Starting phenix.real_space_refine on Fri Aug 22 12:39:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bg9_16027/08_2025/8bg9_16027_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bg9_16027/08_2025/8bg9_16027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bg9_16027/08_2025/8bg9_16027_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bg9_16027/08_2025/8bg9_16027_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bg9_16027/08_2025/8bg9_16027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bg9_16027/08_2025/8bg9_16027.map" } resolution = 3.5 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1074 2.51 5 N 300 2.21 5 O 312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1692 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 0.69, per 1000 atoms: 0.41 Number of scatterers: 1692 At special positions: 0 Unit cell: (86.688, 62.608, 30.1, 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 6 16.00 O 312 8.00 N 300 7.00 C 1074 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: 0.09 Conformation dependent library (CDL) restraints added in 49.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 525 1.34 - 1.46: 483 1.46 - 1.58: 708 1.58 - 1.70: 0 1.70 - 1.82: 12 Bond restraints: 1728 Sorted by residual: bond pdb=" CA SER A 8 " pdb=" CB SER A 8 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.78e-02 3.16e+03 4.06e+00 bond pdb=" CA SER E 8 " pdb=" CB SER E 8 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.78e-02 3.16e+03 4.04e+00 bond pdb=" CA SER D 8 " pdb=" CB SER D 8 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.78e-02 3.16e+03 3.98e+00 bond pdb=" CA SER C 8 " pdb=" CB SER C 8 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.78e-02 3.16e+03 3.98e+00 bond pdb=" CA SER F 8 " pdb=" CB SER F 8 " ideal model delta sigma weight residual 1.529 1.494 0.035 1.78e-02 3.16e+03 3.92e+00 ... (remaining 1723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 1921 1.78 - 3.56: 323 3.56 - 5.33: 51 5.33 - 7.11: 6 7.11 - 8.89: 9 Bond angle restraints: 2310 Sorted by residual: angle pdb=" C TYR E 10 " pdb=" CA TYR E 10 " pdb=" CB TYR E 10 " ideal model delta sigma weight residual 109.72 118.61 -8.89 1.73e+00 3.34e-01 2.64e+01 angle pdb=" C TYR C 10 " pdb=" CA TYR C 10 " pdb=" CB TYR C 10 " ideal model delta sigma weight residual 109.72 118.60 -8.88 1.73e+00 3.34e-01 2.64e+01 angle pdb=" C TYR A 10 " pdb=" CA TYR A 10 " pdb=" CB TYR A 10 " ideal model delta sigma weight residual 109.72 118.60 -8.88 1.73e+00 3.34e-01 2.63e+01 angle pdb=" CB GLU F 11 " pdb=" CG GLU F 11 " pdb=" CD GLU F 11 " ideal model delta sigma weight residual 112.60 120.28 -7.68 1.70e+00 3.46e-01 2.04e+01 angle pdb=" CB GLU D 11 " pdb=" CG GLU D 11 " pdb=" CD GLU D 11 " ideal model delta sigma weight residual 112.60 120.28 -7.68 1.70e+00 3.46e-01 2.04e+01 ... (remaining 2305 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 11.61: 780 11.61 - 23.22: 120 23.22 - 34.82: 42 34.82 - 46.43: 9 46.43 - 58.03: 9 Dihedral angle restraints: 960 sinusoidal: 366 harmonic: 594 Sorted by residual: dihedral pdb=" CA SER F 8 " pdb=" C SER F 8 " pdb=" N GLY F 9 " pdb=" CA GLY F 9 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA SER B 8 " pdb=" C SER B 8 " pdb=" N GLY B 9 " pdb=" CA GLY B 9 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA SER D 8 " pdb=" C SER D 8 " pdb=" N GLY D 9 " pdb=" CA GLY D 9 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 957 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.045: 87 0.045 - 0.087: 62 0.087 - 0.129: 46 0.129 - 0.171: 24 0.171 - 0.213: 15 Chirality restraints: 234 Sorted by residual: chirality pdb=" CA VAL C 18 " pdb=" N VAL C 18 " pdb=" C VAL C 18 " pdb=" CB VAL C 18 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA VAL A 18 " pdb=" N VAL A 18 " pdb=" C VAL A 18 " pdb=" CB VAL A 18 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA VAL E 18 " pdb=" N VAL E 18 " pdb=" C VAL E 18 " pdb=" CB VAL E 18 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 231 not shown) Planarity restraints: 306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 8 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C SER D 8 " -0.028 2.00e-02 2.50e+03 pdb=" O SER D 8 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY D 9 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 8 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C SER B 8 " -0.028 2.00e-02 2.50e+03 pdb=" O SER B 8 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY B 9 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 8 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.58e+00 pdb=" C SER F 8 " -0.028 2.00e-02 2.50e+03 pdb=" O SER F 8 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY F 9 " 0.009 2.00e-02 2.50e+03 ... (remaining 303 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 809 2.97 - 3.45: 1558 3.45 - 3.93: 2520 3.93 - 4.42: 2733 4.42 - 4.90: 4413 Nonbonded interactions: 12033 Sorted by model distance: nonbonded pdb=" OD1 ASP B 7 " pdb=" N GLY B 9 " model vdw 2.484 3.120 nonbonded pdb=" OD1 ASP A 7 " pdb=" N GLY A 9 " model vdw 2.484 3.120 nonbonded pdb=" OD1 ASP D 7 " pdb=" N GLY D 9 " model vdw 2.485 3.120 nonbonded pdb=" OD1 ASP E 7 " pdb=" N GLY E 9 " model vdw 2.485 3.120 nonbonded pdb=" OD1 ASP C 7 " pdb=" N GLY C 9 " model vdw 2.485 3.120 ... (remaining 12028 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.260 Find NCS groups from input model: 0.020 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.008 0.037 1728 Z= 0.474 Angle : 1.465 8.889 2310 Z= 0.953 Chirality : 0.091 0.213 234 Planarity : 0.007 0.043 306 Dihedral : 14.959 58.032 588 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 2.86 % Allowed : 17.14 % Favored : 80.00 % Rotamer: Outliers : 12.50 % Allowed : 23.21 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.16 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.24), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG C 5 TYR 0.020 0.005 TYR D 10 PHE 0.025 0.006 PHE E 19 HIS 0.010 0.003 HIS E 6 Details of bonding type rmsd covalent geometry : bond 0.00760 ( 1728) covalent geometry : angle 1.46463 ( 2310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 35 time to evaluate : 0.037 Fit side-chains REVERT: A 10 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.6820 (t80) REVERT: B 10 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.6877 (t80) REVERT: C 3 GLU cc_start: 0.7759 (mt-10) cc_final: 0.6864 (tt0) REVERT: C 5 ARG cc_start: 0.7757 (ttm170) cc_final: 0.7350 (ttm110) REVERT: C 10 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.6332 (t80) REVERT: D 5 ARG cc_start: 0.7611 (ttt180) cc_final: 0.7382 (mtp180) REVERT: D 10 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.6182 (t80) outliers start: 21 outliers final: 11 residues processed: 55 average time/residue: 0.0337 time to fit residues: 2.1560 Evaluate side-chains 41 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 14 HIS Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 14 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 15 GLN B 13 HIS C 13 HIS C 14 HIS D 13 HIS D 14 HIS E 15 GLN F 13 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.158883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.143982 restraints weight = 2658.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.146799 restraints weight = 1268.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.148740 restraints weight = 802.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.149956 restraints weight = 586.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.150941 restraints weight = 474.973| |-----------------------------------------------------------------------------| r_work (final): 0.4732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 1728 Z= 0.182 Angle : 0.705 7.325 2310 Z= 0.367 Chirality : 0.054 0.144 234 Planarity : 0.003 0.008 306 Dihedral : 9.773 48.202 257 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 8.93 % Allowed : 13.10 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.93 (0.29), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.22), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 5 TYR 0.018 0.004 TYR B 10 PHE 0.011 0.002 PHE F 20 HIS 0.005 0.002 HIS D 13 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 1728) covalent geometry : angle 0.70507 ( 2310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 20 time to evaluate : 0.065 Fit side-chains REVERT: C 5 ARG cc_start: 0.7764 (ttm170) cc_final: 0.7473 (ttm110) REVERT: D 8 SER cc_start: 0.8844 (m) cc_final: 0.8510 (t) REVERT: D 12 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8462 (m) REVERT: E 17 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7857 (tt) outliers start: 15 outliers final: 8 residues processed: 35 average time/residue: 0.0547 time to fit residues: 2.2394 Evaluate side-chains 27 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 17 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain F residue 17 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.0010 chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 overall best weight: 2.3994 ------------------------------------------------------------------------------- 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 = 0.4741 r_free = 0.4741 target = 0.145632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.130354 restraints weight = 2533.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.133371 restraints weight = 1062.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.135424 restraints weight = 638.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.136766 restraints weight = 454.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.137712 restraints weight = 358.630| |-----------------------------------------------------------------------------| r_work (final): 0.4608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 1728 Z= 0.145 Angle : 0.594 6.287 2310 Z= 0.316 Chirality : 0.050 0.147 234 Planarity : 0.002 0.009 306 Dihedral : 7.417 57.223 236 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.76 % Allowed : 13.69 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.21 (0.36), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.27), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 5 TYR 0.020 0.004 TYR B 10 PHE 0.013 0.002 PHE E 4 HIS 0.005 0.001 HIS D 13 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 1728) covalent geometry : angle 0.59419 ( 2310) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.078 Fit side-chains REVERT: C 5 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7527 (ttm170) REVERT: C 8 SER cc_start: 0.8562 (m) cc_final: 0.8237 (t) REVERT: D 5 ARG cc_start: 0.7745 (mtp180) cc_final: 0.7055 (mmm-85) REVERT: D 8 SER cc_start: 0.8834 (m) cc_final: 0.8480 (t) REVERT: D 12 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8064 (m) outliers start: 8 outliers final: 6 residues processed: 28 average time/residue: 0.0652 time to fit residues: 2.1393 Evaluate side-chains 27 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.0060 chunk 2 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- 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 = 0.4764 r_free = 0.4764 target = 0.153391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.138168 restraints weight = 2516.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.141086 restraints weight = 1103.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.142998 restraints weight = 679.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.144362 restraints weight = 492.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.145176 restraints weight = 391.847| |-----------------------------------------------------------------------------| r_work (final): 0.4651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1728 Z= 0.120 Angle : 0.499 5.234 2310 Z= 0.263 Chirality : 0.048 0.139 234 Planarity : 0.001 0.006 306 Dihedral : 6.933 58.679 234 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.17 % Allowed : 14.88 % Favored : 80.95 % 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 aren not related in a simple way. whole: -3.87 (0.40), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.30), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 5 TYR 0.015 0.003 TYR B 10 PHE 0.011 0.002 PHE E 4 HIS 0.004 0.001 HIS D 13 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 1728) covalent geometry : angle 0.49886 ( 2310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.064 Fit side-chains REVERT: C 5 ARG cc_start: 0.8034 (ttm170) cc_final: 0.7455 (mtp180) REVERT: C 8 SER cc_start: 0.8475 (m) cc_final: 0.8188 (t) REVERT: D 5 ARG cc_start: 0.7870 (mtp180) cc_final: 0.7395 (mmm-85) REVERT: D 8 SER cc_start: 0.8713 (m) cc_final: 0.8455 (t) outliers start: 7 outliers final: 7 residues processed: 28 average time/residue: 0.0535 time to fit residues: 1.7614 Evaluate side-chains 25 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 0.0070 chunk 5 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 overall best weight: 2.3604 ------------------------------------------------------------------------------- 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 = 0.4714 r_free = 0.4714 target = 0.148430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.133414 restraints weight = 2638.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.136287 restraints weight = 1144.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.138206 restraints weight = 705.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.139527 restraints weight = 511.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.140332 restraints weight = 408.388| |-----------------------------------------------------------------------------| r_work (final): 0.4596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.6386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1728 Z= 0.134 Angle : 0.511 5.263 2310 Z= 0.272 Chirality : 0.048 0.128 234 Planarity : 0.002 0.007 306 Dihedral : 7.221 59.636 234 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.76 % Allowed : 14.88 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.84 (0.41), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 5 TYR 0.017 0.003 TYR B 10 PHE 0.010 0.001 PHE E 4 HIS 0.004 0.001 HIS D 13 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 1728) covalent geometry : angle 0.51143 ( 2310) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.067 Fit side-chains REVERT: C 5 ARG cc_start: 0.8101 (ttm170) cc_final: 0.7416 (mtp180) REVERT: C 8 SER cc_start: 0.8627 (m) cc_final: 0.8321 (t) REVERT: D 5 ARG cc_start: 0.7996 (mtp180) cc_final: 0.7302 (mmm-85) REVERT: D 8 SER cc_start: 0.8801 (m) cc_final: 0.8504 (t) outliers start: 8 outliers final: 8 residues processed: 26 average time/residue: 0.0611 time to fit residues: 1.8782 Evaluate side-chains 26 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.143326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.129019 restraints weight = 2697.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.131784 restraints weight = 1157.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.133646 restraints weight = 707.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.134855 restraints weight = 512.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.135717 restraints weight = 410.724| |-----------------------------------------------------------------------------| r_work (final): 0.4577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1728 Z= 0.193 Angle : 0.587 5.571 2310 Z= 0.307 Chirality : 0.050 0.136 234 Planarity : 0.002 0.010 306 Dihedral : 7.795 59.930 234 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.76 % Allowed : 15.48 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.99 (0.42), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.32), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 5 TYR 0.022 0.004 TYR B 10 PHE 0.010 0.002 PHE D 20 HIS 0.006 0.002 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 1728) covalent geometry : angle 0.58700 ( 2310) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.065 Fit side-chains REVERT: D 8 SER cc_start: 0.9078 (m) cc_final: 0.8709 (t) outliers start: 8 outliers final: 8 residues processed: 23 average time/residue: 0.0263 time to fit residues: 0.8646 Evaluate side-chains 24 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.138486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.125182 restraints weight = 2681.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.127784 restraints weight = 1188.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.129480 restraints weight = 735.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.130603 restraints weight = 536.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.131402 restraints weight = 429.114| |-----------------------------------------------------------------------------| r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.7291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 1728 Z= 0.266 Angle : 0.670 6.426 2310 Z= 0.350 Chirality : 0.052 0.150 234 Planarity : 0.003 0.011 306 Dihedral : 8.292 59.517 234 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.76 % Allowed : 17.26 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.30 (0.41), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 5 TYR 0.027 0.005 TYR B 10 PHE 0.012 0.002 PHE C 4 HIS 0.007 0.003 HIS E 6 Details of bonding type rmsd covalent geometry : bond 0.00601 ( 1728) covalent geometry : angle 0.66974 ( 2310) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.071 Fit side-chains REVERT: A 3 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7374 (tt0) REVERT: B 5 ARG cc_start: 0.8242 (ttt180) cc_final: 0.8035 (tpp80) REVERT: D 8 SER cc_start: 0.9104 (m) cc_final: 0.8670 (t) outliers start: 8 outliers final: 8 residues processed: 27 average time/residue: 0.0421 time to fit residues: 1.4263 Evaluate side-chains 29 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.4692 r_free = 0.4692 target = 0.145747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.131392 restraints weight = 2590.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.134251 restraints weight = 1136.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.136130 restraints weight = 692.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.137391 restraints weight = 501.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.138293 restraints weight = 399.373| |-----------------------------------------------------------------------------| r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.7538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1728 Z= 0.134 Angle : 0.518 4.663 2310 Z= 0.276 Chirality : 0.048 0.123 234 Planarity : 0.002 0.012 306 Dihedral : 7.355 59.111 234 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.76 % Allowed : 16.07 % Favored : 79.17 % 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 aren not related in a simple way. whole: -4.05 (0.43), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.33), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 5 TYR 0.015 0.003 TYR B 10 PHE 0.007 0.001 PHE E 4 HIS 0.003 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 1728) covalent geometry : angle 0.51773 ( 2310) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.067 Fit side-chains REVERT: A 3 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7311 (tt0) REVERT: E 10 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.6931 (p90) outliers start: 8 outliers final: 7 residues processed: 27 average time/residue: 0.0414 time to fit residues: 1.3743 Evaluate side-chains 26 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.4653 r_free = 0.4653 target = 0.141685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.127513 restraints weight = 2705.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.130316 restraints weight = 1192.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.132103 restraints weight = 732.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.133349 restraints weight = 532.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.134217 restraints weight = 423.688| |-----------------------------------------------------------------------------| r_work (final): 0.4565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.7644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 1728 Z= 0.202 Angle : 0.603 7.567 2310 Z= 0.316 Chirality : 0.050 0.132 234 Planarity : 0.002 0.013 306 Dihedral : 7.890 59.591 234 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 4.76 % Allowed : 17.86 % Favored : 77.38 % 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 aren not related in a simple way. whole: -4.08 (0.43), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.33), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 5 TYR 0.020 0.004 TYR B 10 PHE 0.009 0.002 PHE D 20 HIS 0.005 0.002 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 1728) covalent geometry : angle 0.60350 ( 2310) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.067 Fit side-chains REVERT: A 3 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7204 (tt0) REVERT: E 10 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.6833 (p90) outliers start: 8 outliers final: 7 residues processed: 27 average time/residue: 0.0267 time to fit residues: 1.0036 Evaluate side-chains 28 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.140399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.126313 restraints weight = 2649.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.129026 restraints weight = 1169.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.130766 restraints weight = 726.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.131977 restraints weight = 531.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.132810 restraints weight = 425.136| |-----------------------------------------------------------------------------| r_work (final): 0.4522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.7760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 1728 Z= 0.219 Angle : 0.610 6.890 2310 Z= 0.321 Chirality : 0.050 0.133 234 Planarity : 0.002 0.012 306 Dihedral : 8.014 58.743 234 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.76 % Allowed : 19.05 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.13 (0.42), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.32), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 5 TYR 0.022 0.004 TYR B 10 PHE 0.010 0.002 PHE C 4 HIS 0.006 0.002 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 1728) covalent geometry : angle 0.60986 ( 2310) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.068 Fit side-chains REVERT: A 3 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7326 (tt0) REVERT: E 10 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.6756 (p90) outliers start: 8 outliers final: 7 residues processed: 27 average time/residue: 0.0415 time to fit residues: 1.3999 Evaluate side-chains 28 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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 = 0.4605 r_free = 0.4605 target = 0.138128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.124038 restraints weight = 2754.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.126755 restraints weight = 1222.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.128487 restraints weight = 755.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.129682 restraints weight = 552.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.130520 restraints weight = 441.904| |-----------------------------------------------------------------------------| r_work (final): 0.4517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.7833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 1728 Z= 0.266 Angle : 0.662 8.303 2310 Z= 0.350 Chirality : 0.052 0.140 234 Planarity : 0.003 0.012 306 Dihedral : 8.307 59.089 234 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 4.17 % Allowed : 19.64 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.33 (0.41), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 5 TYR 0.025 0.005 TYR B 10 PHE 0.012 0.002 PHE B 20 HIS 0.007 0.003 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00606 ( 1728) covalent geometry : angle 0.66215 ( 2310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 542.58 seconds wall clock time: 9 minutes 59.60 seconds (599.60 seconds total)