Starting phenix.real_space_refine on Wed Sep 17 23:15:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wz5_21970/09_2025/6wz5_21970.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wz5_21970/09_2025/6wz5_21970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wz5_21970/09_2025/6wz5_21970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wz5_21970/09_2025/6wz5_21970.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wz5_21970/09_2025/6wz5_21970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wz5_21970/09_2025/6wz5_21970.map" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 306 5.49 5 S 12 5.16 5 C 6860 2.51 5 N 2349 2.21 5 O 2916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12443 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 776 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 776 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "I" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3155 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "J" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3118 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Time building chain proxies: 3.10, per 1000 atoms: 0.25 Number of scatterers: 12443 At special positions: 0 Unit cell: (74.2, 116.6, 122.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 306 15.00 O 2916 8.00 N 2349 7.00 C 6860 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: 1.10 Conformation dependent library (CDL) restraints added in 396.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1456 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 71.8% alpha, 3.1% beta 153 base pairs and 280 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.962A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.743A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.335A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 122 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.987A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.706A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.370A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.773A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.695A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.928A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.556A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.789A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.055A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 414 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 392 hydrogen bonds 780 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 280 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1867 1.32 - 1.44: 4639 1.44 - 1.56: 6148 1.56 - 1.68: 610 1.68 - 1.80: 22 Bond restraints: 13286 Sorted by residual: bond pdb=" C LEU D 98 " pdb=" N LEU D 99 " ideal model delta sigma weight residual 1.339 1.251 0.088 5.57e-02 3.22e+02 2.50e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.379 0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.97e+00 bond pdb=" CG1 ILE D 58 " pdb=" CD1 ILE D 58 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.84e+00 bond pdb=" CG1 ILE H 58 " pdb=" CD1 ILE H 58 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.79e+00 ... (remaining 13281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 18574 1.71 - 3.43: 654 3.43 - 5.14: 15 5.14 - 6.85: 4 6.85 - 8.57: 2 Bond angle restraints: 19249 Sorted by residual: angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 113.18 118.95 -5.77 2.37e+00 1.78e-01 5.93e+00 angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 123.83 -3.63 1.50e+00 4.44e-01 5.84e+00 angle pdb=" C3' DC I -26 " pdb=" C2' DC I -26 " pdb=" C1' DC I -26 " ideal model delta sigma weight residual 101.60 98.31 3.29 1.50e+00 4.44e-01 4.82e+00 angle pdb=" C SER H 75 " pdb=" N ARG H 76 " pdb=" CA ARG H 76 " ideal model delta sigma weight residual 121.14 117.37 3.77 1.75e+00 3.27e-01 4.63e+00 angle pdb=" C3' DC I -25 " pdb=" C2' DC I -25 " pdb=" C1' DC I -25 " ideal model delta sigma weight residual 101.60 98.43 3.17 1.50e+00 4.44e-01 4.46e+00 ... (remaining 19244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.12: 5548 33.12 - 66.24: 1634 66.24 - 99.36: 32 99.36 - 132.48: 0 132.48 - 165.60: 2 Dihedral angle restraints: 7216 sinusoidal: 4964 harmonic: 2252 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 54.40 165.60 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 80.87 139.13 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 162.50 17.50 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 7213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1149 0.030 - 0.060: 710 0.060 - 0.090: 252 0.090 - 0.119: 63 0.119 - 0.149: 18 Chirality restraints: 2192 Sorted by residual: chirality pdb=" C4' DA J -35 " pdb=" C5' DA J -35 " pdb=" O4' DA J -35 " pdb=" C3' DA J -35 " both_signs ideal model delta sigma weight residual False -2.53 -2.38 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ARG H 76 " pdb=" N ARG H 76 " pdb=" C ARG H 76 " pdb=" CB ARG H 76 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" C4' DA I 26 " pdb=" C5' DA I 26 " pdb=" O4' DA I 26 " pdb=" C3' DA I 26 " both_signs ideal model delta sigma weight residual False -2.53 -2.39 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 2189 not shown) Planarity restraints: 1372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO E 43 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " 0.028 2.00e-02 2.50e+03 1.22e-02 4.09e+00 pdb=" N9 DA I 47 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " 0.006 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 26 " -0.026 2.00e-02 2.50e+03 1.19e-02 3.92e+00 pdb=" N9 DA I 26 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA I 26 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 26 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 26 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 26 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA I 26 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 26 " 0.001 2.00e-02 2.50e+03 ... (remaining 1369 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2451 2.78 - 3.31: 10584 3.31 - 3.84: 26079 3.84 - 4.37: 31295 4.37 - 4.90: 42128 Nonbonded interactions: 112537 Sorted by model distance: nonbonded pdb=" OE1 GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 2.253 3.120 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.260 3.040 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.320 3.120 nonbonded pdb=" N2 DG I 38 " pdb=" O2 DC J -38 " model vdw 2.329 2.496 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.366 3.040 ... (remaining 112532 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.440 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:8.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 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 0.088 13286 Z= 0.373 Angle : 0.693 8.565 19249 Z= 0.424 Chirality : 0.043 0.149 2192 Planarity : 0.005 0.051 1372 Dihedral : 28.628 165.601 5760 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.93 % Allowed : 3.24 % Favored : 95.83 % 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: -0.00 (0.27), residues: 758 helix: 0.51 (0.20), residues: 552 sheet: None (None), residues: 0 loop : -1.19 (0.35), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 39 TYR 0.014 0.002 TYR G 57 PHE 0.017 0.002 PHE A 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00837 (13286) covalent geometry : angle 0.69294 (19249) hydrogen bonds : bond 0.08467 ( 806) hydrogen bonds : angle 3.42209 ( 1998) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 0.371 Fit side-chains REVERT: G 15 LYS cc_start: 0.7464 (mtpp) cc_final: 0.7220 (mtpt) REVERT: G 24 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7781 (mm-40) REVERT: H 68 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6886 (mp0) outliers start: 6 outliers final: 2 residues processed: 196 average time/residue: 0.9353 time to fit residues: 192.7043 Evaluate side-chains 148 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN C 31 HIS C 104 GLN D 92 GLN E 68 GLN G 31 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 92 GLN H 106 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.111666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.087973 restraints weight = 16905.317| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 0.91 r_work: 0.3141 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13286 Z= 0.230 Angle : 0.663 7.336 19249 Z= 0.393 Chirality : 0.038 0.160 2192 Planarity : 0.005 0.051 1372 Dihedral : 31.498 162.068 4208 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.24 % Allowed : 12.81 % Favored : 83.95 % 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: 1.59 (0.28), residues: 758 helix: 1.72 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.70 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 27 TYR 0.009 0.002 TYR C 57 PHE 0.010 0.002 PHE E 67 HIS 0.011 0.002 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00503 (13286) covalent geometry : angle 0.66308 (19249) hydrogen bonds : bond 0.05244 ( 806) hydrogen bonds : angle 2.98563 ( 1998) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.270 Fit side-chains REVERT: C 15 LYS cc_start: 0.8481 (ttpp) cc_final: 0.7920 (ttmm) REVERT: G 72 ASP cc_start: 0.7892 (m-30) cc_final: 0.7635 (m-30) REVERT: G 104 GLN cc_start: 0.8783 (mt0) cc_final: 0.8515 (mm110) REVERT: H 29 THR cc_start: 0.7832 (t) cc_final: 0.7475 (p) outliers start: 21 outliers final: 0 residues processed: 189 average time/residue: 1.0005 time to fit residues: 198.4478 Evaluate side-chains 162 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN E 68 GLN E 76 GLN G 24 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.108560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.084962 restraints weight = 16830.645| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 0.86 r_work: 0.3079 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.6627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13286 Z= 0.190 Angle : 0.582 7.403 19249 Z= 0.349 Chirality : 0.035 0.127 2192 Planarity : 0.004 0.047 1372 Dihedral : 31.294 163.657 4202 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.70 % Allowed : 13.89 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.29), residues: 758 helix: 2.32 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.44 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.014 0.001 TYR F 51 PHE 0.012 0.002 PHE A 67 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00419 (13286) covalent geometry : angle 0.58215 (19249) hydrogen bonds : bond 0.04487 ( 806) hydrogen bonds : angle 2.78427 ( 1998) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.334 Fit side-chains REVERT: C 15 LYS cc_start: 0.8515 (ttpp) cc_final: 0.7915 (tttm) REVERT: G 73 ASN cc_start: 0.8325 (t0) cc_final: 0.8121 (t0) REVERT: G 74 LYS cc_start: 0.8610 (mppt) cc_final: 0.8376 (mptt) REVERT: H 29 THR cc_start: 0.7866 (t) cc_final: 0.7607 (p) outliers start: 11 outliers final: 6 residues processed: 163 average time/residue: 1.0434 time to fit residues: 178.1541 Evaluate side-chains 158 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 60 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 104 GLN C 110 ASN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.105176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.082019 restraints weight = 16792.056| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 0.89 r_work: 0.3024 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.7322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13286 Z= 0.250 Angle : 0.629 7.152 19249 Z= 0.375 Chirality : 0.038 0.140 2192 Planarity : 0.005 0.050 1372 Dihedral : 31.550 167.285 4202 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.16 % Allowed : 14.51 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.29), residues: 758 helix: 2.25 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.51 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 35 TYR 0.014 0.002 TYR F 51 PHE 0.013 0.002 PHE E 67 HIS 0.006 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00559 (13286) covalent geometry : angle 0.62939 (19249) hydrogen bonds : bond 0.05199 ( 806) hydrogen bonds : angle 2.89957 ( 1998) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.355 Fit side-chains REVERT: C 15 LYS cc_start: 0.8481 (ttpp) cc_final: 0.7892 (ttmm) REVERT: E 94 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: G 73 ASN cc_start: 0.8234 (t0) cc_final: 0.7950 (t0) REVERT: G 74 LYS cc_start: 0.8722 (mppt) cc_final: 0.8493 (mptt) REVERT: G 90 ASP cc_start: 0.8740 (t70) cc_final: 0.8504 (t0) REVERT: H 29 THR cc_start: 0.8035 (t) cc_final: 0.7741 (p) REVERT: H 90 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8231 (mp0) outliers start: 14 outliers final: 10 residues processed: 155 average time/residue: 1.1124 time to fit residues: 180.4623 Evaluate side-chains 160 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.083275 restraints weight = 16937.104| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 0.88 r_work: 0.3052 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13286 Z= 0.194 Angle : 0.584 7.391 19249 Z= 0.351 Chirality : 0.035 0.126 2192 Planarity : 0.005 0.049 1372 Dihedral : 31.308 167.797 4202 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.23 % Allowed : 15.43 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.63 (0.29), residues: 758 helix: 2.47 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.36 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.012 0.001 TYR F 51 PHE 0.013 0.002 PHE A 67 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00428 (13286) covalent geometry : angle 0.58407 (19249) hydrogen bonds : bond 0.04502 ( 806) hydrogen bonds : angle 2.76898 ( 1998) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 0.363 Fit side-chains REVERT: B 24 ASP cc_start: 0.7413 (t70) cc_final: 0.7151 (OUTLIER) REVERT: C 15 LYS cc_start: 0.8415 (ttpp) cc_final: 0.7835 (ttmm) REVERT: G 73 ASN cc_start: 0.8228 (t0) cc_final: 0.7872 (t160) REVERT: G 74 LYS cc_start: 0.8751 (mppt) cc_final: 0.8529 (mptt) REVERT: G 90 ASP cc_start: 0.8678 (t70) cc_final: 0.8453 (t0) REVERT: H 29 THR cc_start: 0.8080 (t) cc_final: 0.7749 (p) REVERT: H 90 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8169 (mp0) outliers start: 8 outliers final: 8 residues processed: 156 average time/residue: 1.0369 time to fit residues: 169.4660 Evaluate side-chains 157 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 92 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.105756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082681 restraints weight = 16730.886| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 0.88 r_work: 0.3040 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.7468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13286 Z= 0.215 Angle : 0.600 7.393 19249 Z= 0.359 Chirality : 0.036 0.125 2192 Planarity : 0.005 0.049 1372 Dihedral : 31.330 168.551 4202 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.01 % Allowed : 14.81 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.29), residues: 758 helix: 2.44 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.32 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 30 TYR 0.011 0.001 TYR F 51 PHE 0.013 0.002 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00479 (13286) covalent geometry : angle 0.59952 (19249) hydrogen bonds : bond 0.04754 ( 806) hydrogen bonds : angle 2.81216 ( 1998) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.334 Fit side-chains REVERT: C 15 LYS cc_start: 0.8375 (ttpp) cc_final: 0.7819 (ttmm) REVERT: G 73 ASN cc_start: 0.8227 (t0) cc_final: 0.7833 (t160) REVERT: G 74 LYS cc_start: 0.8775 (mppt) cc_final: 0.8561 (mptt) REVERT: H 29 THR cc_start: 0.8109 (t) cc_final: 0.7732 (p) REVERT: H 90 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8182 (mp0) outliers start: 13 outliers final: 9 residues processed: 153 average time/residue: 1.1000 time to fit residues: 176.3638 Evaluate side-chains 157 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.106127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.083097 restraints weight = 16623.451| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 0.87 r_work: 0.3046 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.7477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13286 Z= 0.190 Angle : 0.596 7.595 19249 Z= 0.357 Chirality : 0.034 0.126 2192 Planarity : 0.004 0.049 1372 Dihedral : 31.333 168.524 4202 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.39 % Allowed : 15.28 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.29), residues: 758 helix: 2.47 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.31 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 30 TYR 0.011 0.001 TYR B 51 PHE 0.013 0.002 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00418 (13286) covalent geometry : angle 0.59555 (19249) hydrogen bonds : bond 0.04674 ( 806) hydrogen bonds : angle 2.80141 ( 1998) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.363 Fit side-chains REVERT: C 15 LYS cc_start: 0.8368 (ttpp) cc_final: 0.7811 (ttmm) REVERT: G 73 ASN cc_start: 0.8216 (t0) cc_final: 0.7792 (t160) REVERT: G 74 LYS cc_start: 0.8771 (mppt) cc_final: 0.8559 (mptt) REVERT: H 29 THR cc_start: 0.8103 (t) cc_final: 0.7729 (p) REVERT: H 90 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8185 (mp0) outliers start: 9 outliers final: 7 residues processed: 151 average time/residue: 1.1303 time to fit residues: 178.5289 Evaluate side-chains 154 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 63 optimal weight: 0.0770 chunk 92 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.106135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.083108 restraints weight = 16670.096| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 0.87 r_work: 0.3053 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.7483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13286 Z= 0.188 Angle : 0.592 7.394 19249 Z= 0.356 Chirality : 0.034 0.127 2192 Planarity : 0.004 0.049 1372 Dihedral : 31.328 168.643 4202 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.23 % Allowed : 15.90 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.29), residues: 758 helix: 2.46 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.31 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 30 TYR 0.011 0.001 TYR B 51 PHE 0.013 0.002 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00414 (13286) covalent geometry : angle 0.59235 (19249) hydrogen bonds : bond 0.04589 ( 806) hydrogen bonds : angle 2.79439 ( 1998) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.349 Fit side-chains REVERT: C 15 LYS cc_start: 0.8368 (ttpp) cc_final: 0.7818 (ttmm) REVERT: G 73 ASN cc_start: 0.8217 (t0) cc_final: 0.7779 (t160) REVERT: G 74 LYS cc_start: 0.8768 (mppt) cc_final: 0.8556 (mptt) REVERT: H 29 THR cc_start: 0.8105 (t) cc_final: 0.7729 (p) REVERT: H 90 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8183 (mp0) outliers start: 8 outliers final: 9 residues processed: 150 average time/residue: 1.0793 time to fit residues: 169.6348 Evaluate side-chains 156 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.106374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.083318 restraints weight = 16783.308| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 0.89 r_work: 0.3052 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.7522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13286 Z= 0.196 Angle : 0.586 7.288 19249 Z= 0.352 Chirality : 0.035 0.127 2192 Planarity : 0.005 0.048 1372 Dihedral : 31.264 168.979 4202 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.23 % Allowed : 15.59 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.29), residues: 758 helix: 2.51 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.28 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 30 TYR 0.012 0.001 TYR F 51 PHE 0.013 0.002 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00434 (13286) covalent geometry : angle 0.58643 (19249) hydrogen bonds : bond 0.04499 ( 806) hydrogen bonds : angle 2.76540 ( 1998) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.294 Fit side-chains REVERT: C 15 LYS cc_start: 0.8365 (ttpp) cc_final: 0.7817 (ttmm) REVERT: C 90 ASP cc_start: 0.8675 (t70) cc_final: 0.8450 (t0) REVERT: G 73 ASN cc_start: 0.8217 (t0) cc_final: 0.7775 (t160) REVERT: G 74 LYS cc_start: 0.8765 (mppt) cc_final: 0.8557 (mptt) REVERT: H 90 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8161 (mp0) outliers start: 8 outliers final: 8 residues processed: 154 average time/residue: 1.0258 time to fit residues: 165.4942 Evaluate side-chains 157 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 26 optimal weight: 0.0570 chunk 66 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 63 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.106414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083407 restraints weight = 16782.723| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 0.87 r_work: 0.3055 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.7566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13286 Z= 0.195 Angle : 0.589 7.233 19249 Z= 0.353 Chirality : 0.035 0.157 2192 Planarity : 0.005 0.048 1372 Dihedral : 31.227 169.460 4202 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.08 % Allowed : 15.59 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.75 (0.29), residues: 758 helix: 2.58 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.27 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 30 TYR 0.012 0.001 TYR F 51 PHE 0.013 0.002 PHE A 67 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00432 (13286) covalent geometry : angle 0.58854 (19249) hydrogen bonds : bond 0.04482 ( 806) hydrogen bonds : angle 2.76127 ( 1998) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.335 Fit side-chains REVERT: C 15 LYS cc_start: 0.8360 (ttpp) cc_final: 0.7808 (ttmm) REVERT: C 90 ASP cc_start: 0.8684 (t70) cc_final: 0.8448 (t0) REVERT: G 73 ASN cc_start: 0.8216 (t0) cc_final: 0.7780 (t160) REVERT: G 74 LYS cc_start: 0.8764 (mppt) cc_final: 0.8558 (mptt) REVERT: H 29 THR cc_start: 0.8030 (t) cc_final: 0.7690 (p) REVERT: H 90 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8135 (mp0) outliers start: 7 outliers final: 6 residues processed: 154 average time/residue: 1.0464 time to fit residues: 168.8543 Evaluate side-chains 155 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 8 optimal weight: 0.0570 chunk 71 optimal weight: 0.0970 chunk 73 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.106793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.083811 restraints weight = 16683.335| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 0.87 r_work: 0.3062 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.7565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13286 Z= 0.168 Angle : 0.586 7.266 19249 Z= 0.352 Chirality : 0.033 0.149 2192 Planarity : 0.004 0.048 1372 Dihedral : 31.230 169.375 4202 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.54 % Allowed : 15.74 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.78 (0.29), residues: 758 helix: 2.60 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.27 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 96 TYR 0.011 0.001 TYR F 51 PHE 0.012 0.002 PHE A 67 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00365 (13286) covalent geometry : angle 0.58568 (19249) hydrogen bonds : bond 0.04413 ( 806) hydrogen bonds : angle 2.75247 ( 1998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5911.95 seconds wall clock time: 100 minutes 58.39 seconds (6058.39 seconds total)