Starting phenix.real_space_refine on Tue Mar 3 12:19:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zyl_15026/03_2026/7zyl_15026_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyl_15026/03_2026/7zyl_15026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zyl_15026/03_2026/7zyl_15026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyl_15026/03_2026/7zyl_15026.map" model { file = "/net/cci-nas-00/data/ceres_data/7zyl_15026/03_2026/7zyl_15026_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyl_15026/03_2026/7zyl_15026_trim.cif" } resolution = 2.08 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= 0.000 sd= 0.005 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 20 5.16 5 C 2504 2.51 5 N 684 2.21 5 O 784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 3992 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'KFL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'KFL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'KFL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'KFL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.06, per 1000 atoms: 0.27 Number of scatterers: 3992 At special positions: 0 Unit cell: (62.55, 72.45, 66.15, 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 20 16.00 O 784 8.00 N 684 7.00 C 2504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 107 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 107 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 107 " 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 41 " " NAG F 1 " - " ASN B 41 " " NAG G 1 " - " ASN C 41 " " NAG H 1 " - " ASN D 41 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 114.9 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 872 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 4 sheets defined 8.9% alpha, 46.3% 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 79 through 83 removed outlier: 3.532A pdb=" N LYS A 82 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 83 " --> pdb=" O ILE A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 83' Processing helix chain 'A' and resid 129 through 135 removed outlier: 4.617A pdb=" N TRP A 134 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.642A pdb=" N LYS B 82 " --> pdb=" O THR B 79 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG B 83 " --> pdb=" O ILE B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'B' and resid 129 through 135 removed outlier: 4.599A pdb=" N TRP B 134 " --> pdb=" O GLY B 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.636A pdb=" N LYS C 82 " --> pdb=" O THR C 79 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG C 83 " --> pdb=" O ILE C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 83' Processing helix chain 'C' and resid 129 through 135 removed outlier: 4.597A pdb=" N TRP C 134 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 135 removed outlier: 4.602A pdb=" N TRP D 134 " --> pdb=" O GLY D 131 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36 removed outlier: 8.018A pdb=" N GLU A 115 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG A 146 " --> pdb=" O GLU A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 32 through 36 removed outlier: 8.026A pdb=" N GLU B 115 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG B 146 " --> pdb=" O GLU B 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 32 through 36 removed outlier: 7.905A pdb=" N GLU C 115 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG C 146 " --> pdb=" O GLU C 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 32 through 36 removed outlier: 8.038A pdb=" N GLU D 115 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG D 146 " --> pdb=" O GLU D 115 " (cutoff:3.500A) 192 hydrogen bonds defined for protein. 492 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: 0.50 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 636 1.30 - 1.43: 1052 1.43 - 1.56: 2340 1.56 - 1.68: 16 1.68 - 1.81: 28 Bond restraints: 4072 Sorted by residual: bond pdb=" C14 KFL B 201 " pdb=" S15 KFL B 201 " ideal model delta sigma weight residual 1.837 1.394 0.443 2.00e-02 2.50e+03 4.91e+02 bond pdb=" C14 KFL C 201 " pdb=" S15 KFL C 201 " ideal model delta sigma weight residual 1.837 1.395 0.442 2.00e-02 2.50e+03 4.89e+02 bond pdb=" C14 KFL A 201 " pdb=" S15 KFL A 201 " ideal model delta sigma weight residual 1.837 1.395 0.442 2.00e-02 2.50e+03 4.89e+02 bond pdb=" C14 KFL D 201 " pdb=" S15 KFL D 201 " ideal model delta sigma weight residual 1.837 1.395 0.442 2.00e-02 2.50e+03 4.89e+02 bond pdb=" N27 KFL B 201 " pdb=" O28 KFL B 201 " ideal model delta sigma weight residual 1.441 1.171 0.270 2.00e-02 2.50e+03 1.82e+02 ... (remaining 4067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 5413 2.77 - 5.54: 79 5.54 - 8.31: 40 8.31 - 11.09: 0 11.09 - 13.86: 4 Bond angle restraints: 5536 Sorted by residual: angle pdb=" C14 KFL C 201 " pdb=" S15 KFL C 201 " pdb=" C16 KFL C 201 " ideal model delta sigma weight residual 89.59 103.45 -13.86 3.00e+00 1.11e-01 2.13e+01 angle pdb=" C14 KFL A 201 " pdb=" S15 KFL A 201 " pdb=" C16 KFL A 201 " ideal model delta sigma weight residual 89.59 103.45 -13.86 3.00e+00 1.11e-01 2.13e+01 angle pdb=" C14 KFL D 201 " pdb=" S15 KFL D 201 " pdb=" C16 KFL D 201 " ideal model delta sigma weight residual 89.59 103.45 -13.86 3.00e+00 1.11e-01 2.13e+01 angle pdb=" C14 KFL B 201 " pdb=" S15 KFL B 201 " pdb=" C16 KFL B 201 " ideal model delta sigma weight residual 89.59 103.43 -13.84 3.00e+00 1.11e-01 2.13e+01 angle pdb=" C23 KFL B 201 " pdb=" C24 KFL B 201 " pdb=" N27 KFL B 201 " ideal model delta sigma weight residual 106.69 114.68 -7.99 3.00e+00 1.11e-01 7.10e+00 ... (remaining 5531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.74: 2460 33.74 - 67.47: 72 67.47 - 101.21: 40 101.21 - 134.94: 0 134.94 - 168.68: 16 Dihedral angle restraints: 2588 sinusoidal: 1232 harmonic: 1356 Sorted by residual: dihedral pdb=" C07 KFL D 201 " pdb=" C09 KFL D 201 " pdb=" C10 KFL D 201 " pdb=" C11 KFL D 201 " ideal model delta sinusoidal sigma weight residual 290.24 121.56 168.68 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C07 KFL C 201 " pdb=" C09 KFL C 201 " pdb=" C10 KFL C 201 " pdb=" C11 KFL C 201 " ideal model delta sinusoidal sigma weight residual 290.24 121.67 168.57 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C07 KFL B 201 " pdb=" C09 KFL B 201 " pdb=" C10 KFL B 201 " pdb=" C11 KFL B 201 " ideal model delta sinusoidal sigma weight residual 290.24 121.83 168.41 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 2585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 535 0.055 - 0.110: 102 0.110 - 0.165: 11 0.165 - 0.221: 4 0.221 - 0.276: 4 Chirality restraints: 656 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN C 41 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN D 41 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 41 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 653 not shown) Planarity restraints: 676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 41 " 0.027 2.00e-02 2.50e+03 2.46e-02 7.55e+00 pdb=" CG ASN C 41 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN C 41 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 41 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 41 " -0.026 2.00e-02 2.50e+03 2.38e-02 7.10e+00 pdb=" CG ASN A 41 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 41 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 41 " 0.026 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 41 " -0.026 2.00e-02 2.50e+03 2.37e-02 7.01e+00 pdb=" CG ASN D 41 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN D 41 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D 41 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.026 2.00e-02 2.50e+03 ... (remaining 673 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 79 2.66 - 3.22: 3654 3.22 - 3.78: 6727 3.78 - 4.34: 9624 4.34 - 4.90: 15038 Nonbonded interactions: 35122 Sorted by model distance: nonbonded pdb=" OE2 GLU C 98 " pdb=" ND2 ASN D 81 " model vdw 2.104 3.120 nonbonded pdb=" OG SER C 40 " pdb=" O20 KFL C 201 " model vdw 2.329 3.040 nonbonded pdb=" OG SER B 40 " pdb=" O20 KFL B 201 " model vdw 2.337 3.040 nonbonded pdb=" OG SER A 40 " pdb=" O20 KFL A 201 " model vdw 2.338 3.040 nonbonded pdb=" OG SER D 40 " pdb=" O20 KFL D 201 " model vdw 2.338 3.040 ... (remaining 35117 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 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: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.160 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 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 : 0.022 0.443 4084 Z= 1.074 Angle : 0.998 13.858 5568 Z= 0.406 Chirality : 0.050 0.276 656 Planarity : 0.003 0.024 672 Dihedral : 24.651 168.679 1704 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.00 % Allowed : 22.14 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.36), residues: 476 helix: -4.93 (0.17), residues: 24 sheet: 0.53 (0.26), residues: 288 loop : 1.26 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 124 TYR 0.006 0.002 TYR C 57 PHE 0.015 0.002 PHE B 90 TRP 0.008 0.002 TRP C 94 HIS 0.001 0.000 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.02157 ( 4072) covalent geometry : angle 0.97999 ( 5536) SS BOND : bond 0.00407 ( 4) SS BOND : angle 1.23132 ( 8) hydrogen bonds : bond 0.18412 ( 192) hydrogen bonds : angle 8.00523 ( 492) link_BETA1-4 : bond 0.00127 ( 4) link_BETA1-4 : angle 1.80360 ( 12) link_NAG-ASN : bond 0.00847 ( 4) link_NAG-ASN : angle 3.86146 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7153 (pm20) REVERT: C 114 LYS cc_start: 0.7508 (mmmt) cc_final: 0.6839 (mmmt) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.6921 time to fit residues: 48.3439 Evaluate side-chains 66 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 0.0970 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** 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 = 0.3544 r_free = 0.3544 target = 0.122173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.098482 restraints weight = 4717.394| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.37 r_work: 0.3067 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4084 Z= 0.136 Angle : 0.757 9.403 5568 Z= 0.352 Chirality : 0.044 0.124 656 Planarity : 0.003 0.021 672 Dihedral : 23.884 172.938 860 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.67 % Allowed : 21.67 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.36), residues: 476 helix: -4.92 (0.18), residues: 24 sheet: 0.39 (0.27), residues: 292 loop : 1.28 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 146 TYR 0.004 0.001 TYR A 57 PHE 0.011 0.002 PHE D 90 TRP 0.009 0.002 TRP D 121 HIS 0.001 0.001 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4072) covalent geometry : angle 0.75264 ( 5536) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.94690 ( 8) hydrogen bonds : bond 0.04473 ( 192) hydrogen bonds : angle 5.96420 ( 492) link_BETA1-4 : bond 0.00126 ( 4) link_BETA1-4 : angle 1.64777 ( 12) link_NAG-ASN : bond 0.00515 ( 4) link_NAG-ASN : angle 1.05955 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7170 (pm20) REVERT: B 67 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6799 (pm20) REVERT: C 67 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6767 (pm20) REVERT: C 114 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6791 (mtpp) outliers start: 7 outliers final: 0 residues processed: 86 average time/residue: 0.6867 time to fit residues: 60.6120 Evaluate side-chains 70 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 114 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.123171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.100235 restraints weight = 4635.365| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.28 r_work: 0.3158 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 4084 Z= 0.128 Angle : 0.612 4.656 5568 Z= 0.312 Chirality : 0.043 0.123 656 Planarity : 0.003 0.017 672 Dihedral : 22.173 169.013 860 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.67 % Allowed : 21.19 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.37), residues: 476 helix: -4.91 (0.19), residues: 24 sheet: 0.45 (0.27), residues: 292 loop : 1.36 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.004 0.001 TYR A 57 PHE 0.012 0.002 PHE B 90 TRP 0.008 0.001 TRP C 94 HIS 0.001 0.000 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4072) covalent geometry : angle 0.60776 ( 5536) SS BOND : bond 0.00410 ( 4) SS BOND : angle 0.89778 ( 8) hydrogen bonds : bond 0.04246 ( 192) hydrogen bonds : angle 5.75190 ( 492) link_BETA1-4 : bond 0.00239 ( 4) link_BETA1-4 : angle 1.44631 ( 12) link_NAG-ASN : bond 0.00598 ( 4) link_NAG-ASN : angle 0.95247 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7318 (pm20) REVERT: B 67 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6921 (pm20) REVERT: C 50 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.8288 (mtm-85) REVERT: C 67 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: C 95 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8702 (mmtm) REVERT: C 114 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6948 (mtpp) REVERT: D 67 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6859 (pm20) outliers start: 7 outliers final: 2 residues processed: 86 average time/residue: 0.6996 time to fit residues: 61.7303 Evaluate side-chains 80 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 67 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.119025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.094847 restraints weight = 4712.828| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.38 r_work: 0.3052 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 4084 Z= 0.238 Angle : 0.680 4.527 5568 Z= 0.354 Chirality : 0.047 0.127 656 Planarity : 0.004 0.022 672 Dihedral : 21.957 172.229 860 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 4.05 % Allowed : 20.24 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.37), residues: 476 helix: -4.90 (0.19), residues: 24 sheet: 0.40 (0.27), residues: 292 loop : 1.34 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 124 TYR 0.007 0.002 TYR C 57 PHE 0.019 0.003 PHE C 90 TRP 0.009 0.002 TRP C 94 HIS 0.000 0.000 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 4072) covalent geometry : angle 0.67211 ( 5536) SS BOND : bond 0.00494 ( 4) SS BOND : angle 1.38977 ( 8) hydrogen bonds : bond 0.04906 ( 192) hydrogen bonds : angle 6.07974 ( 492) link_BETA1-4 : bond 0.00094 ( 4) link_BETA1-4 : angle 1.42623 ( 12) link_NAG-ASN : bond 0.00922 ( 4) link_NAG-ASN : angle 1.69040 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.177 Fit side-chains REVERT: A 67 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7253 (pm20) REVERT: A 95 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8742 (mmtm) REVERT: B 67 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6886 (pm20) REVERT: C 67 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6856 (pm20) REVERT: C 95 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8766 (mmtm) REVERT: C 114 LYS cc_start: 0.7407 (mmmt) cc_final: 0.6897 (mmmt) REVERT: D 67 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6832 (pm20) REVERT: D 95 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8740 (mmtm) outliers start: 17 outliers final: 3 residues processed: 79 average time/residue: 0.7048 time to fit residues: 57.1243 Evaluate side-chains 78 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 95 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.122184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.098459 restraints weight = 4692.944| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.36 r_work: 0.3149 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4084 Z= 0.123 Angle : 0.603 3.696 5568 Z= 0.311 Chirality : 0.044 0.140 656 Planarity : 0.003 0.016 672 Dihedral : 20.670 167.233 860 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.67 % Allowed : 21.43 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.49 (0.37), residues: 476 helix: -4.89 (0.19), residues: 24 sheet: 0.43 (0.27), residues: 292 loop : 1.35 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 146 TYR 0.005 0.001 TYR D 57 PHE 0.012 0.002 PHE C 90 TRP 0.009 0.002 TRP C 121 HIS 0.001 0.000 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 4072) covalent geometry : angle 0.59853 ( 5536) SS BOND : bond 0.00432 ( 4) SS BOND : angle 0.99545 ( 8) hydrogen bonds : bond 0.04077 ( 192) hydrogen bonds : angle 5.68428 ( 492) link_BETA1-4 : bond 0.00218 ( 4) link_BETA1-4 : angle 1.51581 ( 12) link_NAG-ASN : bond 0.00818 ( 4) link_NAG-ASN : angle 0.61010 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7270 (pm20) REVERT: A 114 LYS cc_start: 0.7388 (ptmm) cc_final: 0.6926 (ptmm) REVERT: B 67 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: B 114 LYS cc_start: 0.7408 (ptmm) cc_final: 0.6897 (ptmm) REVERT: C 67 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6895 (pm20) REVERT: C 114 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6793 (mmmt) REVERT: D 67 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: D 114 LYS cc_start: 0.7385 (ptmm) cc_final: 0.6917 (ptmm) outliers start: 7 outliers final: 0 residues processed: 76 average time/residue: 0.6900 time to fit residues: 53.8583 Evaluate side-chains 76 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 67 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 42 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.122161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.098905 restraints weight = 4704.986| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.30 r_work: 0.3140 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 4084 Z= 0.142 Angle : 0.593 3.754 5568 Z= 0.313 Chirality : 0.045 0.135 656 Planarity : 0.003 0.017 672 Dihedral : 20.194 167.244 860 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.19 % Allowed : 23.33 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.37), residues: 476 helix: -4.88 (0.19), residues: 24 sheet: 0.46 (0.27), residues: 292 loop : 1.35 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 146 TYR 0.005 0.001 TYR A 57 PHE 0.016 0.002 PHE C 90 TRP 0.008 0.001 TRP C 94 HIS 0.000 0.000 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4072) covalent geometry : angle 0.58732 ( 5536) SS BOND : bond 0.00550 ( 4) SS BOND : angle 1.57291 ( 8) hydrogen bonds : bond 0.04186 ( 192) hydrogen bonds : angle 5.74978 ( 492) link_BETA1-4 : bond 0.00172 ( 4) link_BETA1-4 : angle 1.40618 ( 12) link_NAG-ASN : bond 0.00770 ( 4) link_NAG-ASN : angle 0.75973 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7371 (pm20) REVERT: A 114 LYS cc_start: 0.7435 (ptmm) cc_final: 0.6892 (ptmm) REVERT: B 67 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6976 (pm20) REVERT: C 67 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6937 (pm20) REVERT: C 114 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6858 (mmmt) REVERT: D 67 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6920 (pm20) REVERT: D 114 LYS cc_start: 0.7413 (ptmm) cc_final: 0.6865 (ptmm) outliers start: 5 outliers final: 1 residues processed: 71 average time/residue: 0.6992 time to fit residues: 50.9782 Evaluate side-chains 71 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.118511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095009 restraints weight = 4729.836| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.29 r_work: 0.3079 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 4084 Z= 0.279 Angle : 0.698 4.347 5568 Z= 0.372 Chirality : 0.049 0.130 656 Planarity : 0.004 0.023 672 Dihedral : 20.545 169.918 860 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.43 % Allowed : 23.81 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.37), residues: 476 helix: -4.88 (0.20), residues: 24 sheet: 0.38 (0.27), residues: 292 loop : 1.30 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 138 TYR 0.007 0.003 TYR A 57 PHE 0.022 0.003 PHE A 90 TRP 0.008 0.002 TRP C 94 HIS 0.000 0.000 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00606 ( 4072) covalent geometry : angle 0.68830 ( 5536) SS BOND : bond 0.00714 ( 4) SS BOND : angle 1.72271 ( 8) hydrogen bonds : bond 0.05064 ( 192) hydrogen bonds : angle 6.18083 ( 492) link_BETA1-4 : bond 0.00069 ( 4) link_BETA1-4 : angle 1.51720 ( 12) link_NAG-ASN : bond 0.01095 ( 4) link_NAG-ASN : angle 1.79565 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.150 Fit side-chains REVERT: A 67 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7442 (pm20) REVERT: A 114 LYS cc_start: 0.7445 (ptmm) cc_final: 0.6985 (ptmm) REVERT: B 67 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6959 (pm20) REVERT: B 114 LYS cc_start: 0.7368 (ptmm) cc_final: 0.6971 (ptmm) REVERT: C 67 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6920 (pm20) REVERT: C 114 LYS cc_start: 0.7476 (mmmt) cc_final: 0.6858 (mmmt) REVERT: D 67 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6956 (pm20) REVERT: D 114 LYS cc_start: 0.7421 (ptmm) cc_final: 0.6964 (ptmm) outliers start: 6 outliers final: 3 residues processed: 73 average time/residue: 0.6548 time to fit residues: 49.0999 Evaluate side-chains 75 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.122047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.098052 restraints weight = 4704.712| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.40 r_work: 0.3144 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 4084 Z= 0.121 Angle : 0.570 3.665 5568 Z= 0.303 Chirality : 0.045 0.134 656 Planarity : 0.003 0.020 672 Dihedral : 19.833 163.465 860 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.71 % Allowed : 24.76 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.50 (0.37), residues: 476 helix: -4.86 (0.20), residues: 24 sheet: 0.46 (0.27), residues: 292 loop : 1.31 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 138 TYR 0.006 0.001 TYR A 57 PHE 0.012 0.001 PHE C 90 TRP 0.011 0.002 TRP C 121 HIS 0.001 0.000 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 4072) covalent geometry : angle 0.56329 ( 5536) SS BOND : bond 0.00268 ( 4) SS BOND : angle 1.21359 ( 8) hydrogen bonds : bond 0.04064 ( 192) hydrogen bonds : angle 5.66439 ( 492) link_BETA1-4 : bond 0.00226 ( 4) link_BETA1-4 : angle 1.60647 ( 12) link_NAG-ASN : bond 0.01020 ( 4) link_NAG-ASN : angle 0.95044 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7375 (pm20) REVERT: A 114 LYS cc_start: 0.7381 (ptmm) cc_final: 0.6932 (ptmm) REVERT: B 67 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6969 (pm20) REVERT: C 67 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6937 (pm20) REVERT: C 114 LYS cc_start: 0.7318 (mmmt) cc_final: 0.6855 (mmmt) REVERT: D 67 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: D 114 LYS cc_start: 0.7373 (ptmm) cc_final: 0.6874 (ptmm) outliers start: 3 outliers final: 0 residues processed: 71 average time/residue: 0.7453 time to fit residues: 54.3302 Evaluate side-chains 72 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain D residue 67 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 12 optimal weight: 7.9990 chunk 26 optimal weight: 0.1980 chunk 47 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.120732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097438 restraints weight = 4739.734| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.30 r_work: 0.3117 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 4084 Z= 0.179 Angle : 0.606 3.945 5568 Z= 0.325 Chirality : 0.046 0.129 656 Planarity : 0.003 0.021 672 Dihedral : 20.021 164.998 860 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.43 % Allowed : 24.29 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.36), residues: 476 helix: -4.87 (0.20), residues: 24 sheet: 0.43 (0.27), residues: 292 loop : 1.23 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 138 TYR 0.006 0.002 TYR C 57 PHE 0.018 0.002 PHE C 90 TRP 0.008 0.002 TRP C 94 HIS 0.000 0.000 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 4072) covalent geometry : angle 0.60031 ( 5536) SS BOND : bond 0.00386 ( 4) SS BOND : angle 1.19675 ( 8) hydrogen bonds : bond 0.04442 ( 192) hydrogen bonds : angle 5.85860 ( 492) link_BETA1-4 : bond 0.00160 ( 4) link_BETA1-4 : angle 1.49123 ( 12) link_NAG-ASN : bond 0.00898 ( 4) link_NAG-ASN : angle 1.09487 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7417 (pm20) REVERT: A 114 LYS cc_start: 0.7394 (ptmm) cc_final: 0.6950 (ptmm) REVERT: B 67 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6976 (pm20) REVERT: B 114 LYS cc_start: 0.7305 (ptmm) cc_final: 0.6923 (ptmm) REVERT: C 67 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6942 (pm20) REVERT: C 114 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6915 (mmmt) REVERT: D 67 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6947 (pm20) REVERT: D 114 LYS cc_start: 0.7376 (ptmm) cc_final: 0.6881 (ptmm) outliers start: 6 outliers final: 2 residues processed: 74 average time/residue: 0.6933 time to fit residues: 52.6510 Evaluate side-chains 77 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 0.0010 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.120541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.097274 restraints weight = 4659.599| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.29 r_work: 0.3117 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 4084 Z= 0.184 Angle : 0.605 4.137 5568 Z= 0.327 Chirality : 0.046 0.130 656 Planarity : 0.003 0.021 672 Dihedral : 20.083 164.290 860 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.67 % Allowed : 24.05 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.37), residues: 476 helix: -4.87 (0.20), residues: 24 sheet: 0.30 (0.27), residues: 300 loop : 1.52 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 138 TYR 0.006 0.002 TYR C 57 PHE 0.018 0.002 PHE C 90 TRP 0.008 0.002 TRP C 94 HIS 0.000 0.000 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 4072) covalent geometry : angle 0.59899 ( 5536) SS BOND : bond 0.00471 ( 4) SS BOND : angle 1.18156 ( 8) hydrogen bonds : bond 0.04487 ( 192) hydrogen bonds : angle 5.91312 ( 492) link_BETA1-4 : bond 0.00141 ( 4) link_BETA1-4 : angle 1.53755 ( 12) link_NAG-ASN : bond 0.00891 ( 4) link_NAG-ASN : angle 1.10876 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7433 (pm20) REVERT: A 114 LYS cc_start: 0.7351 (ptmm) cc_final: 0.6921 (ptmm) REVERT: B 67 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6976 (pm20) REVERT: B 114 LYS cc_start: 0.7304 (ptmm) cc_final: 0.6921 (ptmm) REVERT: C 67 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: C 114 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6920 (mmmt) REVERT: D 67 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: D 114 LYS cc_start: 0.7354 (ptmm) cc_final: 0.6854 (ptmm) outliers start: 7 outliers final: 2 residues processed: 77 average time/residue: 0.6622 time to fit residues: 52.5075 Evaluate side-chains 74 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 20 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.121931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.098620 restraints weight = 4650.638| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.30 r_work: 0.3140 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4084 Z= 0.144 Angle : 0.592 4.378 5568 Z= 0.317 Chirality : 0.045 0.150 656 Planarity : 0.003 0.020 672 Dihedral : 19.964 162.907 860 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.19 % Allowed : 24.29 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.45 (0.37), residues: 476 helix: -4.87 (0.20), residues: 24 sheet: 0.36 (0.27), residues: 300 loop : 1.49 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 138 TYR 0.005 0.001 TYR D 57 PHE 0.015 0.002 PHE B 90 TRP 0.009 0.002 TRP A 121 HIS 0.000 0.000 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4072) covalent geometry : angle 0.58392 ( 5536) SS BOND : bond 0.00400 ( 4) SS BOND : angle 1.64387 ( 8) hydrogen bonds : bond 0.04227 ( 192) hydrogen bonds : angle 5.76791 ( 492) link_BETA1-4 : bond 0.00212 ( 4) link_BETA1-4 : angle 1.58866 ( 12) link_NAG-ASN : bond 0.00829 ( 4) link_NAG-ASN : angle 1.02259 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2146.18 seconds wall clock time: 37 minutes 19.56 seconds (2239.56 seconds total)