Starting phenix.real_space_refine on Tue Feb 3 12:20:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kzo_62666/02_2026/9kzo_62666.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kzo_62666/02_2026/9kzo_62666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kzo_62666/02_2026/9kzo_62666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kzo_62666/02_2026/9kzo_62666.map" model { file = "/net/cci-nas-00/data/ceres_data/9kzo_62666/02_2026/9kzo_62666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kzo_62666/02_2026/9kzo_62666.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 3 Type Number sf(0) Gaussians C 972 2.51 5 N 303 2.21 5 O 363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1638 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 98 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "E" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 100 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "N" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 135 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "H" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 82 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "K" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 131 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 98 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "D" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 100 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "M" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 135 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "G" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 82 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "J" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 131 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 98 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "F" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 100 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "O" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 135 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "I" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 82 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "L" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 131 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Time building chain proxies: 0.56, per 1000 atoms: 0.34 Number of scatterers: 1638 At special positions: 0 Unit cell: (48.97, 94.62, 33.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 363 8.00 N 303 7.00 C 972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.12 Conformation dependent library (CDL) restraints added in 74.8 milliseconds 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 288 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.527A pdb=" N VAL E 38 " --> pdb=" O ILE F 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 55 through 56 removed outlier: 6.334A pdb=" N VAL N 55 " --> pdb=" O ILE M 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 42 through 44 removed outlier: 6.174A pdb=" N VAL H 43 " --> pdb=" O ILE G 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 57 through 58 removed outlier: 6.616A pdb=" N VAL K 57 " --> pdb=" O ILE J 58 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP K 56 " --> pdb=" O VAL L 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 6 hydrogen bonds defined for protein. 18 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: 0.16 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 354 1.29 - 1.36: 288 1.36 - 1.43: 63 1.43 - 1.49: 281 1.49 - 1.56: 646 Bond restraints: 1632 Sorted by residual: bond pdb=" CB VAL H 43 " pdb=" CG2 VAL H 43 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.75e+00 bond pdb=" CB VAL I 43 " pdb=" CG2 VAL I 43 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.75e+00 bond pdb=" CB VAL G 43 " pdb=" CG2 VAL G 43 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.75e+00 bond pdb=" CA LEU J 48 " pdb=" C LEU J 48 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.80e-02 3.09e+03 1.80e+00 bond pdb=" CA VAL M 58 " pdb=" CB VAL M 58 " ideal model delta sigma weight residual 1.544 1.560 -0.016 1.49e-02 4.50e+03 1.09e+00 ... (remaining 1627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 1944 1.37 - 2.74: 174 2.74 - 4.11: 18 4.11 - 5.48: 11 5.48 - 6.85: 7 Bond angle restraints: 2154 Sorted by residual: angle pdb=" N GLU N 57 " pdb=" CA GLU N 57 " pdb=" C GLU N 57 " ideal model delta sigma weight residual 110.56 117.41 -6.85 1.94e+00 2.66e-01 1.25e+01 angle pdb=" N GLU M 57 " pdb=" CA GLU M 57 " pdb=" C GLU M 57 " ideal model delta sigma weight residual 110.56 117.23 -6.67 1.94e+00 2.66e-01 1.18e+01 angle pdb=" C ILE N 56 " pdb=" N GLU N 57 " pdb=" CA GLU N 57 " ideal model delta sigma weight residual 121.71 117.31 4.40 1.39e+00 5.18e-01 1.00e+01 angle pdb=" CA TYR O 66 " pdb=" CB TYR O 66 " pdb=" CG TYR O 66 " ideal model delta sigma weight residual 113.90 119.12 -5.22 1.80e+00 3.09e-01 8.40e+00 angle pdb=" CA LEU J 48 " pdb=" C LEU J 48 " pdb=" N GLY J 49 " ideal model delta sigma weight residual 118.27 122.62 -4.35 1.59e+00 3.96e-01 7.49e+00 ... (remaining 2149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 728 17.48 - 34.96: 56 34.96 - 52.45: 11 52.45 - 69.93: 6 69.93 - 87.41: 3 Dihedral angle restraints: 804 sinusoidal: 249 harmonic: 555 Sorted by residual: dihedral pdb=" CA GLU N 57 " pdb=" C GLU N 57 " pdb=" N VAL N 58 " pdb=" CA VAL N 58 " ideal model delta harmonic sigma weight residual -180.00 -154.01 -25.99 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA GLU M 57 " pdb=" C GLU M 57 " pdb=" N VAL M 58 " pdb=" CA VAL M 58 " ideal model delta harmonic sigma weight residual 180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA GLU O 57 " pdb=" C GLU O 57 " pdb=" N VAL O 58 " pdb=" CA VAL O 58 " ideal model delta harmonic sigma weight residual 180.00 -156.04 -23.96 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 127 0.049 - 0.098: 24 0.098 - 0.147: 38 0.147 - 0.197: 6 0.197 - 0.246: 3 Chirality restraints: 198 Sorted by residual: chirality pdb=" CB VAL G 43 " pdb=" CA VAL G 43 " pdb=" CG1 VAL G 43 " pdb=" CG2 VAL G 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB VAL H 43 " pdb=" CA VAL H 43 " pdb=" CG1 VAL H 43 " pdb=" CG2 VAL H 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB VAL I 43 " pdb=" CA VAL I 43 " pdb=" CG1 VAL I 43 " pdb=" CG2 VAL I 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 195 not shown) Planarity restraints: 321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 66 " -0.018 2.00e-02 2.50e+03 1.03e-02 2.13e+00 pdb=" CG TYR N 66 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR N 66 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR N 66 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR N 66 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR N 66 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR N 66 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 66 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 66 " -0.016 2.00e-02 2.50e+03 1.01e-02 2.06e+00 pdb=" CG TYR O 66 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR O 66 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR O 66 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR O 66 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR O 66 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR O 66 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR O 66 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 66 " -0.016 2.00e-02 2.50e+03 9.89e-03 1.96e+00 pdb=" CG TYR M 66 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR M 66 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR M 66 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR M 66 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR M 66 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR M 66 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR M 66 " -0.003 2.00e-02 2.50e+03 ... (remaining 318 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 922 3.04 - 3.50: 1302 3.50 - 3.97: 2178 3.97 - 4.43: 2437 4.43 - 4.90: 4747 Nonbonded interactions: 11586 Sorted by model distance: nonbonded pdb=" N GLY H 38 " pdb=" N ALA H 39 " model vdw 2.569 2.560 nonbonded pdb=" N GLY G 38 " pdb=" N ALA G 39 " model vdw 2.569 2.560 nonbonded pdb=" N GLY I 38 " pdb=" N ALA I 39 " model vdw 2.569 2.560 nonbonded pdb=" N ARG E 26 " pdb=" O ARG F 26 " model vdw 2.598 3.120 nonbonded pdb=" N ALA F 34 " pdb=" O ALA F 34 " model vdw 2.613 2.496 ... (remaining 11581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = (chain 'M' and resid 45 through 66) selection = (chain 'N' and resid 45 through 66) selection = (chain 'O' and resid 45 through 66) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.950 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 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 : 0.005 0.055 1632 Z= 0.219 Angle : 0.934 6.855 2154 Z= 0.516 Chirality : 0.073 0.246 198 Planarity : 0.002 0.010 321 Dihedral : 14.968 87.409 516 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.58 % Favored : 86.42 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % 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: -5.82 (0.20), residues: 243 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.43 (0.15), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG F 26 TYR 0.023 0.004 TYR O 66 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 1632) covalent geometry : angle 0.93382 ( 2154) hydrogen bonds : bond 0.28657 ( 6) hydrogen bonds : angle 7.74029 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.054 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0277 time to fit residues: 0.5223 Evaluate side-chains 11 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.149595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.129044 restraints weight = 2078.745| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 2.61 r_work: 0.4170 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.4052 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1632 Z= 0.164 Angle : 0.809 6.079 2154 Z= 0.424 Chirality : 0.065 0.165 198 Planarity : 0.002 0.013 321 Dihedral : 6.424 23.758 270 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 5.13 % Allowed : 12.82 % Favored : 82.05 % 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: -5.28 (0.26), residues: 243 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.20), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 26 TYR 0.028 0.004 TYR N 66 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 1632) covalent geometry : angle 0.80878 ( 2154) hydrogen bonds : bond 0.02470 ( 6) hydrogen bonds : angle 4.88214 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.055 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 14 average time/residue: 0.0255 time to fit residues: 0.5318 Evaluate side-chains 13 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain I residue 43 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 4 optimal weight: 0.0570 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.144230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.123864 restraints weight = 2158.729| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.47 r_work: 0.4154 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4052 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 1632 Z= 0.215 Angle : 0.897 6.146 2154 Z= 0.475 Chirality : 0.065 0.162 198 Planarity : 0.004 0.023 321 Dihedral : 6.866 23.041 270 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.46 % Favored : 83.54 % Rotamer: Outliers : 4.27 % Allowed : 23.93 % Favored : 71.79 % 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: -5.24 (0.26), residues: 243 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.20), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 26 TYR 0.040 0.006 TYR N 66 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 1632) covalent geometry : angle 0.89723 ( 2154) hydrogen bonds : bond 0.02793 ( 6) hydrogen bonds : angle 4.64870 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 12 time to evaluate : 0.055 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 15 average time/residue: 0.0258 time to fit residues: 0.5698 Evaluate side-chains 12 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.0470 chunk 15 optimal weight: 0.0040 overall best weight: 0.3290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.153204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.134639 restraints weight = 2053.856| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 2.30 r_work: 0.4254 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4141 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1632 Z= 0.110 Angle : 0.678 6.024 2154 Z= 0.351 Chirality : 0.059 0.149 198 Planarity : 0.002 0.011 321 Dihedral : 5.491 21.162 270 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.98 % Allowed : 24.79 % Favored : 69.23 % 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: -4.77 (0.29), residues: 243 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.22), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 26 TYR 0.013 0.002 TYR N 66 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 1632) covalent geometry : angle 0.67788 ( 2154) hydrogen bonds : bond 0.01740 ( 6) hydrogen bonds : angle 4.77234 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.055 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 13 average time/residue: 0.0258 time to fit residues: 0.5040 Evaluate side-chains 15 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 9 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain I residue 43 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 14 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- 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 = 0.4479 r_free = 0.4479 target = 0.148503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.128552 restraints weight = 2104.489| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 2.43 r_work: 0.4182 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4067 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1632 Z= 0.167 Angle : 0.784 5.758 2154 Z= 0.411 Chirality : 0.060 0.151 198 Planarity : 0.003 0.016 321 Dihedral : 6.058 22.979 270 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 6.84 % Allowed : 24.79 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.73 (0.29), residues: 243 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.22), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 26 TYR 0.030 0.005 TYR N 66 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 1632) covalent geometry : angle 0.78424 ( 2154) hydrogen bonds : bond 0.01689 ( 6) hydrogen bonds : angle 4.47327 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 9 time to evaluate : 0.055 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 14 average time/residue: 0.0249 time to fit residues: 0.5180 Evaluate side-chains 14 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 9 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain I residue 43 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4470 r_free = 0.4470 target = 0.147777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.128637 restraints weight = 2080.802| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 2.23 r_work: 0.4179 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4072 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1632 Z= 0.171 Angle : 0.807 5.802 2154 Z= 0.422 Chirality : 0.061 0.154 198 Planarity : 0.003 0.019 321 Dihedral : 6.110 23.306 270 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 5.98 % Allowed : 25.64 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.73 (0.29), residues: 243 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.22), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 26 TYR 0.030 0.005 TYR N 66 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 1632) covalent geometry : angle 0.80728 ( 2154) hydrogen bonds : bond 0.01730 ( 6) hydrogen bonds : angle 4.54041 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.055 Fit side-chains REVERT: K 58 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7919 (tt) outliers start: 7 outliers final: 3 residues processed: 13 average time/residue: 0.0251 time to fit residues: 0.4911 Evaluate side-chains 11 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 7 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain I residue 43 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4466 r_free = 0.4466 target = 0.147670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.128275 restraints weight = 2086.857| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 2.24 r_work: 0.4221 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4128 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1632 Z= 0.172 Angle : 0.810 5.720 2154 Z= 0.423 Chirality : 0.061 0.154 198 Planarity : 0.003 0.018 321 Dihedral : 6.115 23.574 270 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.35 % Favored : 87.65 % Rotamer: Outliers : 5.98 % Allowed : 26.50 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.74 (0.29), residues: 243 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.22), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 26 TYR 0.031 0.005 TYR N 66 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 1632) covalent geometry : angle 0.81001 ( 2154) hydrogen bonds : bond 0.01732 ( 6) hydrogen bonds : angle 4.55742 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.054 Fit side-chains REVERT: K 58 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7903 (tt) outliers start: 7 outliers final: 3 residues processed: 13 average time/residue: 0.0251 time to fit residues: 0.4924 Evaluate side-chains 12 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 8 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain I residue 43 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.144437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.123754 restraints weight = 2097.478| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 2.37 r_work: 0.4107 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3997 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 1632 Z= 0.248 Angle : 0.947 6.763 2154 Z= 0.501 Chirality : 0.065 0.168 198 Planarity : 0.004 0.027 321 Dihedral : 6.820 25.662 270 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.99 % Favored : 86.01 % Rotamer: Outliers : 5.13 % Allowed : 26.50 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.93 (0.29), residues: 243 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.22), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 26 TYR 0.044 0.007 TYR N 66 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 1632) covalent geometry : angle 0.94654 ( 2154) hydrogen bonds : bond 0.01890 ( 6) hydrogen bonds : angle 4.54349 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.035 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 13 average time/residue: 0.0164 time to fit residues: 0.3219 Evaluate side-chains 12 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain I residue 43 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 0.0070 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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 = 0.4484 r_free = 0.4484 target = 0.148469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.128240 restraints weight = 2076.848| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 2.39 r_work: 0.4210 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4109 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1632 Z= 0.148 Angle : 0.771 5.566 2154 Z= 0.402 Chirality : 0.061 0.156 198 Planarity : 0.003 0.016 321 Dihedral : 5.884 23.328 270 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 3.42 % Allowed : 29.06 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.29), residues: 243 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.22), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 26 TYR 0.025 0.004 TYR N 66 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 1632) covalent geometry : angle 0.77148 ( 2154) hydrogen bonds : bond 0.01762 ( 6) hydrogen bonds : angle 4.65815 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 9 time to evaluate : 0.054 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 11 average time/residue: 0.0270 time to fit residues: 0.4500 Evaluate side-chains 10 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain I residue 43 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4474 r_free = 0.4474 target = 0.147420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.126821 restraints weight = 2101.822| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.42 r_work: 0.4158 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4043 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1632 Z= 0.177 Angle : 0.829 5.767 2154 Z= 0.432 Chirality : 0.062 0.154 198 Planarity : 0.003 0.018 321 Dihedral : 6.216 24.425 270 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 3.42 % Allowed : 27.35 % Favored : 69.23 % 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: -4.75 (0.29), residues: 243 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.22), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 26 TYR 0.032 0.005 TYR N 66 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 1632) covalent geometry : angle 0.82858 ( 2154) hydrogen bonds : bond 0.01718 ( 6) hydrogen bonds : angle 4.53440 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 9 time to evaluate : 0.032 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 12 average time/residue: 0.0159 time to fit residues: 0.2862 Evaluate side-chains 12 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain I residue 43 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4499 r_free = 0.4499 target = 0.149827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.130658 restraints weight = 2067.657| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 2.26 r_work: 0.4240 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4143 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1632 Z= 0.140 Angle : 0.749 5.522 2154 Z= 0.389 Chirality : 0.060 0.150 198 Planarity : 0.002 0.016 321 Dihedral : 5.728 23.220 270 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 2.56 % Allowed : 29.06 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.64 (0.29), residues: 243 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.22), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 26 TYR 0.024 0.004 TYR N 66 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 1632) covalent geometry : angle 0.74851 ( 2154) hydrogen bonds : bond 0.01680 ( 6) hydrogen bonds : angle 4.57519 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 675.45 seconds wall clock time: 12 minutes 7.63 seconds (727.63 seconds total)