Starting phenix.real_space_refine on Wed Mar 5 23:43:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zyl_15026/03_2025/7zyl_15026_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyl_15026/03_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_15026/03_2025/7zyl_15026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyl_15026/03_2025/7zyl_15026.map" model { file = "/net/cci-nas-00/data/ceres_data/7zyl_15026/03_2025/7zyl_15026_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyl_15026/03_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-5624/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: 4.38, per 1000 atoms: 1.10 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: 1.04 Conformation dependent library (CDL) restraints added in 429.5 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: 0.47 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: 1.10 Time building geometry restraints manager: 1.22 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: 5.620 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: 0.040 Set scattering table: 0.050 Process input model: 15.430 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.680 ------------------------------------------------------------------------------- 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 4072 Z= 1.392 Angle : 0.980 13.858 5536 Z= 0.402 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 *********************** 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 : 0.527 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: 1.4557 time to fit residues: 101.8734 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 : 0.423 ------------------------------------------------------------------------------- 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 4072 Z= 0.287 Angle : 0.787 9.392 5536 Z= 0.379 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 *********************** 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 : 0.651 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: 1.5351 time to fit residues: 131.0751 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 : 0.417 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.9980 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN D 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.122564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.099495 restraints weight = 4622.109| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.28 r_work: 0.3142 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 4072 Z= 0.177 Angle : 0.628 5.192 5536 Z= 0.319 Chirality : 0.044 0.123 656 Planarity : 0.003 0.020 672 Dihedral : 22.680 169.688 860 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.71 % Allowed : 22.62 % 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 (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: 0.41 (0.37), residues: 476 helix: -4.89 (0.19), residues: 24 sheet: 0.39 (0.27), residues: 292 loop : 1.27 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 121 HIS 0.001 0.000 HIS C 74 PHE 0.012 0.002 PHE D 90 TYR 0.005 0.001 TYR B 57 ARG 0.002 0.000 ARG B 146 *********************** 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 : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7379 (pm20) REVERT: B 67 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6923 (pm20) REVERT: C 67 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6890 (pm20) REVERT: C 114 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6896 (mmmt) outliers start: 3 outliers final: 0 residues processed: 83 average time/residue: 1.2894 time to fit residues: 110.2700 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 : 0.412 ------------------------------------------------------------------------------- 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: 10.0000 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.117102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.093396 restraints weight = 4590.900| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.29 r_work: 0.3010 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 4072 Z= 0.443 Angle : 0.741 5.094 5536 Z= 0.389 Chirality : 0.049 0.125 656 Planarity : 0.005 0.026 672 Dihedral : 22.742 171.111 860 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 3.57 % Allowed : 20.48 % Favored : 75.95 % 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: 0.24 (0.36), residues: 476 helix: -4.90 (0.19), residues: 24 sheet: 0.26 (0.27), residues: 292 loop : 1.17 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 94 HIS 0.000 0.000 HIS A 74 PHE 0.021 0.003 PHE D 90 TYR 0.007 0.003 TYR C 57 ARG 0.002 0.001 ARG D 124 *********************** 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: 15 poor density : 70 time to evaluate : 0.483 Fit side-chains REVERT: A 67 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7244 (pm20) REVERT: A 95 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8737 (mmtm) REVERT: B 67 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6823 (pm20) REVERT: B 95 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8657 (mmtm) REVERT: C 67 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6811 (pm20) REVERT: C 114 LYS cc_start: 0.7387 (mmmt) cc_final: 0.6894 (mmmt) REVERT: D 95 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8679 (mmtm) outliers start: 15 outliers final: 3 residues processed: 80 average time/residue: 1.5235 time to fit residues: 125.4915 Evaluate side-chains 79 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 B residue 95 LYS 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: 6.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.119506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.096035 restraints weight = 4719.599| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.30 r_work: 0.3096 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 4072 Z= 0.294 Angle : 0.669 4.766 5536 Z= 0.350 Chirality : 0.047 0.133 656 Planarity : 0.004 0.023 672 Dihedral : 21.520 165.969 860 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: 0.29 (0.36), residues: 476 helix: -4.87 (0.20), residues: 24 sheet: 0.32 (0.27), residues: 292 loop : 1.15 (0.49), 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 0.017 0.002 PHE D 90 TYR 0.006 0.002 TYR A 57 ARG 0.002 0.001 ARG D 138 *********************** 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 78 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7450 (pm20) REVERT: A 114 LYS cc_start: 0.7449 (ptmm) cc_final: 0.7021 (ptmm) REVERT: B 67 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6947 (pm20) REVERT: B 114 LYS cc_start: 0.7450 (ptmm) cc_final: 0.7034 (ptmm) REVERT: C 67 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6914 (pm20) REVERT: C 114 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.6973 (mmmt) REVERT: D 114 LYS cc_start: 0.7467 (ptmm) cc_final: 0.6924 (ptmm) outliers start: 6 outliers final: 3 residues processed: 75 average time/residue: 2.1036 time to fit residues: 162.8871 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 : 0.433 ------------------------------------------------------------------------------- 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: 1.9990 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.120295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.096731 restraints weight = 4596.515| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.29 r_work: 0.3111 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 4072 Z= 0.250 Angle : 0.615 4.041 5536 Z= 0.328 Chirality : 0.046 0.123 656 Planarity : 0.003 0.023 672 Dihedral : 20.537 163.552 860 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.19 % Allowed : 23.10 % 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 (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: 0.36 (0.36), residues: 476 helix: -4.87 (0.20), residues: 24 sheet: 0.37 (0.27), residues: 292 loop : 1.21 (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 C 74 PHE 0.017 0.002 PHE B 90 TYR 0.006 0.002 TYR B 57 ARG 0.003 0.001 ARG A 50 *********************** 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: 5 poor density : 76 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7413 (pm20) REVERT: A 114 LYS cc_start: 0.7425 (ptmm) cc_final: 0.6988 (ptmm) REVERT: B 67 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: B 114 LYS cc_start: 0.7413 (ptmm) cc_final: 0.6999 (ptmm) REVERT: C 67 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6896 (pm20) REVERT: C 114 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.6813 (mmmt) REVERT: D 114 LYS cc_start: 0.7418 (ptmm) cc_final: 0.6970 (ptmm) outliers start: 5 outliers final: 1 residues processed: 77 average time/residue: 1.3296 time to fit residues: 105.5307 Evaluate side-chains 80 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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: 1.9990 chunk 36 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.118043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094691 restraints weight = 4665.925| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.27 r_work: 0.3077 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 4072 Z= 0.375 Angle : 0.687 4.955 5536 Z= 0.366 Chirality : 0.049 0.142 656 Planarity : 0.004 0.026 672 Dihedral : 20.724 164.877 860 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.19 % Allowed : 23.81 % 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: 0.28 (0.36), residues: 476 helix: -4.87 (0.20), residues: 24 sheet: 0.31 (0.27), residues: 292 loop : 1.15 (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 D 74 PHE 0.020 0.003 PHE C 90 TYR 0.007 0.002 TYR B 57 ARG 0.004 0.001 ARG A 138 *********************** 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: 5 poor density : 71 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7428 (pm20) REVERT: A 114 LYS cc_start: 0.7378 (ptmm) cc_final: 0.6976 (ptmm) REVERT: B 67 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6935 (pm20) REVERT: B 114 LYS cc_start: 0.7357 (ptmm) cc_final: 0.6986 (ptmm) REVERT: C 67 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6891 (pm20) REVERT: C 114 LYS cc_start: 0.7457 (mmmt) cc_final: 0.6992 (mmmt) REVERT: D 114 LYS cc_start: 0.7405 (ptmm) cc_final: 0.6951 (ptmm) outliers start: 5 outliers final: 3 residues processed: 74 average time/residue: 1.7487 time to fit residues: 133.0771 Evaluate side-chains 76 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.118282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.095088 restraints weight = 4562.452| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.25 r_work: 0.3086 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 4072 Z= 0.346 Angle : 0.656 4.235 5536 Z= 0.353 Chirality : 0.048 0.126 656 Planarity : 0.004 0.025 672 Dihedral : 20.589 163.357 860 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: 0.27 (0.36), residues: 476 helix: -4.87 (0.20), residues: 24 sheet: 0.31 (0.27), residues: 292 loop : 1.14 (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 0.020 0.003 PHE B 90 TYR 0.007 0.002 TYR A 57 ARG 0.004 0.001 ARG D 138 *********************** 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 81 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7452 (pm20) REVERT: A 114 LYS cc_start: 0.7355 (ptmm) cc_final: 0.6952 (ptmm) REVERT: B 67 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6942 (pm20) REVERT: B 114 LYS cc_start: 0.7306 (ptmm) cc_final: 0.6938 (ptmm) REVERT: C 67 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6902 (pm20) REVERT: C 114 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.6963 (mmmt) REVERT: D 114 LYS cc_start: 0.7367 (ptmm) cc_final: 0.6920 (ptmm) outliers start: 7 outliers final: 3 residues processed: 78 average time/residue: 1.3725 time to fit residues: 110.3190 Evaluate side-chains 80 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.120003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097028 restraints weight = 4619.522| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.26 r_work: 0.3121 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 4072 Z= 0.226 Angle : 0.604 4.122 5536 Z= 0.324 Chirality : 0.046 0.144 656 Planarity : 0.003 0.023 672 Dihedral : 20.249 161.521 860 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.43 % Allowed : 23.33 % 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 0.010 0.002 TRP B 121 HIS 0.000 0.000 HIS C 74 PHE 0.016 0.002 PHE A 90 TYR 0.006 0.002 TYR B 57 ARG 0.004 0.001 ARG A 138 *********************** 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 85 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7438 (pm20) REVERT: A 114 LYS cc_start: 0.7313 (ptmm) cc_final: 0.6902 (ptmm) REVERT: B 67 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6956 (pm20) REVERT: B 114 LYS cc_start: 0.7274 (ptmm) cc_final: 0.6887 (ptmm) REVERT: C 67 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: C 114 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6919 (mmmt) REVERT: D 114 LYS cc_start: 0.7350 (ptmm) cc_final: 0.6876 (ptmm) outliers start: 6 outliers final: 0 residues processed: 82 average time/residue: 1.3426 time to fit residues: 113.4771 Evaluate side-chains 81 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 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 43 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 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 = 0.3577 r_free = 0.3577 target = 0.118960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.095804 restraints weight = 4605.985| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.26 r_work: 0.3097 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 4072 Z= 0.325 Angle : 0.665 4.722 5536 Z= 0.358 Chirality : 0.048 0.147 656 Planarity : 0.004 0.024 672 Dihedral : 20.467 162.864 860 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.71 % Allowed : 23.57 % 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 (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: 0.36 (0.36), residues: 476 helix: -4.88 (0.20), residues: 24 sheet: 0.40 (0.27), residues: 292 loop : 1.12 (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 0.019 0.002 PHE B 90 TYR 0.006 0.002 TYR A 57 ARG 0.004 0.001 ARG A 138 ********************** 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 79 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.404 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: 0.7429 (pm20) REVERT: A 114 LYS cc_start: 0.7323 (ptmm) cc_final: 0.6927 (ptmm) REVERT: B 67 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6938 (pm20) REVERT: B 114 LYS cc_start: 0.7306 (ptmm) cc_final: 0.6919 (ptmm) REVERT: C 67 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6896 (pm20) REVERT: C 114 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6989 (mmmt) REVERT: D 114 LYS cc_start: 0.7346 (ptmm) cc_final: 0.6897 (ptmm) outliers start: 3 outliers final: 0 residues processed: 76 average time/residue: 1.3482 time to fit residues: 105.4880 Evaluate side-chains 78 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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: 4.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.121899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.099035 restraints weight = 4613.833| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.27 r_work: 0.3148 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 4072 Z= 0.178 Angle : 0.591 3.838 5536 Z= 0.317 Chirality : 0.045 0.139 656 Planarity : 0.003 0.022 672 Dihedral : 20.080 160.265 860 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.71 % Allowed : 23.57 % 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 (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: 0.50 (0.37), residues: 476 helix: -4.87 (0.19), residues: 24 sheet: 0.52 (0.27), residues: 292 loop : 1.17 (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 C 74 PHE 0.014 0.002 PHE C 90 TYR 0.005 0.001 TYR A 57 ARG 0.003 0.001 ARG B 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4483.59 seconds wall clock time: 79 minutes 25.77 seconds (4765.77 seconds total)