Starting phenix.real_space_refine on Thu Sep 10 21:34:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7efd_31084/09_2026/7efd_31084.cif Found real_map, /net/cci-nas-00/data/ceres_data/7efd_31084/09_2026/7efd_31084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7efd_31084/09_2026/7efd_31084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7efd_31084/09_2026/7efd_31084.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7efd_31084/09_2026/7efd_31084.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7efd_31084/09_2026/7efd_31084.cif" model { file = "/net/cci-nas-00/data/ceres_data/7efd_31084/09_2026/7efd_31084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7efd_31084/09_2026/7efd_31084.cif" } resolution = 1.77 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= 0.007 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 4 5.16 5 C 2392 2.51 5 N 668 2.21 5 O 940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4004 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 946 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 120, 896 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Conformer: "B" Number of residues, atoms: 120, 896 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} bond proxies already assigned to first conformer: 867 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 40, 55 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1, 'water': 39} Link IDs: {None: 39} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Restraints were copied for chains: B, C, D Residues with excluded nonbonded symmetry interactions: 56 residue: pdb=" N ASER A 45 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 45 " occ=0.50 residue: pdb=" N AALA A 46 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 46 " occ=0.50 residue: pdb=" N AVAL A 47 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 47 " occ=0.50 residue: pdb=" N AGLY A 48 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 48 " occ=0.50 residue: pdb=" N AASN A 49 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 49 " occ=0.50 residue: pdb=" N AALA A 50 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 50 " occ=0.50 residue: pdb=" N AGLU A 51 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 51 " occ=0.50 residue: pdb=" N ASER A 52 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 52 " occ=0.50 residue: pdb=" C10ABTN A5100 " occ=0.50 ... (14 atoms not shown) pdb=" S1 ABTN A5100 " occ=0.50 residue: pdb=" O HOH A5223 " occ=0.50 residue: pdb=" O AHOH A5225 " occ=0.50 residue: pdb=" O AHOH A5226 " occ=0.50 ... (remaining 44 not shown) Time building chain proxies: 1.06, per 1000 atoms: 0.26 Number of scatterers: 4004 At special positions: 0 Unit cell: (68.8516, 64.4096, 58.4869, 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 4 16.00 O 940 8.00 N 668 7.00 C 2392 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: 0.23 Conformation dependent library (CDL) restraints added in 228.6 milliseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 5.8% alpha, 53.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP A 120 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP B 120 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP C 120 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP D 120 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG A 53 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS A 80 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER A 88 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'B' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG B 53 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS B 80 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER B 88 " --> pdb=" O TRP B 79 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG C 53 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS C 80 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER C 88 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'D' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG D 53 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS D 80 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER D 88 " --> pdb=" O TRP D 79 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 540 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: 0.58 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 540 1.28 - 1.42: 876 1.42 - 1.55: 2196 1.55 - 1.68: 324 1.68 - 1.82: 8 Bond restraints: 3944 Sorted by residual: bond pdb=" C THR A 42 " pdb=" O THR A 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C THR B 42 " pdb=" O THR B 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C THR D 42 " pdb=" O THR D 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C THR C 42 " pdb=" O THR C 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C GLY D 94 " pdb=" O GLY D 94 " ideal model delta sigma weight residual 1.232 1.313 -0.082 1.05e-02 9.07e+03 6.03e+01 ... (remaining 3939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 3452 2.76 - 5.51: 1456 5.51 - 8.26: 432 8.26 - 11.01: 40 11.01 - 13.77: 20 Bond angle restraints: 5400 Sorted by residual: angle pdb=" CA PHE A 29 " pdb=" CB PHE A 29 " pdb=" CG PHE A 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA PHE C 29 " pdb=" CB PHE C 29 " pdb=" CG PHE C 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA PHE B 29 " pdb=" CB PHE B 29 " pdb=" CG PHE B 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA PHE D 29 " pdb=" CB PHE D 29 " pdb=" CG PHE D 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA ILE A 17 " pdb=" C ILE A 17 " pdb=" O ILE A 17 " ideal model delta sigma weight residual 120.85 110.32 10.53 1.06e+00 8.90e-01 9.87e+01 ... (remaining 5395 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.60: 1956 16.60 - 33.19: 144 33.19 - 49.79: 28 49.79 - 66.38: 12 66.38 - 82.98: 12 Dihedral angle restraints: 2152 sinusoidal: 728 harmonic: 1424 Sorted by residual: dihedral pdb=" CA ASER C 52 " pdb=" C ASER C 52 " pdb=" N ARG C 53 " pdb=" CA ARG C 53 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASER B 52 " pdb=" C ASER B 52 " pdb=" N ARG B 53 " pdb=" CA ARG B 53 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASER D 52 " pdb=" C ASER D 52 " pdb=" N ARG D 53 " pdb=" CA ARG D 53 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 2149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 424 0.083 - 0.166: 152 0.166 - 0.248: 20 0.248 - 0.331: 0 0.331 - 0.414: 8 Chirality restraints: 604 Sorted by residual: chirality pdb=" CB VAL D 125 " pdb=" CA VAL D 125 " pdb=" CG1 VAL D 125 " pdb=" CG2 VAL D 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB VAL A 125 " pdb=" CA VAL A 125 " pdb=" CG1 VAL A 125 " pdb=" CG2 VAL A 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB VAL C 125 " pdb=" CA VAL C 125 " pdb=" CG1 VAL C 125 " pdb=" CG2 VAL C 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 601 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 ABTN D5100 " 0.059 2.00e-02 2.50e+03 2.01e-01 6.08e+02 pdb=" C4 ABTN D5100 " -0.164 2.00e-02 2.50e+03 pdb=" C5 ABTN D5100 " -0.156 2.00e-02 2.50e+03 pdb=" N1 ABTN D5100 " 0.250 2.00e-02 2.50e+03 pdb=" N2 ABTN D5100 " 0.257 2.00e-02 2.50e+03 pdb=" O3 ABTN D5100 " -0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 ABTN B5100 " 0.059 2.00e-02 2.50e+03 2.01e-01 6.08e+02 pdb=" C4 ABTN B5100 " -0.164 2.00e-02 2.50e+03 pdb=" C5 ABTN B5100 " -0.156 2.00e-02 2.50e+03 pdb=" N1 ABTN B5100 " 0.250 2.00e-02 2.50e+03 pdb=" N2 ABTN B5100 " 0.257 2.00e-02 2.50e+03 pdb=" O3 ABTN B5100 " -0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 ABTN A5100 " -0.059 2.00e-02 2.50e+03 2.01e-01 6.08e+02 pdb=" C4 ABTN A5100 " 0.164 2.00e-02 2.50e+03 pdb=" C5 ABTN A5100 " 0.156 2.00e-02 2.50e+03 pdb=" N1 ABTN A5100 " -0.250 2.00e-02 2.50e+03 pdb=" N2 ABTN A5100 " -0.257 2.00e-02 2.50e+03 pdb=" O3 ABTN A5100 " 0.245 2.00e-02 2.50e+03 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 2 0.98 - 1.96: 0 1.96 - 2.94: 1410 2.94 - 3.92: 11570 3.92 - 4.90: 22800 Warning: very small nonbonded interaction distances. Nonbonded interactions: 35782 Sorted by model distance: nonbonded pdb=" O HOH A5223 " pdb=" O HOH C5223 " model vdw 0.001 3.040 nonbonded pdb=" O HOH B5223 " pdb=" O HOH D5223 " model vdw 0.001 3.040 nonbonded pdb=" O AASN A 49 " pdb=" OD1AASN A 49 " model vdw 2.212 3.040 nonbonded pdb=" O AASN B 49 " pdb=" OD1AASN B 49 " model vdw 2.212 3.040 nonbonded pdb=" O AASN D 49 " pdb=" OD1AASN D 49 " model vdw 2.212 3.040 ... (remaining 35777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.50 max=1.00 mean=0.94 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.910 Find NCS groups from input model: 0.030 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 0.033 0.119 3944 Z= 2.183 Angle : 3.163 13.767 5400 Z= 2.200 Chirality : 0.091 0.414 604 Planarity : 0.015 0.201 684 Dihedral : 15.471 82.977 1264 Min Nonbonded Distance : 0.001 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.85 % Allowed : 1.69 % Favored : 97.46 % Rotamer: Outliers : 2.15 % Allowed : 4.30 % Favored : 93.55 % Cbeta Deviations : 2.70 % 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: -0.54 (0.34), residues: 512 helix: None (None), residues: 0 sheet: 0.53 (0.31), residues: 224 loop : -1.12 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 103 TYR 0.002 0.001 TYR D 60 PHE 0.002 0.001 PHE C 130 TRP 0.004 0.001 TRP B 92 HIS 0.001 0.000 HIS B 127 Details of bonding type rmsd/Z covalent geometry : bond 0.03266 / 2.18 ( 3944) covalent geometry : angle 3.16286 / 2.20 ( 5400) hydrogen bonds : bond 0.15084 / 10.02 ( 208) hydrogen bonds : angle 9.35849 / 6.38 ( 540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8196 (m) cc_final: 0.7701 (p) REVERT: A 103 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7455 (ttp80) REVERT: B 27 SER cc_start: 0.8197 (m) cc_final: 0.7701 (p) REVERT: B 103 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7455 (ttp80) REVERT: C 27 SER cc_start: 0.8195 (m) cc_final: 0.7701 (p) REVERT: C 103 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7454 (ttp80) REVERT: D 27 SER cc_start: 0.8197 (m) cc_final: 0.7702 (p) REVERT: D 103 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7454 (ttp80) outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 0.5914 time to fit residues: 39.0282 Evaluate side-chains 60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 GLN A 118 ASN B 107 GLN B 118 ASN C 107 GLN C 118 ASN D 107 GLN D 118 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.176969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.155179 restraints weight = 4438.571| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.33 r_work: 0.3726 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (11 function evaluations) r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3944 Z= 0.171 Angle : 0.743 7.681 5400 Z= 0.409 Chirality : 0.044 0.130 604 Planarity : 0.003 0.014 684 Dihedral : 8.155 44.744 576 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.85 % Allowed : 0.85 % Favored : 98.31 % Rotamer: Outliers : 1.08 % Allowed : 7.53 % Favored : 91.40 % 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: 0.63 (0.38), residues: 512 helix: None (None), residues: 0 sheet: 0.26 (0.25), residues: 320 loop : 1.02 (0.57), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 103 TYR 0.012 0.002 TYR C 22 PHE 0.021 0.004 PHE A 29 TRP 0.014 0.003 TRP D 21 HIS 0.003 0.002 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 ( 3944) covalent geometry : angle 0.74259 / 0.41 ( 5400) hydrogen bonds : bond 0.04859 / 3.29 ( 208) hydrogen bonds : angle 7.62736 / 5.22 ( 540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7679 (ttp80) REVERT: B 53 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7680 (ttp80) REVERT: C 53 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7683 (ttp80) REVERT: D 53 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7686 (ttp80) outliers start: 4 outliers final: 0 residues processed: 76 average time/residue: 0.5612 time to fit residues: 44.0019 Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.4135 r_free = 0.4135 target = 0.175236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.154826 restraints weight = 3307.303| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 0.94 r_work: 0.3793 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3944 Z= 0.288 Angle : 0.856 7.801 5400 Z= 0.467 Chirality : 0.049 0.143 604 Planarity : 0.005 0.030 684 Dihedral : 7.877 47.796 572 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.85 % Allowed : 3.39 % Favored : 95.76 % Rotamer: Outliers : 2.15 % Allowed : 9.68 % Favored : 88.17 % 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: 1.17 (0.39), residues: 512 helix: None (None), residues: 0 sheet: 0.74 (0.26), residues: 292 loop : 1.07 (0.54), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 103 TYR 0.012 0.004 TYR B 54 PHE 0.034 0.006 PHE A 29 TRP 0.016 0.004 TRP D 92 HIS 0.005 0.003 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.29 ( 3944) covalent geometry : angle 0.85634 / 0.47 ( 5400) hydrogen bonds : bond 0.05706 / 3.85 ( 208) hydrogen bonds : angle 8.04095 / 5.48 ( 540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 68 average time/residue: 0.6737 time to fit residues: 47.0112 Evaluate side-chains 72 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain D residue 107 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.175680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.155123 restraints weight = 4212.352| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.24 r_work: 0.3752 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3944 Z= 0.225 Angle : 0.728 5.694 5400 Z= 0.406 Chirality : 0.046 0.147 604 Planarity : 0.004 0.024 684 Dihedral : 7.573 45.623 572 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.85 % Allowed : 3.39 % Favored : 95.76 % Rotamer: Outliers : 1.08 % Allowed : 11.83 % Favored : 87.10 % 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: 1.04 (0.37), residues: 512 helix: None (None), residues: 0 sheet: 0.78 (0.26), residues: 292 loop : 0.76 (0.50), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 103 TYR 0.012 0.003 TYR C 22 PHE 0.026 0.005 PHE B 29 TRP 0.014 0.003 TRP D 92 HIS 0.004 0.002 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.22 ( 3944) covalent geometry : angle 0.72827 / 0.41 ( 5400) hydrogen bonds : bond 0.05381 / 3.63 ( 208) hydrogen bonds : angle 7.82703 / 5.35 ( 540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8470 (mt0) REVERT: C 107 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8460 (mt0) REVERT: D 107 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8463 (mt0) outliers start: 4 outliers final: 0 residues processed: 64 average time/residue: 0.7316 time to fit residues: 48.0875 Evaluate side-chains 67 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain D residue 107 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.177060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.156390 restraints weight = 4532.198| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.27 r_work: 0.3767 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3944 Z= 0.157 Angle : 0.637 5.284 5400 Z= 0.354 Chirality : 0.043 0.146 604 Planarity : 0.003 0.018 684 Dihedral : 6.976 41.500 572 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.08 % Allowed : 11.83 % Favored : 87.10 % 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: 1.24 (0.37), residues: 512 helix: None (None), residues: 0 sheet: 0.81 (0.26), residues: 296 loop : 1.06 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 103 TYR 0.012 0.002 TYR B 22 PHE 0.018 0.003 PHE C 29 TRP 0.012 0.002 TRP A 108 HIS 0.003 0.001 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 ( 3944) covalent geometry : angle 0.63662 / 0.35 ( 5400) hydrogen bonds : bond 0.04859 / 3.30 ( 208) hydrogen bonds : angle 7.58181 / 5.19 ( 540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8350 (mt0) REVERT: C 107 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8359 (mt0) REVERT: D 107 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8353 (mt0) outliers start: 4 outliers final: 0 residues processed: 64 average time/residue: 0.6875 time to fit residues: 45.1942 Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain D residue 107 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 4 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 0.0870 chunk 47 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN B 82 ASN C 82 ASN D 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.175456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.155518 restraints weight = 4101.167| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.20 r_work: 0.3745 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3944 Z= 0.210 Angle : 0.699 5.560 5400 Z= 0.387 Chirality : 0.046 0.147 604 Planarity : 0.004 0.021 684 Dihedral : 7.409 45.090 572 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.85 % Allowed : 3.39 % Favored : 95.76 % Rotamer: Outliers : 0.81 % Allowed : 13.17 % Favored : 86.02 % 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: 1.16 (0.37), residues: 512 helix: None (None), residues: 0 sheet: 0.74 (0.26), residues: 296 loop : 1.05 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 103 TYR 0.012 0.003 TYR D 22 PHE 0.016 0.003 PHE B 29 TRP 0.013 0.003 TRP D 92 HIS 0.003 0.002 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.21 ( 3944) covalent geometry : angle 0.69928 / 0.39 ( 5400) hydrogen bonds : bond 0.05318 / 3.61 ( 208) hydrogen bonds : angle 7.79685 / 5.33 ( 540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 64 average time/residue: 0.7699 time to fit residues: 50.4889 Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN B 82 ASN C 82 ASN D 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.175117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.155336 restraints weight = 4007.843| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.18 r_work: 0.3756 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3944 Z= 0.230 Angle : 0.714 5.337 5400 Z= 0.397 Chirality : 0.046 0.145 604 Planarity : 0.004 0.024 684 Dihedral : 7.464 45.385 572 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.85 % Allowed : 2.54 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 13.98 % Favored : 86.02 % 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: 1.11 (0.37), residues: 512 helix: None (None), residues: 0 sheet: 0.75 (0.26), residues: 296 loop : 0.93 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 103 TYR 0.012 0.003 TYR D 22 PHE 0.017 0.004 PHE C 29 TRP 0.014 0.003 TRP C 92 HIS 0.004 0.002 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.23 ( 3944) covalent geometry : angle 0.71359 / 0.40 ( 5400) hydrogen bonds : bond 0.05405 / 3.66 ( 208) hydrogen bonds : angle 7.84836 / 5.36 ( 540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.7272 time to fit residues: 47.8043 Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN B 82 ASN C 82 ASN D 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.175717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.156540 restraints weight = 3736.350| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.12 r_work: 0.3769 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3944 Z= 0.191 Angle : 0.666 5.070 5400 Z= 0.371 Chirality : 0.044 0.144 604 Planarity : 0.004 0.019 684 Dihedral : 7.302 44.309 572 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.85 % Allowed : 2.54 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 15.05 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.17 (0.37), residues: 512 helix: None (None), residues: 0 sheet: 0.80 (0.26), residues: 296 loop : 0.96 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 103 TYR 0.012 0.002 TYR B 22 PHE 0.014 0.003 PHE B 29 TRP 0.013 0.003 TRP C 92 HIS 0.003 0.002 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 ( 3944) covalent geometry : angle 0.66557 / 0.37 ( 5400) hydrogen bonds : bond 0.05129 / 3.48 ( 208) hydrogen bonds : angle 7.74315 / 5.30 ( 540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.7013 time to fit residues: 48.8781 Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 42 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN B 82 ASN C 82 ASN D 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.176240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.157140 restraints weight = 3752.463| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.05 r_work: 0.3793 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3944 Z= 0.169 Angle : 0.661 7.161 5400 Z= 0.360 Chirality : 0.044 0.143 604 Planarity : 0.003 0.017 684 Dihedral : 7.106 42.844 572 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 15.05 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.27 (0.37), residues: 512 helix: None (None), residues: 0 sheet: 0.83 (0.26), residues: 296 loop : 1.08 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 103 TYR 0.013 0.002 TYR C 22 PHE 0.012 0.003 PHE C 29 TRP 0.012 0.003 TRP C 92 HIS 0.003 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 ( 3944) covalent geometry : angle 0.66126 / 0.36 ( 5400) hydrogen bonds : bond 0.04960 / 3.36 ( 208) hydrogen bonds : angle 7.67569 / 5.25 ( 540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.6926 time to fit residues: 48.3309 Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN B 82 ASN C 82 ASN D 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.175923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.156216 restraints weight = 3992.724| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.18 r_work: 0.3755 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3944 Z= 0.178 Angle : 0.670 6.718 5400 Z= 0.367 Chirality : 0.045 0.164 604 Planarity : 0.004 0.018 684 Dihedral : 7.181 43.603 572 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 15.05 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.22 (0.37), residues: 512 helix: None (None), residues: 0 sheet: 0.84 (0.26), residues: 296 loop : 0.98 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 103 TYR 0.013 0.002 TYR C 22 PHE 0.014 0.003 PHE C 29 TRP 0.012 0.003 TRP D 92 HIS 0.003 0.001 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 ( 3944) covalent geometry : angle 0.67036 / 0.37 ( 5400) hydrogen bonds : bond 0.05060 / 3.43 ( 208) hydrogen bonds : angle 7.71484 / 5.28 ( 540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.7664 time to fit residues: 50.2785 Evaluate side-chains 60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 20 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 0.0070 chunk 31 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 overall best weight: 1.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN B 82 ASN C 82 ASN D 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.176094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.151150 restraints weight = 5206.486| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.30 r_work: 0.3761 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3944 Z= 0.129 Angle : 0.614 7.597 5400 Z= 0.332 Chirality : 0.043 0.143 604 Planarity : 0.003 0.013 684 Dihedral : 6.660 39.875 572 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 15.05 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.29 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.95 (0.26), residues: 296 loop : 0.90 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.010 0.002 TYR B 22 PHE 0.011 0.003 PHE C 29 TRP 0.012 0.002 TRP A 108 HIS 0.002 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 3944) covalent geometry : angle 0.61418 / 0.33 ( 5400) hydrogen bonds : bond 0.04598 / 3.12 ( 208) hydrogen bonds : angle 7.43185 / 5.10 ( 540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2222.16 seconds wall clock time: 38 minutes 50.25 seconds (2330.25 seconds total)