Starting phenix.real_space_refine on Wed Sep 17 02:56:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kap_62213/09_2025/9kap_62213.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kap_62213/09_2025/9kap_62213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kap_62213/09_2025/9kap_62213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kap_62213/09_2025/9kap_62213.map" model { file = "/net/cci-nas-00/data/ceres_data/9kap_62213/09_2025/9kap_62213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kap_62213/09_2025/9kap_62213.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 12 5.16 5 C 540 2.51 5 N 60 2.21 5 O 192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 804 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'BDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'BDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'BDP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'BDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'BDP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'BDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'BDP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'BDP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'BDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'BDP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'BDP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'BDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.17, per 1000 atoms: 0.21 Number of scatterers: 804 At special positions: 0 Unit cell: (47.7, 48.76, 42.4, 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 12 16.00 O 192 8.00 N 60 7.00 C 540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS B 3 " distance=2.09 Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS F 3 " distance=2.09 Simple disulfide: pdb=" SG CYS I 3 " - pdb=" SG CYS J 3 " distance=2.09 Simple disulfide: pdb=" SG CYS M 3 " - pdb=" SG CYS N 3 " distance=2.09 Simple disulfide: pdb=" SG CYS Q 3 " - pdb=" SG CYS R 3 " distance=2.09 Simple disulfide: pdb=" SG CYS U 3 " - pdb=" SG CYS V 3 " distance=2.09 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 10.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 120 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 3 sheets defined 0.0% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'I' and resid 2 through 4 Processing sheet with id=AA3, first strand: chain 'Q' and resid 2 through 4 30 hydrogen bonds defined for protein. 54 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.05 Time building geometry restraints manager: 0.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 209 1.26 - 1.40: 319 1.40 - 1.54: 276 1.54 - 1.68: 24 1.68 - 1.82: 12 Bond restraints: 840 Sorted by residual: bond pdb=" CE1 TYR N 5 " pdb=" CZ TYR N 5 " ideal model delta sigma weight residual 1.378 1.216 0.162 2.40e-02 1.74e+03 4.58e+01 bond pdb=" CE1 TYR F 5 " pdb=" CZ TYR F 5 " ideal model delta sigma weight residual 1.378 1.216 0.162 2.40e-02 1.74e+03 4.58e+01 bond pdb=" CE1 TYR B 5 " pdb=" CZ TYR B 5 " ideal model delta sigma weight residual 1.378 1.216 0.162 2.40e-02 1.74e+03 4.57e+01 bond pdb=" CE1 TYR J 5 " pdb=" CZ TYR J 5 " ideal model delta sigma weight residual 1.378 1.216 0.162 2.40e-02 1.74e+03 4.56e+01 bond pdb=" CE1 TYR R 5 " pdb=" CZ TYR R 5 " ideal model delta sigma weight residual 1.378 1.216 0.162 2.40e-02 1.74e+03 4.56e+01 ... (remaining 835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 840 2.68 - 5.35: 192 5.35 - 8.03: 84 8.03 - 10.70: 24 10.70 - 13.37: 12 Bond angle restraints: 1152 Sorted by residual: angle pdb=" C TYR B 4 " pdb=" N TYR B 5 " pdb=" CA TYR B 5 " ideal model delta sigma weight residual 121.70 112.15 9.55 1.80e+00 3.09e-01 2.81e+01 angle pdb=" C TYR F 4 " pdb=" N TYR F 5 " pdb=" CA TYR F 5 " ideal model delta sigma weight residual 121.70 112.16 9.54 1.80e+00 3.09e-01 2.81e+01 angle pdb=" C TYR J 4 " pdb=" N TYR J 5 " pdb=" CA TYR J 5 " ideal model delta sigma weight residual 121.70 112.17 9.53 1.80e+00 3.09e-01 2.80e+01 angle pdb=" C TYR N 4 " pdb=" N TYR N 5 " pdb=" CA TYR N 5 " ideal model delta sigma weight residual 121.70 112.19 9.51 1.80e+00 3.09e-01 2.79e+01 angle pdb=" C TYR V 4 " pdb=" N TYR V 5 " pdb=" CA TYR V 5 " ideal model delta sigma weight residual 121.70 112.19 9.51 1.80e+00 3.09e-01 2.79e+01 ... (remaining 1147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.86: 492 9.86 - 19.71: 54 19.71 - 29.57: 0 29.57 - 39.42: 12 39.42 - 49.28: 72 Dihedral angle restraints: 630 sinusoidal: 426 harmonic: 204 Sorted by residual: dihedral pdb=" N TYR F 1 " pdb=" C TYR F 1 " pdb=" CA TYR F 1 " pdb=" CB TYR F 1 " ideal model delta harmonic sigma weight residual 122.80 115.61 7.19 0 2.50e+00 1.60e-01 8.27e+00 dihedral pdb=" N TYR V 1 " pdb=" C TYR V 1 " pdb=" CA TYR V 1 " pdb=" CB TYR V 1 " ideal model delta harmonic sigma weight residual 122.80 115.64 7.16 0 2.50e+00 1.60e-01 8.20e+00 dihedral pdb=" N TYR N 1 " pdb=" C TYR N 1 " pdb=" CA TYR N 1 " pdb=" CB TYR N 1 " ideal model delta harmonic sigma weight residual 122.80 115.64 7.16 0 2.50e+00 1.60e-01 8.19e+00 ... (remaining 627 not shown) Histogram of chiral volume deviations from ideal: 0.006 - 0.065: 48 0.065 - 0.125: 0 0.125 - 0.184: 42 0.184 - 0.244: 6 0.244 - 0.304: 24 Chirality restraints: 120 Sorted by residual: chirality pdb=" CA TYR I 5 " pdb=" N TYR I 5 " pdb=" C TYR I 5 " pdb=" CB TYR I 5 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA TYR E 5 " pdb=" N TYR E 5 " pdb=" C TYR E 5 " pdb=" CB TYR E 5 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA TYR R 5 " pdb=" N TYR R 5 " pdb=" C TYR R 5 " pdb=" CB TYR R 5 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 117 not shown) Planarity restraints: 120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 5 " -0.052 2.00e-02 2.50e+03 2.65e-02 1.40e+01 pdb=" CG TYR R 5 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR R 5 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR R 5 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR R 5 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR R 5 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR R 5 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR R 5 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 5 " -0.052 2.00e-02 2.50e+03 2.65e-02 1.40e+01 pdb=" CG TYR V 5 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR V 5 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR V 5 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR V 5 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR V 5 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR V 5 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR V 5 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 5 " -0.052 2.00e-02 2.50e+03 2.64e-02 1.40e+01 pdb=" CG TYR F 5 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR F 5 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR F 5 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR F 5 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR F 5 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR F 5 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR F 5 " -0.028 2.00e-02 2.50e+03 ... (remaining 117 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 264 2.72 - 3.27: 511 3.27 - 3.81: 1176 3.81 - 4.36: 1487 4.36 - 4.90: 2488 Nonbonded interactions: 5926 Sorted by model distance: nonbonded pdb=" CE2 TYR I 4 " pdb=" O5 BDP I 101 " model vdw 2.177 3.340 nonbonded pdb=" CE2 TYR A 4 " pdb=" O5 BDP A 101 " model vdw 2.177 3.340 nonbonded pdb=" CE2 TYR U 4 " pdb=" O5 BDP U 101 " model vdw 2.177 3.340 nonbonded pdb=" CE2 TYR E 4 " pdb=" O5 BDP E 101 " model vdw 2.178 3.340 nonbonded pdb=" CE2 TYR Q 4 " pdb=" O5 BDP Q 101 " model vdw 2.178 3.340 ... (remaining 5921 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' } 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: 0.280 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: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 1.940 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 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 : 0.088 0.200 858 Z= 3.961 Angle : 3.284 13.374 1164 Z= 1.636 Chirality : 0.171 0.304 120 Planarity : 0.015 0.026 120 Dihedral : 19.333 49.275 492 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 26.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.69), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.52), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.052 0.015 TYR R 5 Details of bonding type rmsd covalent geometry : bond 0.08867 ( 840) covalent geometry : angle 3.18782 ( 1152) SS BOND : bond 0.06297 ( 6) SS BOND : angle 8.38881 ( 12) hydrogen bonds : bond 0.23054 ( 30) hydrogen bonds : angle 5.83615 ( 54) Misc. bond : bond 0.01365 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.014 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0071 time to fit residues: 0.1296 Evaluate side-chains 12 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.144755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114362 restraints weight = 903.344| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.37 r_work: 0.3246 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.130 0.370 858 Z= 5.656 Angle : 4.904 27.682 1164 Z= 2.238 Chirality : 0.251 0.750 120 Planarity : 0.026 0.065 120 Dihedral : 27.526 89.857 384 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.00 % Allowed : 18.33 % Favored : 76.67 % Cbeta Deviations : 15.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.35 (0.82), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.63), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.090 0.024 TYR B 5 Details of bonding type rmsd covalent geometry : bond 0.13102 ( 840) covalent geometry : angle 4.78958 ( 1152) SS BOND : bond 0.10563 ( 6) SS BOND : angle 11.43498 ( 12) hydrogen bonds : bond 0.22870 ( 30) hydrogen bonds : angle 7.88173 ( 54) Misc. bond : bond 0.01054 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.014 Fit side-chains REVERT: R 1 TYR cc_start: 0.8775 (t80) cc_final: 0.8512 (t80) outliers start: 3 outliers final: 0 residues processed: 14 average time/residue: 0.0097 time to fit residues: 0.1853 Evaluate side-chains 12 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.143188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112915 restraints weight = 897.880| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.42 r_work: 0.3240 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.131 0.377 858 Z= 5.682 Angle : 5.110 28.458 1164 Z= 2.351 Chirality : 0.264 0.750 120 Planarity : 0.027 0.078 120 Dihedral : 27.325 89.644 384 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.67 % Allowed : 28.33 % Favored : 65.00 % Cbeta Deviations : 20.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.73 (0.81), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.62), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.087 0.024 TYR B 5 Details of bonding type rmsd covalent geometry : bond 0.13164 ( 840) covalent geometry : angle 4.97557 ( 1152) SS BOND : bond 0.13879 ( 6) SS BOND : angle 12.50517 ( 12) hydrogen bonds : bond 0.24345 ( 30) hydrogen bonds : angle 9.20361 ( 54) Misc. bond : bond 0.01076 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1 TYR cc_start: 0.8830 (t80) cc_final: 0.8509 (t80) outliers start: 4 outliers final: 3 residues processed: 20 average time/residue: 0.0087 time to fit residues: 0.2361 Evaluate side-chains 16 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 TYR Chi-restraints excluded: chain E residue 4 TYR Chi-restraints excluded: chain N residue 4 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.143094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.112407 restraints weight = 918.500| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.49 r_work: 0.3260 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.130 0.373 858 Z= 5.658 Angle : 5.176 28.640 1164 Z= 2.383 Chirality : 0.268 0.741 120 Planarity : 0.026 0.066 120 Dihedral : 27.445 88.367 384 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 16.67 % Allowed : 18.33 % Favored : 65.00 % Cbeta Deviations : 21.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.66 (0.87), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.66), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.087 0.024 TYR B 5 Details of bonding type rmsd covalent geometry : bond 0.13034 ( 840) covalent geometry : angle 5.09170 ( 1152) SS BOND : bond 0.14823 ( 6) SS BOND : angle 10.46932 ( 12) hydrogen bonds : bond 0.24245 ( 30) hydrogen bonds : angle 9.12234 ( 54) Misc. bond : bond 0.01041 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 16 time to evaluate : 0.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 2 TYR cc_start: 0.9307 (OUTLIER) cc_final: 0.8882 (p90) REVERT: R 1 TYR cc_start: 0.8771 (t80) cc_final: 0.8495 (t80) outliers start: 10 outliers final: 5 residues processed: 23 average time/residue: 0.0105 time to fit residues: 0.3141 Evaluate side-chains 19 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 TYR Chi-restraints excluded: chain E residue 4 TYR Chi-restraints excluded: chain M residue 2 TYR Chi-restraints excluded: chain M residue 4 TYR Chi-restraints excluded: chain N residue 4 TYR Chi-restraints excluded: chain Q residue 2 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.144205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113035 restraints weight = 943.522| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.74 r_work: 0.3262 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.129 0.374 858 Z= 5.657 Angle : 5.339 42.414 1164 Z= 2.458 Chirality : 0.277 0.768 120 Planarity : 0.026 0.068 120 Dihedral : 27.514 87.372 384 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 20.00 % Allowed : 18.33 % Favored : 61.67 % Cbeta Deviations : 23.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.83 (0.90), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.68), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.088 0.024 TYR B 5 Details of bonding type rmsd covalent geometry : bond 0.13015 ( 840) covalent geometry : angle 5.27358 ( 1152) SS BOND : bond 0.14878 ( 6) SS BOND : angle 9.74940 ( 12) hydrogen bonds : bond 0.24882 ( 30) hydrogen bonds : angle 9.25042 ( 54) Misc. bond : bond 0.01057 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 15 time to evaluate : 0.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 2 TYR cc_start: 0.9274 (OUTLIER) cc_final: 0.8792 (p90) REVERT: R 1 TYR cc_start: 0.8751 (t80) cc_final: 0.8477 (t80) outliers start: 12 outliers final: 5 residues processed: 22 average time/residue: 0.0124 time to fit residues: 0.3689 Evaluate side-chains 19 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 TYR Chi-restraints excluded: chain E residue 4 TYR Chi-restraints excluded: chain M residue 2 TYR Chi-restraints excluded: chain M residue 4 TYR Chi-restraints excluded: chain N residue 4 TYR Chi-restraints excluded: chain Q residue 2 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.143693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112228 restraints weight = 958.157| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.82 r_work: 0.3216 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.129 0.374 858 Z= 5.654 Angle : 5.462 40.920 1164 Z= 2.510 Chirality : 0.286 0.771 120 Planarity : 0.027 0.072 120 Dihedral : 27.560 88.124 384 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 23.33 % Allowed : 15.00 % Favored : 61.67 % Cbeta Deviations : 21.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.50 (0.91), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.69), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.089 0.024 TYR B 5 Details of bonding type rmsd covalent geometry : bond 0.12992 ( 840) covalent geometry : angle 5.43019 ( 1152) SS BOND : bond 0.14531 ( 6) SS BOND : angle 7.94547 ( 12) hydrogen bonds : bond 0.25700 ( 30) hydrogen bonds : angle 9.15962 ( 54) Misc. bond : bond 0.01081 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 15 time to evaluate : 0.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 2 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.8642 (p90) REVERT: R 1 TYR cc_start: 0.8749 (t80) cc_final: 0.8482 (t80) outliers start: 14 outliers final: 6 residues processed: 24 average time/residue: 0.0091 time to fit residues: 0.2880 Evaluate side-chains 22 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 15 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain B residue 4 TYR Chi-restraints excluded: chain E residue 4 TYR Chi-restraints excluded: chain M residue 2 TYR Chi-restraints excluded: chain M residue 4 TYR Chi-restraints excluded: chain N residue 4 TYR Chi-restraints excluded: chain Q residue 2 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.145397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113841 restraints weight = 946.734| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.75 r_work: 0.3242 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.129 0.376 858 Z= 5.647 Angle : 5.590 43.339 1164 Z= 2.569 Chirality : 0.294 0.787 120 Planarity : 0.027 0.079 120 Dihedral : 27.599 88.639 384 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 20.00 % Allowed : 15.00 % Favored : 65.00 % Cbeta Deviations : 23.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.41 (0.90), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.68), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.089 0.024 TYR B 5 Details of bonding type rmsd covalent geometry : bond 0.12956 ( 840) covalent geometry : angle 5.59309 ( 1152) SS BOND : bond 0.13665 ( 6) SS BOND : angle 5.29148 ( 12) hydrogen bonds : bond 0.25932 ( 30) hydrogen bonds : angle 9.12884 ( 54) Misc. bond : bond 0.01090 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 17 time to evaluate : 0.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 2 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.8667 (p90) REVERT: R 1 TYR cc_start: 0.8733 (t80) cc_final: 0.8405 (t80) outliers start: 12 outliers final: 7 residues processed: 25 average time/residue: 0.0111 time to fit residues: 0.3599 Evaluate side-chains 25 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain B residue 4 TYR Chi-restraints excluded: chain E residue 4 TYR Chi-restraints excluded: chain M residue 2 TYR Chi-restraints excluded: chain M residue 4 TYR Chi-restraints excluded: chain N residue 4 TYR Chi-restraints excluded: chain Q residue 2 TYR Chi-restraints excluded: chain Q residue 4 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.145710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113591 restraints weight = 958.001| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.88 r_work: 0.3223 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.129 0.376 858 Z= 5.651 Angle : 5.739 44.495 1164 Z= 2.639 Chirality : 0.299 0.761 120 Planarity : 0.028 0.085 120 Dihedral : 27.630 89.074 384 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 13.33 % Allowed : 20.00 % Favored : 66.67 % Cbeta Deviations : 21.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.91), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.69), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.089 0.024 TYR B 5 Details of bonding type rmsd covalent geometry : bond 0.12962 ( 840) covalent geometry : angle 5.75417 ( 1152) SS BOND : bond 0.13344 ( 6) SS BOND : angle 3.96920 ( 12) hydrogen bonds : bond 0.26309 ( 30) hydrogen bonds : angle 9.13074 ( 54) Misc. bond : bond 0.01109 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 2 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8511 (p90) REVERT: R 1 TYR cc_start: 0.8747 (t80) cc_final: 0.8518 (t80) outliers start: 8 outliers final: 6 residues processed: 24 average time/residue: 0.0089 time to fit residues: 0.2822 Evaluate side-chains 22 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 15 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain B residue 4 TYR Chi-restraints excluded: chain E residue 4 TYR Chi-restraints excluded: chain M residue 2 TYR Chi-restraints excluded: chain M residue 4 TYR Chi-restraints excluded: chain N residue 4 TYR Chi-restraints excluded: chain Q residue 2 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.146768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115663 restraints weight = 934.052| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.72 r_work: 0.3239 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.129 0.376 858 Z= 5.659 Angle : 5.828 44.485 1164 Z= 2.684 Chirality : 0.304 0.741 120 Planarity : 0.028 0.086 120 Dihedral : 27.639 89.364 384 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 15.00 % Allowed : 18.33 % Favored : 66.67 % Cbeta Deviations : 21.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.44 (0.89), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.68), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.088 0.024 TYR B 5 Details of bonding type rmsd covalent geometry : bond 0.12991 ( 840) covalent geometry : angle 5.84387 ( 1152) SS BOND : bond 0.12636 ( 6) SS BOND : angle 4.01363 ( 12) hydrogen bonds : bond 0.26408 ( 30) hydrogen bonds : angle 9.17776 ( 54) Misc. bond : bond 0.01111 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 17 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 2 TYR cc_start: 0.9166 (OUTLIER) cc_final: 0.8507 (p90) REVERT: R 1 TYR cc_start: 0.8812 (t80) cc_final: 0.8576 (t80) outliers start: 9 outliers final: 8 residues processed: 25 average time/residue: 0.0105 time to fit residues: 0.3581 Evaluate side-chains 23 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 14 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain B residue 4 TYR Chi-restraints excluded: chain E residue 4 TYR Chi-restraints excluded: chain M residue 2 TYR Chi-restraints excluded: chain M residue 4 TYR Chi-restraints excluded: chain N residue 4 TYR Chi-restraints excluded: chain Q residue 2 TYR Chi-restraints excluded: chain Q residue 4 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.147607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.116136 restraints weight = 969.040| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.91 r_work: 0.3231 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.129 0.376 858 Z= 5.666 Angle : 5.870 44.301 1164 Z= 2.707 Chirality : 0.305 0.741 120 Planarity : 0.028 0.084 120 Dihedral : 27.645 89.583 384 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 16.67 % Allowed : 21.67 % Favored : 61.67 % Cbeta Deviations : 20.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.41 (0.90), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.68), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.088 0.024 TYR B 5 Details of bonding type rmsd covalent geometry : bond 0.13017 ( 840) covalent geometry : angle 5.88079 ( 1152) SS BOND : bond 0.12780 ( 6) SS BOND : angle 4.67634 ( 12) hydrogen bonds : bond 0.26612 ( 30) hydrogen bonds : angle 9.25040 ( 54) Misc. bond : bond 0.01113 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 16 time to evaluate : 0.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 2 TYR cc_start: 0.9163 (OUTLIER) cc_final: 0.8504 (p90) REVERT: R 1 TYR cc_start: 0.8811 (t80) cc_final: 0.8574 (t80) outliers start: 10 outliers final: 9 residues processed: 24 average time/residue: 0.0091 time to fit residues: 0.2895 Evaluate side-chains 24 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 14 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain B residue 4 TYR Chi-restraints excluded: chain E residue 4 TYR Chi-restraints excluded: chain M residue 2 TYR Chi-restraints excluded: chain M residue 3 CYS Chi-restraints excluded: chain M residue 4 TYR Chi-restraints excluded: chain N residue 4 TYR Chi-restraints excluded: chain Q residue 2 TYR Chi-restraints excluded: chain Q residue 4 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.148112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116676 restraints weight = 945.590| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 3.86 r_work: 0.3229 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.129 0.377 858 Z= 5.657 Angle : 5.885 44.362 1164 Z= 2.711 Chirality : 0.306 0.742 120 Planarity : 0.028 0.085 120 Dihedral : 27.645 89.680 384 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 15.00 % Allowed : 23.33 % Favored : 61.67 % Cbeta Deviations : 21.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.38 (0.90), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.69), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.088 0.024 TYR B 5 Details of bonding type rmsd covalent geometry : bond 0.13004 ( 840) covalent geometry : angle 5.89815 ( 1152) SS BOND : bond 0.12578 ( 6) SS BOND : angle 4.48456 ( 12) hydrogen bonds : bond 0.26328 ( 30) hydrogen bonds : angle 9.29782 ( 54) Misc. bond : bond 0.01118 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 154.74 seconds wall clock time: 3 minutes 30.92 seconds (210.92 seconds total)