 / 3.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8718 (mp) cc_final: 0.8491 (mm) REVERT: H 72 ASP cc_start: 0.7392 (t0) cc_final: 0.6045 (t0) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0914 time to fit residues: 10.0933 Evaluate side-chains 69 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.094682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.086127 restraints weight = 23028.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.088014 restraints weight = 14212.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.089266 restraints weight = 9687.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.090159 restraints weight = 7109.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.090792 restraints weight = 5492.944| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3999 r_free = 0.3999 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3999 r_free = 0.3999 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4998 Z= 0.149 Angle : 0.787 11.317 6815 Z= 0.393 Chirality : 0.049 0.163 763 Planarity : 0.005 0.050 867 Dihedral : 5.869 21.334 678 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.26 % Favored : 84.58 % Rotamer: Outliers : 1.12 % Allowed : 11.78 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.22 (0.30), residues: 616 helix: -4.16 (0.49), residues: 26 sheet: -2.29 (0.39), residues: 168 loop : -3.13 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 71 TYR 0.015 0.002 TYR H 96 PHE 0.024 0.002 PHE H 27 TRP 0.021 0.002 TRP L 35 HIS 0.004 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 4984) covalent geometry : angle 0.76380 / 0.39 ( 6782) SS BOND : bond 0.00601 / 0.30 ( 9) SS BOND : angle 1.58993 / 0.81 ( 18) hydrogen bonds : bond 0.04962 / 3.41 ( 68) hydrogen bonds : angle 8.70943 / 6.19 ( 171) link_ALPHA1-3 : bond 0.00858 / 0.45 ( 1) link_ALPHA1-3 : angle 1.58654 / 0.78 ( 3) link_ALPHA1-6 : bond 0.00292 / 0.15 ( 1) link_ALPHA1-6 : angle 1.47746 / 0.66 ( 3) link_BETA1-4 : bond 0.00900 / 0.46 ( 2) link_BETA1-4 : angle 2.45464 / 1.36 ( 6) link_NAG-ASN : bond 0.00590 / 0.31 ( 1) link_NAG-ASN : angle 7.50753 / 3.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.185 Fit side-chains REVERT: A 402 ILE cc_start: 0.8801 (mp) cc_final: 0.8555 (mm) REVERT: H 72 ASP cc_start: 0.8157 (t0) cc_final: 0.7674 (t0) outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.0743 time to fit residues: 7.5871 Evaluate side-chains 75 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 37 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 = 0.4061 r_free = 0.4061 target = 0.093741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.085381 restraints weight = 23079.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.087193 restraints weight = 14312.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.088429 restraints weight = 9782.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.089259 restraints weight = 7171.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.089868 restraints weight = 5587.974| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3983 r_free = 0.3983 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4998 Z= 0.159 Angle : 0.773 11.644 6815 Z= 0.387 Chirality : 0.048 0.164 763 Planarity : 0.005 0.048 867 Dihedral : 5.825 21.437 678 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 17.21 % Favored : 82.63 % Rotamer: Outliers : 1.31 % Allowed : 16.45 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.38 (0.29), residues: 616 helix: -3.90 (0.56), residues: 26 sheet: -2.38 (0.39), residues: 165 loop : -3.28 (0.26), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 71 TYR 0.012 0.001 TYR A 453 PHE 0.026 0.002 PHE H 27 TRP 0.021 0.002 TRP H 47 HIS 0.004 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 4984) covalent geometry : angle 0.74977 / 0.38 ( 6782) SS BOND : bond 0.00515 / 0.27 ( 9) SS BOND : angle 1.15213 / 0.60 ( 18) hydrogen bonds : bond 0.04191 / 2.84 ( 68) hydrogen bonds : angle 8.00222 / 5.63 ( 171) link_ALPHA1-3 : bond 0.01028 / 0.54 ( 1) link_ALPHA1-3 : angle 1.51397 / 0.75 ( 3) link_ALPHA1-6 : bond 0.00463 / 0.24 ( 1) link_ALPHA1-6 : angle 1.53970 / 0.66 ( 3) link_BETA1-4 : bond 0.00842 / 0.43 ( 2) link_BETA1-4 : angle 2.47362 / 1.34 ( 6) link_NAG-ASN : bond 0.00422 / 0.22 ( 1) link_NAG-ASN : angle 7.87642 / 3.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.190 Fit side-chains REVERT: A 402 ILE cc_start: 0.8860 (mp) cc_final: 0.8585 (mm) REVERT: H 72 ASP cc_start: 0.8223 (t0) cc_final: 0.7934 (t0) outliers start: 7 outliers final: 5 residues processed: 82 average time/residue: 0.0827 time to fit residues: 8.5638 Evaluate side-chains 73 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 37 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 = 0.4056 r_free = 0.4056 target = 0.093367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.085018 restraints weight = 22792.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.086851 restraints weight = 14198.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.088054 restraints weight = 9718.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.088919 restraints weight = 7148.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.089530 restraints weight = 5526.862| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3979 r_free = 0.3979 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3979 r_free = 0.3979 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 4998 Z= 0.164 Angle : 0.785 11.795 6815 Z= 0.392 Chirality : 0.047 0.160 763 Planarity : 0.005 0.048 867 Dihedral : 5.822 21.422 678 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 17.37 % Favored : 82.47 % Rotamer: Outliers : 2.80 % Allowed : 17.76 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.36 (0.29), residues: 616 helix: -3.89 (0.57), residues: 27 sheet: -2.36 (0.39), residues: 163 loop : -3.27 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 457 TYR 0.018 0.002 TYR L 140 PHE 0.030 0.002 PHE H 27 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 4984) covalent geometry : angle 0.76027 / 0.39 ( 6782) SS BOND : bond 0.00612 / 0.29 ( 9) SS BOND : angle 1.59312 / 0.90 ( 18) hydrogen bonds : bond 0.03818 / 2.56 ( 68) hydrogen bonds : angle 7.99239 / 5.62 ( 171) link_ALPHA1-3 : bond 0.00848 / 0.45 ( 1) link_ALPHA1-3 : angle 1.48142 / 0.72 ( 3) link_ALPHA1-6 : bond 0.00406 / 0.21 ( 1) link_ALPHA1-6 : angle 1.49065 / 0.65 ( 3) link_BETA1-4 : bond 0.00851 / 0.43 ( 2) link_BETA1-4 : angle 2.44617 / 1.32 ( 6) link_NAG-ASN : bond 0.00553 / 0.29 ( 1) link_NAG-ASN : angle 7.89907 / 3.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.182 Fit side-chains REVERT: A 402 ILE cc_start: 0.8886 (mp) cc_final: 0.8612 (mm) REVERT: H 72 ASP cc_start: 0.8114 (t0) cc_final: 0.7825 (t0) REVERT: H 144 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8048 (t0) outliers start: 15 outliers final: 9 residues processed: 90 average time/residue: 0.0726 time to fit residues: 8.4573 Evaluate side-chains 82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 0.0010 chunk 8 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 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 = 0.4038 r_free = 0.4038 target = 0.093430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.084123 restraints weight = 22401.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.086230 restraints weight = 13247.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.087670 restraints weight = 8729.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.088699 restraints weight = 6194.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.089360 restraints weight = 4662.000| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3970 r_free = 0.3970 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3970 r_free = 0.3970 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4998 Z= 0.157 Angle : 0.774 11.654 6815 Z= 0.390 Chirality : 0.049 0.261 763 Planarity : 0.005 0.049 867 Dihedral : 5.746 20.841 678 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.88 % Favored : 82.95 % Rotamer: Outliers : 3.18 % Allowed : 19.63 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.33 (0.30), residues: 616 helix: -3.66 (0.62), residues: 27 sheet: -2.33 (0.40), residues: 163 loop : -3.28 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 71 TYR 0.017 0.002 TYR L 140 PHE 0.031 0.002 PHE H 27 TRP 0.023 0.002 TRP H 47 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 4984) covalent geometry : angle 0.74953 / 0.38 ( 6782) SS BOND : bond 0.00474 / 0.24 ( 9) SS BOND : angle 1.47969 / 0.82 ( 18) hydrogen bonds : bond 0.03591 / 2.41 ( 68) hydrogen bonds : angle 7.64236 / 5.40 ( 171) link_ALPHA1-3 : bond 0.00811 / 0.43 ( 1) link_ALPHA1-3 : angle 1.45768 / 0.71 ( 3) link_ALPHA1-6 : bond 0.00389 / 0.20 ( 1) link_ALPHA1-6 : angle 1.47639 / 0.65 ( 3) link_BETA1-4 : bond 0.00838 / 0.43 ( 2) link_BETA1-4 : angle 2.41972 / 1.31 ( 6) link_NAG-ASN : bond 0.00557 / 0.29 ( 1) link_NAG-ASN : angle 7.85681 / 3.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8892 (mp) cc_final: 0.8630 (mm) REVERT: H 72 ASP cc_start: 0.8077 (t0) cc_final: 0.7776 (t0) REVERT: H 100 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6828 (t80) REVERT: H 117 LYS cc_start: 0.7402 (pptt) cc_final: 0.6201 (pptt) REVERT: H 144 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7366 (t0) outliers start: 17 outliers final: 9 residues processed: 91 average time/residue: 0.0818 time to fit residues: 9.5186 Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 0.0010 chunk 20 optimal weight: 0.0060 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 58 ASN ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.093966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.085622 restraints weight = 23393.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.087447 restraints weight = 14397.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.088717 restraints weight = 9818.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.089593 restraints weight = 7166.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.090200 restraints weight = 5527.480| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3992 r_free = 0.3992 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3992 r_free = 0.3992 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4998 Z= 0.133 Angle : 0.764 11.323 6815 Z= 0.385 Chirality : 0.047 0.187 763 Planarity : 0.005 0.048 867 Dihedral : 5.637 20.320 678 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.58 % Favored : 84.25 % Rotamer: Outliers : 3.18 % Allowed : 20.37 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.29 (0.30), residues: 616 helix: -3.60 (0.64), residues: 27 sheet: -2.37 (0.39), residues: 164 loop : -3.21 (0.26), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 71 TYR 0.016 0.001 TYR L 140 PHE 0.034 0.002 PHE H 27 TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 4984) covalent geometry : angle 0.74149 / 0.38 ( 6782) SS BOND : bond 0.00433 / 0.22 ( 9) SS BOND : angle 1.26564 / 0.68 ( 18) hydrogen bonds : bond 0.03391 / 2.28 ( 68) hydrogen bonds : angle 7.39505 / 5.21 ( 171) link_ALPHA1-3 : bond 0.00870 / 0.46 ( 1) link_ALPHA1-3 : angle 1.35135 / 0.66 ( 3) link_ALPHA1-6 : bond 0.00411 / 0.22 ( 1) link_ALPHA1-6 : angle 1.40770 / 0.64 ( 3) link_BETA1-4 : bond 0.00881 / 0.45 ( 2) link_BETA1-4 : angle 2.29441 / 1.25 ( 6) link_NAG-ASN : bond 0.00405 / 0.21 ( 1) link_NAG-ASN : angle 7.78584 / 3.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8891 (mp) cc_final: 0.8619 (mm) REVERT: H 72 ASP cc_start: 0.8056 (t0) cc_final: 0.7759 (t0) REVERT: H 117 LYS cc_start: 0.7332 (pptt) cc_final: 0.6146 (pptt) REVERT: H 144 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7476 (t0) outliers start: 17 outliers final: 8 residues processed: 86 average time/residue: 0.0769 time to fit residues: 8.3442 Evaluate side-chains 80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 49 optimal weight: 0.0870 chunk 7 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 HIS ** 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 = 0.4080 r_free = 0.4080 target = 0.094491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.086193 restraints weight = 23195.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.088044 restraints weight = 14296.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.089288 restraints weight = 9737.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.090160 restraints weight = 7117.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.090785 restraints weight = 5484.319| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4006 r_free = 0.4006 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4006 r_free = 0.4006 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4998 Z= 0.126 Angle : 0.769 11.278 6815 Z= 0.379 Chirality : 0.047 0.165 763 Planarity : 0.005 0.048 867 Dihedral : 5.471 19.821 678 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.94 % Favored : 84.90 % Rotamer: Outliers : 2.43 % Allowed : 21.31 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.21 (0.30), residues: 616 helix: -3.46 (0.68), residues: 27 sheet: -2.32 (0.40), residues: 164 loop : -3.16 (0.26), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 18 TYR 0.019 0.001 TYR H 96 PHE 0.036 0.002 PHE H 27 TRP 0.029 0.002 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 4984) covalent geometry : angle 0.74709 / 0.37 ( 6782) SS BOND : bond 0.00408 / 0.20 ( 9) SS BOND : angle 1.30114 / 0.68 ( 18) hydrogen bonds : bond 0.03489 / 2.35 ( 68) hydrogen bonds : angle 7.07183 / 4.98 ( 171) link_ALPHA1-3 : bond 0.00887 / 0.47 ( 1) link_ALPHA1-3 : angle 1.33682 / 0.65 ( 3) link_ALPHA1-6 : bond 0.00417 / 0.22 ( 1) link_ALPHA1-6 : angle 1.44769 / 0.65 ( 3) link_BETA1-4 : bond 0.00827 / 0.42 ( 2) link_BETA1-4 : angle 2.14487 / 1.16 ( 6) link_NAG-ASN : bond 0.00634 / 0.33 ( 1) link_NAG-ASN : angle 7.55338 / 3.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8864 (mp) cc_final: 0.8596 (mm) REVERT: A 524 VAL cc_start: 0.6273 (OUTLIER) cc_final: 0.6069 (m) REVERT: H 72 ASP cc_start: 0.8144 (t0) cc_final: 0.7859 (t0) REVERT: H 117 LYS cc_start: 0.7191 (pptt) cc_final: 0.6014 (pptt) REVERT: H 144 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7473 (t0) outliers start: 13 outliers final: 8 residues processed: 89 average time/residue: 0.0647 time to fit residues: 7.4060 Evaluate side-chains 83 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 49 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 37 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 = 0.4052 r_free = 0.4052 target = 0.093341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.084952 restraints weight = 23271.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.086806 restraints weight = 14355.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.088062 restraints weight = 9812.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.088946 restraints weight = 7187.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.089580 restraints weight = 5548.828| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4998 Z= 0.157 Angle : 0.778 10.964 6815 Z= 0.389 Chirality : 0.047 0.146 763 Planarity : 0.005 0.047 867 Dihedral : 5.598 20.530 678 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 17.37 % Favored : 82.47 % Rotamer: Outliers : 2.24 % Allowed : 22.62 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.20 (0.30), residues: 616 helix: -3.35 (0.72), residues: 26 sheet: -2.30 (0.40), residues: 164 loop : -3.18 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 71 TYR 0.019 0.001 TYR L 140 PHE 0.034 0.002 PHE H 27 TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 4984) covalent geometry : angle 0.75574 / 0.38 ( 6782) SS BOND : bond 0.00469 / 0.25 ( 9) SS BOND : angle 1.53334 / 0.79 ( 18) hydrogen bonds : bond 0.03508 / 2.33 ( 68) hydrogen bonds : angle 7.02876 / 4.95 ( 171) link_ALPHA1-3 : bond 0.00643 / 0.34 ( 1) link_ALPHA1-3 : angle 1.43096 / 0.69 ( 3) link_ALPHA1-6 : bond 0.00211 / 0.11 ( 1) link_ALPHA1-6 : angle 1.40279 / 0.59 ( 3) link_BETA1-4 : bond 0.00701 / 0.36 ( 2) link_BETA1-4 : angle 2.21452 / 1.19 ( 6) link_NAG-ASN : bond 0.00475 / 0.25 ( 1) link_NAG-ASN : angle 7.41899 / 3.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8906 (mp) cc_final: 0.8625 (mm) REVERT: A 524 VAL cc_start: 0.6291 (OUTLIER) cc_final: 0.6067 (m) REVERT: H 72 ASP cc_start: 0.8118 (t0) cc_final: 0.7815 (t0) REVERT: H 117 LYS cc_start: 0.7363 (pptt) cc_final: 0.6116 (pptt) REVERT: H 144 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7433 (t0) outliers start: 12 outliers final: 8 residues processed: 78 average time/residue: 0.0739 time to fit residues: 7.4056 Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 0.0030 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.0570 chunk 20 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 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 = 0.4075 r_free = 0.4075 target = 0.094325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.085991 restraints weight = 22929.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.087839 restraints weight = 14198.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.089053 restraints weight = 9706.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.089938 restraints weight = 7135.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.090533 restraints weight = 5525.225| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4000 r_free = 0.4000 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4000 r_free = 0.4000 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4998 Z= 0.129 Angle : 0.765 10.967 6815 Z= 0.381 Chirality : 0.049 0.379 763 Planarity : 0.005 0.049 867 Dihedral : 5.450 20.241 678 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.80 % Favored : 86.04 % Rotamer: Outliers : 2.06 % Allowed : 23.18 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.13 (0.30), residues: 616 helix: -3.34 (0.71), residues: 27 sheet: -2.35 (0.40), residues: 167 loop : -3.06 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 71 TYR 0.016 0.001 TYR L 140 PHE 0.036 0.002 PHE H 27 TRP 0.017 0.001 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 4984) covalent geometry : angle 0.74531 / 0.38 ( 6782) SS BOND : bond 0.00377 / 0.18 ( 9) SS BOND : angle 1.08944 / 0.56 ( 18) hydrogen bonds : bond 0.03316 / 2.24 ( 68) hydrogen bonds : angle 6.84580 / 4.81 ( 171) link_ALPHA1-3 : bond 0.00730 / 0.38 ( 1) link_ALPHA1-3 : angle 1.31452 / 0.64 ( 3) link_ALPHA1-6 : bond 0.00446 / 0.23 ( 1) link_ALPHA1-6 : angle 1.42820 / 0.66 ( 3) link_BETA1-4 : bond 0.00811 / 0.41 ( 2) link_BETA1-4 : angle 2.12020 / 1.15 ( 6) link_NAG-ASN : bond 0.00587 / 0.31 ( 1) link_NAG-ASN : angle 7.32962 / 3.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8878 (mp) cc_final: 0.8606 (mm) REVERT: A 524 VAL cc_start: 0.6227 (OUTLIER) cc_final: 0.5997 (m) REVERT: H 72 ASP cc_start: 0.8139 (t0) cc_final: 0.7843 (t0) REVERT: H 105 GLN cc_start: 0.7634 (pm20) cc_final: 0.7387 (pm20) outliers start: 11 outliers final: 8 residues processed: 82 average time/residue: 0.0603 time to fit residues: 6.3218 Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 3 optimal weight: 0.0270 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 0.0030 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 chunk 48 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.2848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 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 = 0.4095 r_free = 0.4095 target = 0.095333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.087043 restraints weight = 23189.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.088866 restraints weight = 14330.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.090112 restraints weight = 9808.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.090995 restraints weight = 7176.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.091595 restraints weight = 5530.564| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4022 r_free = 0.4022 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4022 r_free = 0.4022 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4998 Z= 0.125 Angle : 0.764 10.446 6815 Z= 0.379 Chirality : 0.047 0.246 763 Planarity : 0.005 0.046 867 Dihedral : 5.262 19.355 678 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.61 % Favored : 85.23 % Rotamer: Outliers : 1.68 % Allowed : 24.11 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.09 (0.31), residues: 616 helix: -3.54 (0.66), residues: 27 sheet: -2.32 (0.38), residues: 178 loop : -3.02 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 71 TYR 0.018 0.001 TYR H 96 PHE 0.033 0.002 PHE H 27 TRP 0.043 0.002 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 4984) covalent geometry : angle 0.74613 / 0.37 ( 6782) SS BOND : bond 0.00320 / 0.16 ( 9) SS BOND : angle 1.18267 / 0.62 ( 18) hydrogen bonds : bond 0.03290 / 2.30 ( 68) hydrogen bonds : angle 6.65310 / 4.67 ( 171) link_ALPHA1-3 : bond 0.00733 / 0.39 ( 1) link_ALPHA1-3 : angle 1.25468 / 0.62 ( 3) link_ALPHA1-6 : bond 0.00383 / 0.20 ( 1) link_ALPHA1-6 : angle 1.40260 / 0.64 ( 3) link_BETA1-4 : bond 0.00800 / 0.41 ( 2) link_BETA1-4 : angle 1.95180 / 1.05 ( 6) link_NAG-ASN : bond 0.00560 / 0.29 ( 1) link_NAG-ASN : angle 6.96204 / 3.33 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8847 (mp) cc_final: 0.8564 (mm) REVERT: A 524 VAL cc_start: 0.6241 (OUTLIER) cc_final: 0.6003 (m) REVERT: H 72 ASP cc_start: 0.8186 (t0) cc_final: 0.7898 (t0) REVERT: H 144 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7820 (t0) REVERT: L 117 ILE cc_start: 0.6965 (tt) cc_final: 0.6584 (tt) outliers start: 9 outliers final: 7 residues processed: 88 average time/residue: 0.0768 time to fit residues: 8.5018 Evaluate side-chains 85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 0.0870 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 0.0000 chunk 57 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 37 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 = 0.4075 r_free = 0.4075 target = 0.094355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.086016 restraints weight = 23092.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.087823 restraints weight = 14331.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.089044 restraints weight = 9859.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.089902 restraints weight = 7246.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.090536 restraints weight = 5618.465| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4000 r_free = 0.4000 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4000 r_free = 0.4000 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4998 Z= 0.141 Angle : 0.790 10.595 6815 Z= 0.395 Chirality : 0.048 0.224 763 Planarity : 0.005 0.049 867 Dihedral : 5.256 19.520 678 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.45 % Favored : 85.39 % Rotamer: Outliers : 2.06 % Allowed : 24.49 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -4.10 (0.31), residues: 616 helix: -3.48 (0.67), residues: 27 sheet: -2.34 (0.38), residues: 171 loop : -3.02 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 71 TYR 0.011 0.001 TYR A 453 PHE 0.033 0.002 PHE H 27 TRP 0.032 0.002 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 4984) covalent geometry : angle 0.77332 / 0.39 ( 6782) SS BOND : bond 0.00424 / 0.22 ( 9) SS BOND : angle 1.06767 / 0.56 ( 18) hydrogen bonds : bond 0.03283 / 2.27 ( 68) hydrogen bonds : angle 6.57499 / 4.63 ( 171) link_ALPHA1-3 : bond 0.00642 / 0.34 ( 1) link_ALPHA1-3 : angle 1.34867 / 0.65 ( 3) link_ALPHA1-6 : bond 0.00395 / 0.21 ( 1) link_ALPHA1-6 : angle 1.47203 / 0.65 ( 3) link_BETA1-4 : bond 0.00708 / 0.36 ( 2) link_BETA1-4 : angle 1.97244 / 1.06 ( 6) link_NAG-ASN : bond 0.00592 / 0.31 ( 1) link_NAG-ASN : angle 6.99664 / 3.36 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1205.96 seconds wall clock time: 21 minutes 39.39 seconds (1299.39 seconds total)