Starting phenix.real_space_refine on Thu Oct 22 17:11:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kap_62213/10_2026/9kap_62213.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kap_62213/10_2026/9kap_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_62213/10_2026/9kap_62213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kap_62213/10_2026/9kap_62213.map" model { file = "/net/cci-nas-00/data/ceres_data/9kap_62213/10_2026/9kap_62213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kap_62213/10_2026/9kap_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-2.3rc1-6221/lib/python3.11/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: 0.23 Conformation dependent library (CDL) restraints added in 12.1 milliseconds 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: 0.06 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: 0.06 Time building geometry restraints manager: 0.18 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 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: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 2.070 Find NCS groups from input model: 0.000 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: 3.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 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 are 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/Z covalent geometry : bond 0.08867 / 3.99 ( 840) covalent geometry : angle 3.18782 / 1.59 ( 1152) SS BOND : bond 0.06297 / 3.43 ( 6) SS BOND : angle 8.38881 / 4.73 ( 12) hydrogen bonds : bond 0.23054 / 12.85 ( 30) hydrogen bonds : angle 5.83615 / 3.56 ( 54) Misc. bond : bond 0.01365 / 0.66 ( 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 : 0.013 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0065 time to fit residues: 0.1202 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: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.206706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.179481 restraints weight = 687.837| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.57 r_work: 0.4002 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 858 Z= 0.217 Angle : 1.144 14.428 1164 Z= 0.552 Chirality : 0.055 0.284 120 Planarity : 0.002 0.005 120 Dihedral : 5.714 26.202 384 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.00 % Allowed : 0.00 % Favored : 95.00 % 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 are not related in a simple way. whole: -2.71 (0.45), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.34), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR Q 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.21 ( 840) covalent geometry : angle 1.07449 / 0.52 ( 1152) SS BOND : bond 0.01092 / 0.57 ( 6) SS BOND : angle 4.02445 / 2.23 ( 12) hydrogen bonds : bond 0.04400 / 2.72 ( 30) hydrogen bonds : angle 6.06068 / 3.66 ( 54) Misc. bond : bond 0.00211 / 0.10 ( 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 9 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.013 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 9 average time/residue: 0.0122 time to fit residues: 0.1816 Evaluate side-chains 5 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.184784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.155795 restraints weight = 659.897| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 3.00 r_work: 0.3730 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.055 858 Z= 0.420 Angle : 1.249 13.289 1164 Z= 0.611 Chirality : 0.060 0.321 120 Planarity : 0.003 0.007 120 Dihedral : 7.585 38.903 384 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.00 % Allowed : 0.00 % Favored : 95.00 % 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 are not related in a simple way. whole: -2.86 (0.48), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.37), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR M 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00996 / 0.42 ( 840) covalent geometry : angle 1.19654 / 0.59 ( 1152) SS BOND : bond 0.01414 / 0.74 ( 6) SS BOND : angle 3.72486 / 1.97 ( 12) hydrogen bonds : bond 0.05907 / 3.64 ( 30) hydrogen bonds : angle 5.90569 / 3.56 ( 54) Misc. bond : bond 0.00078 / 0.04 ( 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 10 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.013 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 10 average time/residue: 0.0069 time to fit residues: 0.1077 Evaluate side-chains 6 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.187153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.156348 restraints weight = 651.403| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 3.12 r_work: 0.3732 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 858 Z= 0.298 Angle : 1.200 14.473 1164 Z= 0.599 Chirality : 0.058 0.297 120 Planarity : 0.002 0.006 120 Dihedral : 5.623 37.951 384 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.00 % Allowed : 0.00 % Favored : 95.00 % 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 are not related in a simple way. whole: -2.72 (0.46), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.35), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR E 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.30 ( 840) covalent geometry : angle 1.13524 / 0.57 ( 1152) SS BOND : bond 0.01455 / 0.78 ( 6) SS BOND : angle 4.00407 / 2.12 ( 12) hydrogen bonds : bond 0.05679 / 3.45 ( 30) hydrogen bonds : angle 5.48919 / 3.32 ( 54) Misc. bond : bond 0.00102 / 0.05 ( 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 9 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.013 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 9 average time/residue: 0.0109 time to fit residues: 0.1527 Evaluate side-chains 5 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.187087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.154656 restraints weight = 673.058| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 3.33 r_work: 0.3706 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.056 858 Z= 0.419 Angle : 1.347 15.658 1164 Z= 0.664 Chirality : 0.065 0.306 120 Planarity : 0.003 0.008 120 Dihedral : 6.763 42.107 384 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.00 % Allowed : 0.00 % Favored : 95.00 % 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 are not related in a simple way. whole: -2.74 (0.48), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.37), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYR M 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00988 / 0.42 ( 840) covalent geometry : angle 1.28096 / 0.63 ( 1152) SS BOND : bond 0.01746 / 0.92 ( 6) SS BOND : angle 4.30907 / 2.37 ( 12) hydrogen bonds : bond 0.06296 / 3.85 ( 30) hydrogen bonds : angle 6.13520 / 3.70 ( 54) Misc. bond : bond 0.00061 / 0.03 ( 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 10 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.016 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 10 average time/residue: 0.0080 time to fit residues: 0.1299 Evaluate side-chains 5 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.189867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.159403 restraints weight = 663.664| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 3.10 r_work: 0.3763 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 858 Z= 0.297 Angle : 1.447 16.233 1164 Z= 0.721 Chirality : 0.069 0.337 120 Planarity : 0.002 0.007 120 Dihedral : 5.735 40.695 384 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.67 % Allowed : 0.00 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.61), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.46), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR E 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.29 ( 840) covalent geometry : angle 1.33158 / 0.67 ( 1152) SS BOND : bond 0.01496 / 0.78 ( 6) SS BOND : angle 5.72954 / 2.95 ( 12) hydrogen bonds : bond 0.05988 / 3.73 ( 30) hydrogen bonds : angle 5.70065 / 3.42 ( 54) Misc. bond : bond 0.00056 / 0.03 ( 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 10 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 6 time to evaluate : 0.013 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 10 average time/residue: 0.0070 time to fit residues: 0.1097 Evaluate side-chains 6 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.186700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.153849 restraints weight = 664.752| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 3.32 r_work: 0.3694 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.048 858 Z= 0.412 Angle : 1.630 19.813 1164 Z= 0.805 Chirality : 0.079 0.380 120 Planarity : 0.003 0.008 120 Dihedral : 6.358 41.836 384 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.00 % Allowed : 6.67 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.75), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.57), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYR M 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00950 / 0.41 ( 840) covalent geometry : angle 1.51076 / 0.75 ( 1152) SS BOND : bond 0.01893 / 1.00 ( 6) SS BOND : angle 6.20751 / 3.22 ( 12) hydrogen bonds : bond 0.06731 / 4.25 ( 30) hydrogen bonds : angle 5.99456 / 3.56 ( 54) Misc. bond : bond 0.00066 / 0.03 ( 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 9 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.013 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 9 average time/residue: 0.0070 time to fit residues: 0.1006 Evaluate side-chains 7 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.188121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.156995 restraints weight = 672.002| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.22 r_work: 0.3722 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 858 Z= 0.310 Angle : 1.656 17.547 1164 Z= 0.826 Chirality : 0.080 0.359 120 Planarity : 0.002 0.006 120 Dihedral : 5.634 42.447 384 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.00 % Allowed : 11.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.67), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.51), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR E 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.30 ( 840) covalent geometry : angle 1.51861 / 0.76 ( 1152) SS BOND : bond 0.01689 / 0.93 ( 6) SS BOND : angle 6.67352 / 3.29 ( 12) hydrogen bonds : bond 0.06503 / 3.98 ( 30) hydrogen bonds : angle 5.86776 / 3.49 ( 54) Misc. bond : bond 0.00056 / 0.03 ( 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 8 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 5 time to evaluate : 0.013 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 7 average time/residue: 0.0072 time to fit residues: 0.0845 Evaluate side-chains 6 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 5 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.185733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.154752 restraints weight = 651.681| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 3.15 r_work: 0.3695 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.055 858 Z= 0.419 Angle : 1.794 22.035 1164 Z= 0.888 Chirality : 0.086 0.397 120 Planarity : 0.003 0.008 120 Dihedral : 6.202 44.876 384 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.00 % Allowed : 10.00 % Favored : 85.00 % 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 are not related in a simple way. whole: -1.65 (0.78), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.59), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYR M 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00961 / 0.41 ( 840) covalent geometry : angle 1.65787 / 0.83 ( 1152) SS BOND : bond 0.02059 / 1.12 ( 6) SS BOND : angle 6.94515 / 3.48 ( 12) hydrogen bonds : bond 0.07177 / 4.42 ( 30) hydrogen bonds : angle 6.20719 / 3.71 ( 54) Misc. bond : bond 0.00066 / 0.03 ( 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 9 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.014 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 9 average time/residue: 0.0084 time to fit residues: 0.1229 Evaluate side-chains 7 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.187214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.155679 restraints weight = 671.516| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 3.27 r_work: 0.3736 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 858 Z= 0.313 Angle : 1.756 21.074 1164 Z= 0.873 Chirality : 0.083 0.398 120 Planarity : 0.002 0.006 120 Dihedral : 5.659 44.354 384 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.67 % Allowed : 13.33 % Favored : 85.00 % 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 are not related in a simple way. whole: -1.19 (0.84), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.89 (0.64), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR M 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.31 ( 840) covalent geometry : angle 1.61184 / 0.81 ( 1152) SS BOND : bond 0.01792 / 0.97 ( 6) SS BOND : angle 7.04908 / 3.51 ( 12) hydrogen bonds : bond 0.06869 / 4.25 ( 30) hydrogen bonds : angle 6.13887 / 3.66 ( 54) Misc. bond : bond 0.00058 / 0.03 ( 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 5 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.016 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 5 average time/residue: 0.0079 time to fit residues: 0.0719 Evaluate side-chains 5 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.184228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.153890 restraints weight = 666.072| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 3.09 r_work: 0.3716 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.052 858 Z= 0.416 Angle : 1.831 21.493 1164 Z= 0.906 Chirality : 0.087 0.401 120 Planarity : 0.003 0.008 120 Dihedral : 6.236 46.086 384 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.67 % Allowed : 13.33 % Favored : 85.00 % 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 are not related in a simple way. whole: -1.18 (0.86), residues: 36 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.89 (0.65), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYR M 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00949 / 0.41 ( 840) covalent geometry : angle 1.69023 / 0.84 ( 1152) SS BOND : bond 0.02063 / 1.13 ( 6) SS BOND : angle 7.14862 / 3.59 ( 12) hydrogen bonds : bond 0.07325 / 4.56 ( 30) hydrogen bonds : angle 6.32327 / 3.79 ( 54) Misc. bond : bond 0.00064 / 0.03 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 159.34 seconds wall clock time: 3 minutes 39.94 seconds (219.94 seconds total)