Starting phenix.real_space_refine on Tue Mar 3 13:22:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lrs_23498/03_2026/7lrs_23498.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lrs_23498/03_2026/7lrs_23498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lrs_23498/03_2026/7lrs_23498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lrs_23498/03_2026/7lrs_23498.map" model { file = "/net/cci-nas-00/data/ceres_data/7lrs_23498/03_2026/7lrs_23498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lrs_23498/03_2026/7lrs_23498.cif" } resolution = 3.89 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 3100 2.51 5 N 812 2.21 5 O 978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4912 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" 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: "D" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1625 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1636 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "A" 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.14, per 1000 atoms: 0.23 Number of scatterers: 4912 At special positions: 0 Unit cell: (79.515, 66.69, 140.22, 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 978 8.00 N 812 7.00 C 3100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 100B" distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " 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 ALPHA1-3 " BMA A 3 " - " MAN A 4 " ALPHA1-6 " BMA A 3 " - " MAN A 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 1 " - " ASN C 343 " " NAG B 1 " - " ASN D 96 " Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 294.2 milliseconds 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 16 sheets defined 3.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 4.186A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.795A pdb=" N THR D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 202 removed outlier: 3.664A pdb=" N LEU E 201 " --> pdb=" O HIS E 198 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER E 202 " --> pdb=" O GLN E 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 202' Processing sheet with id=AA1, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.768A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.749A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 5 " --> pdb=" O LYS D 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.736A pdb=" N THR D 110 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS D 12 " --> pdb=" O THR D 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 33 through 36 removed outlier: 3.786A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AA7, first strand: chain 'D' and resid 93 through 94 removed outlier: 3.505A pdb=" N ILE D 102 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 97 through 98 removed outlier: 3.631A pdb=" N VAL D 100A" --> pdb=" O SER D 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.515A pdb=" N GLY D 139 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 180 " --> pdb=" O CYS D 140 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.515A pdb=" N GLY D 139 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 180 " --> pdb=" O CYS D 140 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 151 through 152 removed outlier: 4.133A pdb=" N THR D 151 " --> pdb=" O ASN D 199 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN D 199 " --> pdb=" O THR D 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'E' and resid 20 through 22 Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 49 removed outlier: 6.681A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 85 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.594A pdb=" N PHE E 116 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL E 133 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL E 132 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 145 through 148 removed outlier: 4.106A pdb=" N LYS E 145 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR E 197 " --> pdb=" O LYS E 145 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 225 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: 0.61 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1550 1.34 - 1.46: 1294 1.46 - 1.58: 2160 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 5030 Sorted by residual: bond pdb=" C1 MAN A 4 " pdb=" C2 MAN A 4 " ideal model delta sigma weight residual 1.526 1.580 -0.054 2.00e-02 2.50e+03 7.27e+00 bond pdb=" C1 MAN A 5 " pdb=" C2 MAN A 5 " ideal model delta sigma weight residual 1.526 1.567 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C1 MAN A 4 " pdb=" O5 MAN A 4 " ideal model delta sigma weight residual 1.399 1.437 -0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" C5 MAN A 5 " pdb=" O5 MAN A 5 " ideal model delta sigma weight residual 1.418 1.455 -0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.40e+00 ... (remaining 5025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 6592 1.66 - 3.31: 200 3.31 - 4.97: 43 4.97 - 6.63: 10 6.63 - 8.28: 2 Bond angle restraints: 6847 Sorted by residual: angle pdb=" CA GLY C 502 " pdb=" C GLY C 502 " pdb=" N VAL C 503 " ideal model delta sigma weight residual 114.23 116.84 -2.61 8.80e-01 1.29e+00 8.77e+00 angle pdb=" C PHE C 486 " pdb=" N ASN C 487 " pdb=" CA ASN C 487 " ideal model delta sigma weight residual 122.08 126.25 -4.17 1.47e+00 4.63e-01 8.06e+00 angle pdb=" C THR E 109 " pdb=" N VAL E 110 " pdb=" CA VAL E 110 " ideal model delta sigma weight residual 121.97 126.69 -4.72 1.80e+00 3.09e-01 6.87e+00 angle pdb=" N LYS D 201 " pdb=" CA LYS D 201 " pdb=" C LYS D 201 " ideal model delta sigma weight residual 109.81 115.60 -5.79 2.21e+00 2.05e-01 6.87e+00 angle pdb=" CA ASP E 185 " pdb=" C ASP E 185 " pdb=" N TYR E 186 " ideal model delta sigma weight residual 119.71 116.70 3.01 1.17e+00 7.31e-01 6.64e+00 ... (remaining 6842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.68: 2866 22.68 - 45.36: 190 45.36 - 68.03: 15 68.03 - 90.71: 23 90.71 - 113.39: 10 Dihedral angle restraints: 3104 sinusoidal: 1291 harmonic: 1813 Sorted by residual: 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 93.00 163.08 -70.08 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 143.13 -50.13 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -133.21 47.21 1 1.00e+01 1.00e-02 3.08e+01 ... (remaining 3101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 638 0.055 - 0.110: 121 0.110 - 0.165: 22 0.165 - 0.220: 2 0.220 - 0.276: 3 Chirality restraints: 786 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 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 783 not shown) Planarity restraints: 871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 146 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO D 147 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 147 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 147 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 79 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.10e+00 pdb=" N PRO E 80 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 80 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 80 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO C 521 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.020 5.00e-02 4.00e+02 ... (remaining 868 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 297 2.72 - 3.27: 4858 3.27 - 3.81: 7198 3.81 - 4.36: 8340 4.36 - 4.90: 14373 Nonbonded interactions: 35066 Sorted by model distance: nonbonded pdb=" OD2 ASP E 82 " pdb=" OH TYR E 86 " model vdw 2.181 3.040 nonbonded pdb=" O SER E 171 " pdb=" OG SER E 171 " model vdw 2.240 3.040 nonbonded pdb=" OG SER E 182 " pdb=" NZ LYS E 188 " model vdw 2.245 3.120 nonbonded pdb=" O4 MAN A 5 " pdb=" O6 MAN A 5 " model vdw 2.266 3.040 nonbonded pdb=" OE2 GLU E 105 " pdb=" NE2 GLN E 166 " model vdw 2.302 3.120 ... (remaining 35061 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: 12.570 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: 0.120 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 6.180 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 : 0.003 0.054 5047 Z= 0.168 Angle : 0.728 8.282 6889 Z= 0.353 Chirality : 0.048 0.276 786 Planarity : 0.005 0.043 869 Dihedral : 16.973 113.391 1917 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.70 % Favored : 88.65 % Rotamer: Outliers : 0.19 % Allowed : 0.37 % Favored : 99.44 % 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: -2.85 (0.33), residues: 617 helix: -4.54 (0.94), residues: 13 sheet: -1.37 (0.38), residues: 207 loop : -2.18 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 44 TYR 0.011 0.001 TYR D 145 PHE 0.013 0.001 PHE E 118 TRP 0.020 0.001 TRP C 353 HIS 0.003 0.001 HIS D 200 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 5030) covalent geometry : angle 0.71932 ( 6847) SS BOND : bond 0.00288 ( 9) SS BOND : angle 1.46575 ( 18) hydrogen bonds : bond 0.29489 ( 75) hydrogen bonds : angle 10.62608 ( 225) link_ALPHA1-3 : bond 0.00729 ( 1) link_ALPHA1-3 : angle 1.09259 ( 3) link_ALPHA1-6 : bond 0.00969 ( 1) link_ALPHA1-6 : angle 1.52289 ( 3) link_BETA1-4 : bond 0.00370 ( 4) link_BETA1-4 : angle 2.05235 ( 12) link_NAG-ASN : bond 0.00285 ( 2) link_NAG-ASN : angle 0.99703 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.134 Fit side-chains REVERT: D 82 LEU cc_start: 0.8695 (mt) cc_final: 0.8348 (mm) REVERT: D 90 TYR cc_start: 0.8121 (m-10) cc_final: 0.7531 (m-80) REVERT: D 155 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8180 (t0) REVERT: D 201 LYS cc_start: 0.8906 (pptt) cc_final: 0.8631 (pptt) REVERT: E 82 ASP cc_start: 0.8046 (t70) cc_final: 0.7828 (t0) REVERT: E 123 GLU cc_start: 0.8605 (tp30) cc_final: 0.8373 (tp30) outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 0.0747 time to fit residues: 9.7542 Evaluate side-chains 82 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 155 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.0010 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.0030 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN D 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.067406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.058394 restraints weight = 19664.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.060226 restraints weight = 10690.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.061499 restraints weight = 6665.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062300 restraints weight = 4570.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062888 restraints weight = 3418.860| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5047 Z= 0.146 Angle : 0.740 10.151 6889 Z= 0.357 Chirality : 0.046 0.165 786 Planarity : 0.005 0.044 869 Dihedral : 13.565 90.828 839 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.21 % Favored : 89.14 % Rotamer: Outliers : 0.93 % Allowed : 10.58 % Favored : 88.50 % 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: -2.76 (0.32), residues: 617 helix: -4.08 (1.11), residues: 13 sheet: -0.90 (0.40), residues: 189 loop : -2.36 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 41 TYR 0.021 0.001 TYR C 380 PHE 0.015 0.001 PHE E 118 TRP 0.012 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5030) covalent geometry : angle 0.72726 ( 6847) SS BOND : bond 0.00400 ( 9) SS BOND : angle 1.49666 ( 18) hydrogen bonds : bond 0.04863 ( 75) hydrogen bonds : angle 7.65169 ( 225) link_ALPHA1-3 : bond 0.01390 ( 1) link_ALPHA1-3 : angle 2.42628 ( 3) link_ALPHA1-6 : bond 0.01476 ( 1) link_ALPHA1-6 : angle 2.13509 ( 3) link_BETA1-4 : bond 0.00510 ( 4) link_BETA1-4 : angle 2.54065 ( 12) link_NAG-ASN : bond 0.00340 ( 2) link_NAG-ASN : angle 0.97002 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: C 389 ASP cc_start: 0.8419 (p0) cc_final: 0.8125 (p0) REVERT: D 155 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8312 (t0) REVERT: D 176 TYR cc_start: 0.7977 (m-10) cc_final: 0.7701 (m-10) REVERT: D 194 TYR cc_start: 0.3533 (m-80) cc_final: 0.3292 (m-10) REVERT: E 123 GLU cc_start: 0.8711 (tp30) cc_final: 0.8414 (tp30) REVERT: E 167 ASP cc_start: 0.8254 (t70) cc_final: 0.8051 (m-30) outliers start: 5 outliers final: 2 residues processed: 91 average time/residue: 0.0702 time to fit residues: 8.2871 Evaluate side-chains 84 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 198 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.065456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.056310 restraints weight = 19524.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.058191 restraints weight = 10445.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.059452 restraints weight = 6464.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.060247 restraints weight = 4437.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060837 restraints weight = 3322.853| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5047 Z= 0.159 Angle : 0.718 11.033 6889 Z= 0.344 Chirality : 0.046 0.155 786 Planarity : 0.005 0.045 869 Dihedral : 11.840 82.333 839 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.70 % Favored : 88.49 % Rotamer: Outliers : 1.67 % Allowed : 13.36 % Favored : 84.97 % 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: -2.68 (0.33), residues: 617 helix: -2.04 (2.23), residues: 7 sheet: -0.93 (0.39), residues: 189 loop : -2.34 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 41 TYR 0.025 0.001 TYR C 380 PHE 0.012 0.001 PHE D 146 TRP 0.015 0.001 TRP C 436 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 5030) covalent geometry : angle 0.70463 ( 6847) SS BOND : bond 0.00367 ( 9) SS BOND : angle 1.36141 ( 18) hydrogen bonds : bond 0.03402 ( 75) hydrogen bonds : angle 6.76587 ( 225) link_ALPHA1-3 : bond 0.01418 ( 1) link_ALPHA1-3 : angle 1.93047 ( 3) link_ALPHA1-6 : bond 0.02026 ( 1) link_ALPHA1-6 : angle 2.38349 ( 3) link_BETA1-4 : bond 0.00498 ( 4) link_BETA1-4 : angle 2.58277 ( 12) link_NAG-ASN : bond 0.00357 ( 2) link_NAG-ASN : angle 1.15791 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: D 155 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8301 (t0) REVERT: D 176 TYR cc_start: 0.8039 (m-10) cc_final: 0.7664 (m-10) REVERT: E 82 ASP cc_start: 0.8873 (t0) cc_final: 0.8635 (t0) REVERT: E 123 GLU cc_start: 0.8711 (tp30) cc_final: 0.8470 (tp30) REVERT: E 167 ASP cc_start: 0.8239 (t70) cc_final: 0.7982 (m-30) outliers start: 9 outliers final: 4 residues processed: 89 average time/residue: 0.0665 time to fit residues: 7.7751 Evaluate side-chains 85 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.0670 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.064734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.055619 restraints weight = 19513.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.057503 restraints weight = 10486.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.058758 restraints weight = 6496.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.059598 restraints weight = 4443.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.060151 restraints weight = 3286.679| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5047 Z= 0.161 Angle : 0.711 11.579 6889 Z= 0.343 Chirality : 0.046 0.145 786 Planarity : 0.005 0.046 869 Dihedral : 10.694 76.363 839 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.37 % Favored : 88.82 % Rotamer: Outliers : 2.23 % Allowed : 15.58 % Favored : 82.19 % 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: -2.67 (0.33), residues: 617 helix: -1.87 (2.27), residues: 7 sheet: -0.92 (0.40), residues: 189 loop : -2.34 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 454 TYR 0.026 0.001 TYR C 380 PHE 0.007 0.001 PHE C 392 TRP 0.015 0.001 TRP C 436 HIS 0.005 0.002 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5030) covalent geometry : angle 0.69817 ( 6847) SS BOND : bond 0.00526 ( 9) SS BOND : angle 1.25948 ( 18) hydrogen bonds : bond 0.03013 ( 75) hydrogen bonds : angle 6.42851 ( 225) link_ALPHA1-3 : bond 0.01562 ( 1) link_ALPHA1-3 : angle 2.12160 ( 3) link_ALPHA1-6 : bond 0.01875 ( 1) link_ALPHA1-6 : angle 2.44720 ( 3) link_BETA1-4 : bond 0.00455 ( 4) link_BETA1-4 : angle 2.54779 ( 12) link_NAG-ASN : bond 0.00317 ( 2) link_NAG-ASN : angle 1.20518 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: D 155 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8294 (t0) REVERT: D 176 TYR cc_start: 0.8087 (m-10) cc_final: 0.7679 (m-10) REVERT: E 82 ASP cc_start: 0.8882 (t0) cc_final: 0.8531 (t0) REVERT: E 123 GLU cc_start: 0.8702 (tp30) cc_final: 0.8445 (tp30) REVERT: E 167 ASP cc_start: 0.8305 (t70) cc_final: 0.8009 (m-30) REVERT: E 186 TYR cc_start: 0.7607 (t80) cc_final: 0.7364 (t80) outliers start: 12 outliers final: 8 residues processed: 88 average time/residue: 0.0691 time to fit residues: 7.9457 Evaluate side-chains 88 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.0060 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.063363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.054373 restraints weight = 19845.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.056236 restraints weight = 10566.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.057481 restraints weight = 6518.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.058295 restraints weight = 4444.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.058874 restraints weight = 3294.444| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5047 Z= 0.196 Angle : 0.739 12.417 6889 Z= 0.357 Chirality : 0.046 0.153 786 Planarity : 0.005 0.047 869 Dihedral : 10.297 74.151 839 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.97 % Allowed : 11.67 % Favored : 87.36 % Rotamer: Outliers : 2.23 % Allowed : 16.88 % Favored : 80.89 % 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: -2.72 (0.33), residues: 617 helix: -1.78 (2.31), residues: 7 sheet: -0.97 (0.39), residues: 189 loop : -2.37 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 41 TYR 0.024 0.001 TYR C 380 PHE 0.016 0.001 PHE D 146 TRP 0.015 0.001 TRP C 436 HIS 0.004 0.002 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 5030) covalent geometry : angle 0.72408 ( 6847) SS BOND : bond 0.00403 ( 9) SS BOND : angle 1.60493 ( 18) hydrogen bonds : bond 0.03033 ( 75) hydrogen bonds : angle 6.37577 ( 225) link_ALPHA1-3 : bond 0.01545 ( 1) link_ALPHA1-3 : angle 2.06116 ( 3) link_ALPHA1-6 : bond 0.02310 ( 1) link_ALPHA1-6 : angle 2.55127 ( 3) link_BETA1-4 : bond 0.00467 ( 4) link_BETA1-4 : angle 2.55324 ( 12) link_NAG-ASN : bond 0.00414 ( 2) link_NAG-ASN : angle 1.43299 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 86 ASP cc_start: 0.8203 (t0) cc_final: 0.8002 (t0) REVERT: D 146 PHE cc_start: 0.7696 (t80) cc_final: 0.7489 (t80) REVERT: D 155 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8236 (t0) REVERT: E 82 ASP cc_start: 0.8920 (t0) cc_final: 0.8503 (t0) REVERT: E 123 GLU cc_start: 0.8666 (tp30) cc_final: 0.8443 (tp30) REVERT: E 167 ASP cc_start: 0.8348 (t70) cc_final: 0.8010 (m-30) outliers start: 12 outliers final: 9 residues processed: 88 average time/residue: 0.0779 time to fit residues: 8.7845 Evaluate side-chains 90 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 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 = 0.3255 r_free = 0.3255 target = 0.064032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.054913 restraints weight = 19736.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.056765 restraints weight = 10779.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.057975 restraints weight = 6747.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.058800 restraints weight = 4664.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.059416 restraints weight = 3477.208| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5047 Z= 0.164 Angle : 0.717 12.329 6889 Z= 0.348 Chirality : 0.046 0.167 786 Planarity : 0.005 0.047 869 Dihedral : 9.648 69.394 839 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.97 % Allowed : 10.37 % Favored : 88.65 % Rotamer: Outliers : 2.60 % Allowed : 17.81 % Favored : 79.59 % 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: -2.83 (0.32), residues: 617 helix: -3.49 (1.29), residues: 13 sheet: -1.00 (0.40), residues: 187 loop : -2.40 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 61 TYR 0.017 0.001 TYR D 194 PHE 0.011 0.001 PHE C 392 TRP 0.014 0.001 TRP C 436 HIS 0.005 0.002 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5030) covalent geometry : angle 0.70413 ( 6847) SS BOND : bond 0.00485 ( 9) SS BOND : angle 1.60894 ( 18) hydrogen bonds : bond 0.02832 ( 75) hydrogen bonds : angle 6.45762 ( 225) link_ALPHA1-3 : bond 0.01547 ( 1) link_ALPHA1-3 : angle 1.93566 ( 3) link_ALPHA1-6 : bond 0.02238 ( 1) link_ALPHA1-6 : angle 2.37588 ( 3) link_BETA1-4 : bond 0.00407 ( 4) link_BETA1-4 : angle 2.35708 ( 12) link_NAG-ASN : bond 0.00351 ( 2) link_NAG-ASN : angle 1.27479 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: D 176 TYR cc_start: 0.8126 (m-10) cc_final: 0.7806 (m-10) REVERT: E 82 ASP cc_start: 0.8997 (t0) cc_final: 0.8585 (t0) REVERT: E 123 GLU cc_start: 0.8585 (tp30) cc_final: 0.8375 (tp30) REVERT: E 167 ASP cc_start: 0.8419 (t70) cc_final: 0.8080 (m-30) outliers start: 14 outliers final: 7 residues processed: 88 average time/residue: 0.0740 time to fit residues: 8.3637 Evaluate side-chains 86 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 0.0020 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 519 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.063693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.054678 restraints weight = 19579.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.056513 restraints weight = 10626.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.057720 restraints weight = 6644.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.058544 restraints weight = 4590.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.059136 restraints weight = 3425.674| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5047 Z= 0.166 Angle : 0.743 12.449 6889 Z= 0.361 Chirality : 0.046 0.192 786 Planarity : 0.005 0.049 869 Dihedral : 9.118 66.149 837 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.18 % Favored : 88.01 % Rotamer: Outliers : 2.60 % Allowed : 19.11 % Favored : 78.29 % 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: -2.82 (0.32), residues: 617 helix: -3.48 (1.29), residues: 13 sheet: -1.01 (0.39), residues: 187 loop : -2.38 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 41 TYR 0.020 0.001 TYR C 380 PHE 0.033 0.001 PHE D 146 TRP 0.013 0.001 TRP C 436 HIS 0.005 0.002 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5030) covalent geometry : angle 0.73216 ( 6847) SS BOND : bond 0.00310 ( 9) SS BOND : angle 1.49110 ( 18) hydrogen bonds : bond 0.02820 ( 75) hydrogen bonds : angle 6.41578 ( 225) link_ALPHA1-3 : bond 0.01400 ( 1) link_ALPHA1-3 : angle 1.85328 ( 3) link_ALPHA1-6 : bond 0.02286 ( 1) link_ALPHA1-6 : angle 2.17577 ( 3) link_BETA1-4 : bond 0.00394 ( 4) link_BETA1-4 : angle 2.25767 ( 12) link_NAG-ASN : bond 0.00348 ( 2) link_NAG-ASN : angle 1.25594 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 176 TYR cc_start: 0.8155 (m-10) cc_final: 0.7888 (m-10) REVERT: E 82 ASP cc_start: 0.8936 (t0) cc_final: 0.8550 (t0) REVERT: E 167 ASP cc_start: 0.8325 (t70) cc_final: 0.7926 (m-30) outliers start: 14 outliers final: 11 residues processed: 87 average time/residue: 0.0744 time to fit residues: 8.2478 Evaluate side-chains 90 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.064445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.055386 restraints weight = 19707.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.057248 restraints weight = 10654.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058486 restraints weight = 6617.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.059298 restraints weight = 4540.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.059890 restraints weight = 3397.111| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5047 Z= 0.144 Angle : 0.754 12.292 6889 Z= 0.365 Chirality : 0.045 0.193 786 Planarity : 0.005 0.048 869 Dihedral : 8.727 63.072 837 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.70 % Favored : 88.49 % Rotamer: Outliers : 2.41 % Allowed : 20.22 % Favored : 77.37 % 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: -2.81 (0.32), residues: 617 helix: -3.49 (1.28), residues: 13 sheet: -1.03 (0.39), residues: 187 loop : -2.36 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 142 TYR 0.025 0.001 TYR C 380 PHE 0.010 0.001 PHE E 118 TRP 0.013 0.001 TRP C 436 HIS 0.008 0.002 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5030) covalent geometry : angle 0.74453 ( 6847) SS BOND : bond 0.00318 ( 9) SS BOND : angle 1.36580 ( 18) hydrogen bonds : bond 0.02656 ( 75) hydrogen bonds : angle 6.28970 ( 225) link_ALPHA1-3 : bond 0.01478 ( 1) link_ALPHA1-3 : angle 1.85327 ( 3) link_ALPHA1-6 : bond 0.02272 ( 1) link_ALPHA1-6 : angle 1.99547 ( 3) link_BETA1-4 : bond 0.00394 ( 4) link_BETA1-4 : angle 2.11433 ( 12) link_NAG-ASN : bond 0.00287 ( 2) link_NAG-ASN : angle 1.11405 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.186 Fit side-chains REVERT: C 465 GLU cc_start: 0.8748 (tp30) cc_final: 0.8445 (tp30) REVERT: D 175 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7747 (pp) REVERT: D 176 TYR cc_start: 0.8131 (m-10) cc_final: 0.7832 (m-10) REVERT: E 82 ASP cc_start: 0.8933 (t0) cc_final: 0.8545 (t0) REVERT: E 167 ASP cc_start: 0.8338 (t70) cc_final: 0.7932 (m-30) outliers start: 13 outliers final: 8 residues processed: 88 average time/residue: 0.0708 time to fit residues: 8.0427 Evaluate side-chains 85 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 35 optimal weight: 0.0270 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 519 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.064499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.055477 restraints weight = 19394.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.057322 restraints weight = 10527.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.058551 restraints weight = 6549.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.059398 restraints weight = 4502.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.059948 restraints weight = 3338.611| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5047 Z= 0.149 Angle : 0.759 12.168 6889 Z= 0.371 Chirality : 0.046 0.213 786 Planarity : 0.005 0.055 869 Dihedral : 8.343 60.042 837 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.21 % Favored : 88.98 % Rotamer: Outliers : 2.23 % Allowed : 20.78 % Favored : 76.99 % 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: -2.77 (0.32), residues: 617 helix: -3.49 (1.28), residues: 13 sheet: -1.07 (0.39), residues: 187 loop : -2.30 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 54 TYR 0.024 0.001 TYR C 380 PHE 0.006 0.001 PHE C 392 TRP 0.012 0.001 TRP C 436 HIS 0.005 0.002 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5030) covalent geometry : angle 0.74987 ( 6847) SS BOND : bond 0.00298 ( 9) SS BOND : angle 1.53637 ( 18) hydrogen bonds : bond 0.02709 ( 75) hydrogen bonds : angle 6.24608 ( 225) link_ALPHA1-3 : bond 0.01374 ( 1) link_ALPHA1-3 : angle 1.88437 ( 3) link_ALPHA1-6 : bond 0.02353 ( 1) link_ALPHA1-6 : angle 1.78056 ( 3) link_BETA1-4 : bond 0.00395 ( 4) link_BETA1-4 : angle 1.98017 ( 12) link_NAG-ASN : bond 0.00274 ( 2) link_NAG-ASN : angle 1.05974 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.127 Fit side-chains REVERT: C 388 ASN cc_start: 0.7785 (m-40) cc_final: 0.7472 (m-40) REVERT: C 406 GLU cc_start: 0.8688 (tt0) cc_final: 0.8340 (tp30) REVERT: C 465 GLU cc_start: 0.8748 (tp30) cc_final: 0.8460 (tp30) REVERT: D 175 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7752 (pp) REVERT: D 176 TYR cc_start: 0.8099 (m-10) cc_final: 0.7805 (m-10) REVERT: E 58 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8628 (pt) REVERT: E 82 ASP cc_start: 0.8944 (t0) cc_final: 0.8505 (t0) REVERT: E 167 ASP cc_start: 0.8309 (t70) cc_final: 0.7913 (m-30) outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 0.0809 time to fit residues: 8.6737 Evaluate side-chains 91 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 519 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.063043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.054015 restraints weight = 19583.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.055874 restraints weight = 10453.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.057112 restraints weight = 6442.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.057931 restraints weight = 4387.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.058541 restraints weight = 3263.932| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 5047 Z= 0.215 Angle : 0.800 12.668 6889 Z= 0.388 Chirality : 0.047 0.228 786 Planarity : 0.006 0.065 869 Dihedral : 8.522 60.977 837 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.97 % Allowed : 11.35 % Favored : 87.68 % Rotamer: Outliers : 2.23 % Allowed : 21.15 % Favored : 76.62 % 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: -2.85 (0.33), residues: 617 helix: -3.48 (1.29), residues: 13 sheet: -1.16 (0.39), residues: 192 loop : -2.34 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 142 TYR 0.035 0.002 TYR C 380 PHE 0.021 0.002 PHE E 62 TRP 0.013 0.001 TRP C 436 HIS 0.005 0.002 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 5030) covalent geometry : angle 0.78940 ( 6847) SS BOND : bond 0.00346 ( 9) SS BOND : angle 1.64126 ( 18) hydrogen bonds : bond 0.02881 ( 75) hydrogen bonds : angle 6.24724 ( 225) link_ALPHA1-3 : bond 0.01802 ( 1) link_ALPHA1-3 : angle 2.15159 ( 3) link_ALPHA1-6 : bond 0.02459 ( 1) link_ALPHA1-6 : angle 1.95874 ( 3) link_BETA1-4 : bond 0.00450 ( 4) link_BETA1-4 : angle 2.13930 ( 12) link_NAG-ASN : bond 0.00438 ( 2) link_NAG-ASN : angle 1.40874 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.185 Fit side-chains REVERT: C 388 ASN cc_start: 0.7861 (m-40) cc_final: 0.7543 (m-40) REVERT: C 465 GLU cc_start: 0.8824 (tp30) cc_final: 0.8535 (tp30) REVERT: D 175 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7810 (pp) REVERT: D 176 TYR cc_start: 0.8135 (m-10) cc_final: 0.7747 (m-10) REVERT: E 82 ASP cc_start: 0.9042 (t0) cc_final: 0.8640 (t0) REVERT: E 167 ASP cc_start: 0.8417 (t70) cc_final: 0.8037 (m-30) outliers start: 12 outliers final: 9 residues processed: 85 average time/residue: 0.0711 time to fit residues: 7.6967 Evaluate side-chains 88 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 519 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** 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 = 0.3263 r_free = 0.3263 target = 0.064380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.055461 restraints weight = 19687.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.057264 restraints weight = 10671.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.058482 restraints weight = 6651.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.059306 restraints weight = 4568.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.059829 restraints weight = 3389.526| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5047 Z= 0.147 Angle : 0.762 12.374 6889 Z= 0.373 Chirality : 0.046 0.216 786 Planarity : 0.006 0.078 869 Dihedral : 8.079 59.013 837 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.97 % Allowed : 9.40 % Favored : 89.63 % Rotamer: Outliers : 1.86 % Allowed : 21.89 % Favored : 76.25 % 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: -2.79 (0.33), residues: 617 helix: -3.52 (1.26), residues: 13 sheet: -1.15 (0.39), residues: 187 loop : -2.27 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 41 TYR 0.029 0.001 TYR C 380 PHE 0.008 0.001 PHE E 118 TRP 0.012 0.001 TRP C 436 HIS 0.008 0.002 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5030) covalent geometry : angle 0.75365 ( 6847) SS BOND : bond 0.00273 ( 9) SS BOND : angle 1.43864 ( 18) hydrogen bonds : bond 0.02618 ( 75) hydrogen bonds : angle 6.21202 ( 225) link_ALPHA1-3 : bond 0.01412 ( 1) link_ALPHA1-3 : angle 1.85246 ( 3) link_ALPHA1-6 : bond 0.02273 ( 1) link_ALPHA1-6 : angle 1.57260 ( 3) link_BETA1-4 : bond 0.00401 ( 4) link_BETA1-4 : angle 1.94409 ( 12) link_NAG-ASN : bond 0.00302 ( 2) link_NAG-ASN : angle 1.09735 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1035.80 seconds wall clock time: 18 minutes 35.59 seconds (1115.59 seconds total)