Starting phenix.real_space_refine on Wed Jul 23 19:08:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zyl_15026/07_2025/7zyl_15026_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyl_15026/07_2025/7zyl_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_15026/07_2025/7zyl_15026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyl_15026/07_2025/7zyl_15026.map" model { file = "/net/cci-nas-00/data/ceres_data/7zyl_15026/07_2025/7zyl_15026_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyl_15026/07_2025/7zyl_15026_trim.cif" } resolution = 2.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.65, per 1000 atoms: 1.16 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: 1.15 Conformation dependent library (CDL) restraints added in 444.1 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: 0.48 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: 1.12 Time building geometry restraints manager: 1.35 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: 0.01 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: 4.140 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.090 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.370 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.002 TRP C 94 HIS 0.001 0.000 HIS B 74 PHE 0.015 0.002 PHE B 90 TYR 0.006 0.002 TYR C 57 ARG 0.002 0.001 ARG A 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00847 ( 4) link_NAG-ASN : angle 3.86146 ( 12) link_BETA1-4 : bond 0.00127 ( 4) link_BETA1-4 : angle 1.80360 ( 12) hydrogen bonds : bond 0.18412 ( 192) hydrogen bonds : angle 8.00523 ( 492) SS BOND : bond 0.00407 ( 4) SS BOND : angle 1.23132 ( 8) covalent geometry : bond 0.02157 ( 4072) covalent geometry : angle 0.97999 ( 5536) *********************** 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 : 0.449 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: 1.4452 time to fit residues: 101.1653 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 : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3498 r_free = 0.3498 target = 0.118627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.095052 restraints weight = 4608.146| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.32 r_work: 0.3009 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4084 Z= 0.212 Angle : 0.792 9.392 5568 Z= 0.380 Chirality : 0.047 0.126 656 Planarity : 0.004 0.025 672 Dihedral : 25.184 175.774 860 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.86 % Allowed : 19.52 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.36), residues: 476 helix: -4.91 (0.19), residues: 24 sheet: 0.39 (0.27), residues: 292 loop : 1.23 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 121 HIS 0.001 0.001 HIS D 74 PHE 0.015 0.002 PHE D 90 TYR 0.005 0.002 TYR A 57 ARG 0.003 0.001 ARG D 138 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 4) link_NAG-ASN : angle 1.63538 ( 12) link_BETA1-4 : bond 0.00102 ( 4) link_BETA1-4 : angle 1.58843 ( 12) hydrogen bonds : bond 0.05084 ( 192) hydrogen bonds : angle 6.24862 ( 492) SS BOND : bond 0.00380 ( 4) SS BOND : angle 1.00467 ( 8) covalent geometry : bond 0.00446 ( 4072) covalent geometry : angle 0.78665 ( 5536) *********************** 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 88 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.557 Fit side-chains REVERT: A 67 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7192 (pm20) REVERT: B 67 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6795 (pm20) REVERT: C 67 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: C 114 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6681 (mmmt) outliers start: 12 outliers final: 3 residues processed: 83 average time/residue: 1.3382 time to fit residues: 114.4330 Evaluate side-chains 81 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 114 LYS Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN B 93 ASN C 93 ASN D 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.121980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.098755 restraints weight = 4622.084| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.29 r_work: 0.3133 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 4084 Z= 0.151 Angle : 0.638 4.882 5568 Z= 0.325 Chirality : 0.045 0.123 656 Planarity : 0.003 0.022 672 Dihedral : 22.709 169.905 860 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.71 % Allowed : 21.90 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.37), residues: 476 helix: -4.89 (0.19), residues: 24 sheet: 0.38 (0.27), residues: 292 loop : 1.26 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 94 HIS 0.000 0.000 HIS C 74 PHE 0.013 0.002 PHE D 90 TYR 0.005 0.001 TYR B 57 ARG 0.002 0.001 ARG B 146 Details of bonding type rmsd link_NAG-ASN : bond 0.00854 ( 4) link_NAG-ASN : angle 0.58501 ( 12) link_BETA1-4 : bond 0.00166 ( 4) link_BETA1-4 : angle 1.61720 ( 12) hydrogen bonds : bond 0.04429 ( 192) hydrogen bonds : angle 5.83607 ( 492) SS BOND : bond 0.00259 ( 4) SS BOND : angle 1.25140 ( 8) covalent geometry : bond 0.00310 ( 4072) covalent geometry : angle 0.63318 ( 5536) *********************** 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 86 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7395 (pm20) REVERT: B 50 ARG cc_start: 0.8558 (mtm-85) cc_final: 0.8354 (mtm-85) REVERT: B 67 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6928 (pm20) REVERT: C 50 ARG cc_start: 0.8542 (mtm-85) cc_final: 0.8342 (mtm-85) REVERT: C 67 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6901 (pm20) REVERT: C 114 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.6943 (mmmt) REVERT: D 50 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8340 (mtm-85) outliers start: 3 outliers final: 0 residues processed: 83 average time/residue: 1.7225 time to fit residues: 147.4246 Evaluate side-chains 73 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 0.0000 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.119479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.096134 restraints weight = 4608.456| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.26 r_work: 0.3098 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 4084 Z= 0.219 Angle : 0.664 4.601 5568 Z= 0.346 Chirality : 0.046 0.123 656 Planarity : 0.004 0.020 672 Dihedral : 22.101 169.511 860 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 3.33 % Allowed : 21.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.37), residues: 476 helix: -4.90 (0.19), residues: 24 sheet: 0.33 (0.27), residues: 292 loop : 1.25 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 94 HIS 0.000 0.000 HIS B 74 PHE 0.018 0.002 PHE B 90 TYR 0.006 0.002 TYR C 57 ARG 0.002 0.001 ARG D 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00922 ( 4) link_NAG-ASN : angle 1.34600 ( 12) link_BETA1-4 : bond 0.00091 ( 4) link_BETA1-4 : angle 1.42517 ( 12) hydrogen bonds : bond 0.04778 ( 192) hydrogen bonds : angle 6.06650 ( 492) SS BOND : bond 0.00506 ( 4) SS BOND : angle 1.26494 ( 8) covalent geometry : bond 0.00468 ( 4072) covalent geometry : angle 0.65774 ( 5536) *********************** 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 86 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7383 (pm20) REVERT: A 95 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8822 (mmtm) REVERT: B 67 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6912 (pm20) REVERT: C 67 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: C 114 LYS cc_start: 0.7472 (mmmt) cc_final: 0.6987 (mmmt) REVERT: D 95 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8796 (mmtm) outliers start: 14 outliers final: 3 residues processed: 81 average time/residue: 1.5483 time to fit residues: 128.8577 Evaluate side-chains 79 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 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 5 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.120411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.096721 restraints weight = 4690.777| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.31 r_work: 0.3112 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 4084 Z= 0.188 Angle : 0.651 4.398 5568 Z= 0.339 Chirality : 0.046 0.123 656 Planarity : 0.003 0.020 672 Dihedral : 21.159 166.895 860 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.43 % Allowed : 22.14 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.37), residues: 476 helix: -4.90 (0.19), residues: 24 sheet: 0.40 (0.27), residues: 292 loop : 1.17 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 94 HIS 0.000 0.000 HIS D 74 PHE 0.017 0.002 PHE D 90 TYR 0.006 0.002 TYR B 57 ARG 0.002 0.001 ARG A 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00848 ( 4) link_NAG-ASN : angle 1.05679 ( 12) link_BETA1-4 : bond 0.00081 ( 4) link_BETA1-4 : angle 1.52280 ( 12) hydrogen bonds : bond 0.04522 ( 192) hydrogen bonds : angle 5.95388 ( 492) SS BOND : bond 0.00312 ( 4) SS BOND : angle 1.55122 ( 8) covalent geometry : bond 0.00396 ( 4072) covalent geometry : angle 0.64493 ( 5536) *********************** 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 82 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7385 (pm20) REVERT: A 114 LYS cc_start: 0.7461 (ptmm) cc_final: 0.7017 (ptmm) REVERT: B 67 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6957 (pm20) REVERT: B 114 LYS cc_start: 0.7464 (ptmm) cc_final: 0.6961 (ptmm) REVERT: C 67 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6905 (pm20) REVERT: C 114 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.6955 (mmmt) REVERT: D 114 LYS cc_start: 0.7461 (ptmm) cc_final: 0.6997 (ptmm) outliers start: 6 outliers final: 3 residues processed: 79 average time/residue: 1.5525 time to fit residues: 126.5848 Evaluate side-chains 82 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 114 LYS Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.121115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.097624 restraints weight = 4697.290| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.33 r_work: 0.3136 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 4084 Z= 0.148 Angle : 0.586 3.754 5568 Z= 0.310 Chirality : 0.044 0.123 656 Planarity : 0.003 0.019 672 Dihedral : 20.090 163.977 860 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.95 % Allowed : 23.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.37), residues: 476 helix: -4.89 (0.20), residues: 24 sheet: 0.44 (0.27), residues: 292 loop : 1.24 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 121 HIS 0.001 0.000 HIS B 74 PHE 0.015 0.002 PHE C 90 TYR 0.005 0.002 TYR C 57 ARG 0.002 0.001 ARG A 146 Details of bonding type rmsd link_NAG-ASN : bond 0.00775 ( 4) link_NAG-ASN : angle 0.72274 ( 12) link_BETA1-4 : bond 0.00220 ( 4) link_BETA1-4 : angle 1.50119 ( 12) hydrogen bonds : bond 0.04160 ( 192) hydrogen bonds : angle 5.78250 ( 492) SS BOND : bond 0.00497 ( 4) SS BOND : angle 1.48876 ( 8) covalent geometry : bond 0.00308 ( 4072) covalent geometry : angle 0.57957 ( 5536) *********************** 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 81 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7317 (pm20) REVERT: A 114 LYS cc_start: 0.7400 (ptmm) cc_final: 0.6931 (ptmm) REVERT: B 67 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6944 (pm20) REVERT: B 114 LYS cc_start: 0.7367 (ptmm) cc_final: 0.6929 (ptmm) REVERT: C 67 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6896 (pm20) REVERT: C 114 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6853 (mmmt) REVERT: D 114 LYS cc_start: 0.7371 (ptmm) cc_final: 0.6891 (ptmm) outliers start: 4 outliers final: 1 residues processed: 78 average time/residue: 1.4983 time to fit residues: 120.2623 Evaluate side-chains 77 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.117768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.094436 restraints weight = 4669.100| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.27 r_work: 0.3072 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 4084 Z= 0.299 Angle : 0.704 4.336 5568 Z= 0.375 Chirality : 0.050 0.131 656 Planarity : 0.004 0.024 672 Dihedral : 20.585 167.143 860 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.67 % Allowed : 23.33 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.36), residues: 476 helix: -4.88 (0.20), residues: 24 sheet: 0.35 (0.27), residues: 292 loop : 1.12 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 94 HIS 0.000 0.000 HIS C 74 PHE 0.022 0.003 PHE C 90 TYR 0.007 0.003 TYR A 57 ARG 0.004 0.001 ARG D 138 Details of bonding type rmsd link_NAG-ASN : bond 0.01163 ( 4) link_NAG-ASN : angle 1.90315 ( 12) link_BETA1-4 : bond 0.00055 ( 4) link_BETA1-4 : angle 1.64396 ( 12) hydrogen bonds : bond 0.05092 ( 192) hydrogen bonds : angle 6.24830 ( 492) SS BOND : bond 0.00638 ( 4) SS BOND : angle 1.47609 ( 8) covalent geometry : bond 0.00654 ( 4072) covalent geometry : angle 0.69449 ( 5536) *********************** 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 77 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.657 Fit side-chains REVERT: A 67 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7438 (pm20) REVERT: A 114 LYS cc_start: 0.7401 (ptmm) cc_final: 0.6959 (ptmm) REVERT: B 67 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6948 (pm20) REVERT: B 114 LYS cc_start: 0.7348 (ptmm) cc_final: 0.6971 (ptmm) REVERT: C 67 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6913 (pm20) REVERT: C 114 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.6872 (mmmt) REVERT: D 114 LYS cc_start: 0.7399 (ptmm) cc_final: 0.6935 (ptmm) outliers start: 7 outliers final: 3 residues processed: 73 average time/residue: 2.2388 time to fit residues: 169.0145 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 : 0.593 ------------------------------------------------------------------------------- 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 114 LYS 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 16 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.119720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.096652 restraints weight = 4561.575| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.25 r_work: 0.3111 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 4084 Z= 0.185 Angle : 0.610 4.046 5568 Z= 0.327 Chirality : 0.046 0.126 656 Planarity : 0.003 0.023 672 Dihedral : 20.191 163.541 860 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.95 % Allowed : 23.81 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.36), residues: 476 helix: -4.88 (0.20), residues: 24 sheet: 0.38 (0.27), residues: 292 loop : 1.19 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 121 HIS 0.000 0.000 HIS C 74 PHE 0.017 0.002 PHE D 90 TYR 0.006 0.002 TYR D 57 ARG 0.003 0.001 ARG B 138 Details of bonding type rmsd link_NAG-ASN : bond 0.00962 ( 4) link_NAG-ASN : angle 1.25421 ( 12) link_BETA1-4 : bond 0.00163 ( 4) link_BETA1-4 : angle 1.66767 ( 12) hydrogen bonds : bond 0.04504 ( 192) hydrogen bonds : angle 5.95426 ( 492) SS BOND : bond 0.00367 ( 4) SS BOND : angle 1.15873 ( 8) covalent geometry : bond 0.00388 ( 4072) covalent geometry : angle 0.60259 ( 5536) *********************** 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 79 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7451 (pm20) REVERT: A 114 LYS cc_start: 0.7388 (ptmm) cc_final: 0.6933 (ptmm) REVERT: B 67 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6968 (pm20) REVERT: B 114 LYS cc_start: 0.7308 (ptmm) cc_final: 0.6924 (ptmm) REVERT: C 67 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6923 (pm20) REVERT: C 114 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6933 (mmmt) REVERT: D 114 LYS cc_start: 0.7381 (ptmm) cc_final: 0.6899 (ptmm) outliers start: 4 outliers final: 1 residues processed: 76 average time/residue: 2.5225 time to fit residues: 198.5793 Evaluate side-chains 79 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.118704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095544 restraints weight = 4620.430| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.26 r_work: 0.3093 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1347 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= 0.234 Angle : 0.649 4.188 5568 Z= 0.348 Chirality : 0.047 0.128 656 Planarity : 0.004 0.024 672 Dihedral : 20.386 164.291 860 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.67 % Allowed : 23.10 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.36), residues: 476 helix: -4.89 (0.20), residues: 24 sheet: 0.37 (0.27), residues: 292 loop : 1.15 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 94 HIS 0.000 0.000 HIS C 74 PHE 0.019 0.002 PHE D 90 TYR 0.007 0.002 TYR B 57 ARG 0.004 0.001 ARG D 138 Details of bonding type rmsd link_NAG-ASN : bond 0.01044 ( 4) link_NAG-ASN : angle 1.40214 ( 12) link_BETA1-4 : bond 0.00100 ( 4) link_BETA1-4 : angle 1.62685 ( 12) hydrogen bonds : bond 0.04785 ( 192) hydrogen bonds : angle 6.11158 ( 492) SS BOND : bond 0.00455 ( 4) SS BOND : angle 1.12498 ( 8) covalent geometry : bond 0.00499 ( 4072) covalent geometry : angle 0.64153 ( 5536) *********************** 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 82 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7427 (pm20) REVERT: A 114 LYS cc_start: 0.7376 (ptmm) cc_final: 0.6940 (ptmm) REVERT: B 67 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: B 114 LYS cc_start: 0.7310 (ptmm) cc_final: 0.6925 (ptmm) REVERT: C 67 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: C 114 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6833 (mmmt) REVERT: D 114 LYS cc_start: 0.7376 (ptmm) cc_final: 0.6899 (ptmm) outliers start: 7 outliers final: 3 residues processed: 79 average time/residue: 1.4153 time to fit residues: 115.2226 Evaluate side-chains 81 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 114 LYS 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 43 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.120755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.097805 restraints weight = 4618.198| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.27 r_work: 0.3091 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4084 Z= 0.152 Angle : 0.591 4.744 5568 Z= 0.317 Chirality : 0.045 0.157 656 Planarity : 0.003 0.022 672 Dihedral : 20.106 161.972 860 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.71 % Allowed : 24.05 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.37), residues: 476 helix: -4.89 (0.20), residues: 24 sheet: 0.43 (0.27), residues: 292 loop : 1.22 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 121 HIS 0.001 0.000 HIS C 74 PHE 0.015 0.002 PHE C 90 TYR 0.006 0.002 TYR D 57 ARG 0.004 0.001 ARG A 138 Details of bonding type rmsd link_NAG-ASN : bond 0.00855 ( 4) link_NAG-ASN : angle 0.86364 ( 12) link_BETA1-4 : bond 0.00194 ( 4) link_BETA1-4 : angle 1.68217 ( 12) hydrogen bonds : bond 0.04274 ( 192) hydrogen bonds : angle 5.83524 ( 492) SS BOND : bond 0.00606 ( 4) SS BOND : angle 1.65065 ( 8) covalent geometry : bond 0.00314 ( 4072) covalent geometry : angle 0.58279 ( 5536) ********************** 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 82 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7330 (pm20) REVERT: A 114 LYS cc_start: 0.7276 (ptmm) cc_final: 0.6805 (ptmm) REVERT: B 67 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: B 114 LYS cc_start: 0.7205 (ptmm) cc_final: 0.6817 (ptmm) REVERT: C 67 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: C 114 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6803 (mmmt) REVERT: D 114 LYS cc_start: 0.7283 (ptmm) cc_final: 0.6774 (ptmm) outliers start: 3 outliers final: 0 residues processed: 79 average time/residue: 1.4529 time to fit residues: 118.0735 Evaluate side-chains 80 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.122204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.099413 restraints weight = 4635.228| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.27 r_work: 0.3158 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 4084 Z= 0.128 Angle : 0.570 3.894 5568 Z= 0.304 Chirality : 0.044 0.133 656 Planarity : 0.003 0.022 672 Dihedral : 19.970 160.790 860 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.71 % Allowed : 24.29 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.37), residues: 476 helix: -4.89 (0.19), residues: 24 sheet: 0.49 (0.27), residues: 292 loop : 1.21 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 121 HIS 0.001 0.000 HIS D 74 PHE 0.014 0.002 PHE C 90 TYR 0.005 0.001 TYR B 57 ARG 0.003 0.001 ARG A 138 Details of bonding type rmsd link_NAG-ASN : bond 0.00787 ( 4) link_NAG-ASN : angle 0.63087 ( 12) link_BETA1-4 : bond 0.00229 ( 4) link_BETA1-4 : angle 1.55104 ( 12) hydrogen bonds : bond 0.04003 ( 192) hydrogen bonds : angle 5.67682 ( 492) SS BOND : bond 0.00356 ( 4) SS BOND : angle 1.48623 ( 8) covalent geometry : bond 0.00266 ( 4072) covalent geometry : angle 0.56319 ( 5536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5215.32 seconds wall clock time: 94 minutes 10.30 seconds (5650.30 seconds total)