Starting phenix.real_space_refine on Fri Sep 11 16:51:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xnp_33322/09_2026/7xnp_33322.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnp_33322/09_2026/7xnp_33322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xnp_33322/09_2026/7xnp_33322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnp_33322/09_2026/7xnp_33322.map" model { file = "/net/cci-nas-00/data/ceres_data/7xnp_33322/09_2026/7xnp_33322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnp_33322/09_2026/7xnp_33322.cif" } resolution = 2.9 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= 0.008 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 245 5.49 5 S 12 5.16 5 C 6107 2.51 5 N 2058 2.21 5 O 2521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10943 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 750 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2535 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "J" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2505 Classifications: {'DNA': 123} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 122} Time building chain proxies: 2.78, per 1000 atoms: 0.25 Number of scatterers: 10943 At special positions: 0 Unit cell: (97.836, 123.084, 109.408, 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 245 15.00 O 2521 8.00 N 2058 7.00 C 6107 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: 0.83 Conformation dependent library (CDL) restraints added in 231.3 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 9 sheets defined 72.0% alpha, 2.9% beta 123 base pairs and 227 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.580A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) 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: 3.804A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.570A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.437A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.517A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 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 removed outlier: 3.504A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.653A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.814A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.624A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.302A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.550A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.627A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.522A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.098A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.216A 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 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.869A 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: 6.938A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 395 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 318 hydrogen bonds 632 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 227 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2006 1.33 - 1.45: 3792 1.45 - 1.57: 5324 1.57 - 1.69: 489 1.69 - 1.81: 22 Bond restraints: 11633 Sorted by residual: bond pdb=" C3' DT J 34 " pdb=" C2' DT J 34 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DG I 4 " pdb=" C2' DG I 4 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" C5' DA I 47 " pdb=" C4' DA I 47 " ideal model delta sigma weight residual 1.512 1.537 -0.025 7.00e-03 2.04e+04 1.25e+01 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.435 1.480 -0.045 1.30e-02 5.92e+03 1.21e+01 bond pdb=" C5' DC I -26 " pdb=" C4' DC I -26 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.20e+01 ... (remaining 11628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 15517 1.71 - 3.41: 1178 3.41 - 5.12: 51 5.12 - 6.82: 9 6.82 - 8.53: 7 Bond angle restraints: 16762 Sorted by residual: angle pdb=" O5' DA I 47 " pdb=" C5' DA I 47 " pdb=" C4' DA I 47 " ideal model delta sigma weight residual 109.40 113.19 -3.79 8.00e-01 1.56e+00 2.25e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.73 -2.83 6.00e-01 2.78e+00 2.23e+01 angle pdb=" N3 DT I 67 " pdb=" C4 DT I 67 " pdb=" O4 DT I 67 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" O5' DG I 57 " pdb=" C5' DG I 57 " pdb=" C4' DG I 57 " ideal model delta sigma weight residual 109.40 113.01 -3.61 8.00e-01 1.56e+00 2.04e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 ... (remaining 16757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 5149 35.05 - 70.10: 1191 70.10 - 105.15: 17 105.15 - 140.20: 1 140.20 - 175.25: 2 Dihedral angle restraints: 6360 sinusoidal: 4201 harmonic: 2159 Sorted by residual: 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 -159.08 -20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 35.25 -175.25 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC J 21 " pdb=" C3' DC J 21 " pdb=" O3' DC J 21 " pdb=" P DC J 22 " ideal model delta sinusoidal sigma weight residual 220.00 72.16 147.84 1 3.50e+01 8.16e-04 1.45e+01 ... (remaining 6357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1378 0.051 - 0.101: 442 0.101 - 0.152: 81 0.152 - 0.203: 10 0.203 - 0.254: 2 Chirality restraints: 1913 Sorted by residual: chirality pdb=" CA GLU H 110 " pdb=" N GLU H 110 " pdb=" C GLU H 110 " pdb=" CB GLU H 110 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" P DC J 22 " pdb=" OP1 DC J 22 " pdb=" OP2 DC J 22 " pdb=" O5' DC J 22 " both_signs ideal model delta sigma weight residual True 2.34 -2.56 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C3' DG I 4 " pdb=" C4' DG I 4 " pdb=" O3' DG I 4 " pdb=" C2' DG I 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.03e-01 ... (remaining 1910 not shown) Planarity restraints: 1271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO C 80 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO G 80 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -26 " 0.031 2.00e-02 2.50e+03 1.60e-02 5.75e+00 pdb=" N1 DC I -26 " -0.032 2.00e-02 2.50e+03 pdb=" C2 DC I -26 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC I -26 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC I -26 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DC I -26 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC I -26 " 0.011 2.00e-02 2.50e+03 pdb=" C5 DC I -26 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DC I -26 " -0.003 2.00e-02 2.50e+03 ... (remaining 1268 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2503 2.82 - 3.34: 8917 3.34 - 3.86: 21917 3.86 - 4.38: 25725 4.38 - 4.90: 36485 Nonbonded interactions: 95547 Sorted by model distance: nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.297 3.040 nonbonded pdb=" N2 DG I -21 " pdb=" O2 DC J 21 " model vdw 2.326 2.496 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.371 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.376 3.040 nonbonded pdb=" NH2 ARG C 88 " pdb=" O VAL C 100 " model vdw 2.387 3.120 ... (remaining 95542 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' and resid 43 through 133) selection = (chain 'E' and resid 43 through 133) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 117) } 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: 0.830 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.650 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 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 : 0.006 0.048 11633 Z= 0.562 Angle : 0.889 8.527 16762 Z= 0.740 Chirality : 0.050 0.254 1913 Planarity : 0.006 0.070 1271 Dihedral : 27.194 175.251 4968 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.27), residues: 730 helix: -0.52 (0.19), residues: 534 sheet: None (None), residues: 0 loop : -0.46 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 49 TYR 0.019 0.002 TYR B 88 PHE 0.014 0.002 PHE H 67 HIS 0.006 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.56 (11633) covalent geometry : angle 0.88885 / 0.74 (16762) hydrogen bonds : bond 0.10344 / 7.04 ( 713) hydrogen bonds : angle 4.30712 / 3.08 ( 1805) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.289 Fit side-chains REVERT: A 118 THR cc_start: 0.8782 (m) cc_final: 0.8543 (m) REVERT: C 95 LYS cc_start: 0.7302 (mmpt) cc_final: 0.7097 (mtmt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.8725 time to fit residues: 97.2903 Evaluate side-chains 91 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 93 GLN C 89 ASN G 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.192910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.161952 restraints weight = 10611.286| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 0.71 r_work: 0.3550 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11633 Z= 0.143 Angle : 0.655 7.911 16762 Z= 0.382 Chirality : 0.048 0.241 1913 Planarity : 0.005 0.053 1271 Dihedral : 30.664 171.100 3504 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.62 % Allowed : 7.11 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.29), residues: 730 helix: 1.09 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.34 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.014 0.001 TYR G 57 PHE 0.008 0.001 PHE H 67 HIS 0.002 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (11633) covalent geometry : angle 0.65542 / 0.38 (16762) hydrogen bonds : bond 0.05170 / 3.59 ( 713) hydrogen bonds : angle 3.11434 / 2.21 ( 1805) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.278 Fit side-chains REVERT: C 88 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6906 (mpt90) REVERT: C 95 LYS cc_start: 0.7335 (mmpt) cc_final: 0.7048 (mmpt) REVERT: F 91 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7808 (ttpp) REVERT: G 92 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7789 (mt-10) outliers start: 10 outliers final: 3 residues processed: 100 average time/residue: 0.7808 time to fit residues: 82.5028 Evaluate side-chains 98 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 44 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 66 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 73 optimal weight: 40.0000 chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN D 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.187219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.155265 restraints weight = 10630.833| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 0.64 r_work: 0.3498 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11633 Z= 0.220 Angle : 0.726 8.569 16762 Z= 0.410 Chirality : 0.052 0.232 1913 Planarity : 0.006 0.050 1271 Dihedral : 30.930 172.625 3504 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.55 % Allowed : 8.56 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.29), residues: 730 helix: 1.33 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.48 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 96 TYR 0.017 0.002 TYR D 37 PHE 0.016 0.003 PHE H 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.22 (11633) covalent geometry : angle 0.72631 / 0.41 (16762) hydrogen bonds : bond 0.05864 / 4.01 ( 713) hydrogen bonds : angle 3.15513 / 2.21 ( 1805) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: C 88 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.7090 (mmp80) REVERT: C 95 LYS cc_start: 0.7357 (mmpt) cc_final: 0.7028 (mmpt) REVERT: E 64 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8105 (mptt) REVERT: E 76 GLN cc_start: 0.7863 (tt0) cc_final: 0.7511 (pt0) REVERT: E 120 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7579 (mtt) REVERT: G 92 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: H 90 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6080 (mp0) outliers start: 22 outliers final: 9 residues processed: 103 average time/residue: 0.8085 time to fit residues: 87.9439 Evaluate side-chains 109 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 89 ASN D 92 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.189032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.156734 restraints weight = 10660.616| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 0.68 r_work: 0.3503 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11633 Z= 0.151 Angle : 0.665 8.249 16762 Z= 0.382 Chirality : 0.049 0.235 1913 Planarity : 0.005 0.045 1271 Dihedral : 30.939 171.161 3504 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.75 % Allowed : 9.69 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.29), residues: 730 helix: 1.72 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.38 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 96 TYR 0.017 0.001 TYR G 57 PHE 0.012 0.002 PHE F 61 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (11633) covalent geometry : angle 0.66481 / 0.38 (16762) hydrogen bonds : bond 0.05109 / 3.52 ( 713) hydrogen bonds : angle 2.99228 / 2.10 ( 1805) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.296 Fit side-chains REVERT: B 52 GLU cc_start: 0.7336 (tp30) cc_final: 0.6859 (mp0) REVERT: C 88 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.7079 (mmp80) REVERT: C 95 LYS cc_start: 0.7351 (mmpt) cc_final: 0.7015 (mmpt) REVERT: E 64 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8027 (mptt) REVERT: E 76 GLN cc_start: 0.7868 (tt0) cc_final: 0.7484 (pt0) REVERT: E 120 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7508 (mtt) REVERT: F 91 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7867 (ttmt) REVERT: G 92 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: H 90 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6556 (mp0) outliers start: 17 outliers final: 7 residues processed: 103 average time/residue: 0.7536 time to fit residues: 82.2345 Evaluate side-chains 105 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 62 optimal weight: 0.0020 chunk 41 optimal weight: 0.9980 overall best weight: 1.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 89 ASN D 92 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.189304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.157108 restraints weight = 10616.107| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 0.67 r_work: 0.3512 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11633 Z= 0.141 Angle : 0.655 7.978 16762 Z= 0.378 Chirality : 0.048 0.227 1913 Planarity : 0.004 0.044 1271 Dihedral : 30.936 171.002 3504 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.58 % Allowed : 11.47 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.30), residues: 730 helix: 1.84 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.37 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 96 TYR 0.016 0.001 TYR G 57 PHE 0.012 0.002 PHE F 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (11633) covalent geometry : angle 0.65457 / 0.38 (16762) hydrogen bonds : bond 0.05048 / 3.48 ( 713) hydrogen bonds : angle 2.96995 / 2.09 ( 1805) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: C 88 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7112 (mmp80) REVERT: C 95 LYS cc_start: 0.7321 (mmpt) cc_final: 0.6964 (mmpt) REVERT: E 64 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8022 (mptt) REVERT: E 76 GLN cc_start: 0.7843 (tt0) cc_final: 0.7442 (pt0) REVERT: E 120 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7519 (mtt) REVERT: F 91 LYS cc_start: 0.8193 (ttpt) cc_final: 0.7858 (ttmt) REVERT: G 92 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: H 90 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6157 (mp0) outliers start: 16 outliers final: 8 residues processed: 98 average time/residue: 0.7594 time to fit residues: 78.7623 Evaluate side-chains 106 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 18 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 89 ASN D 92 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.189373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.157219 restraints weight = 10638.301| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 0.67 r_work: 0.3513 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11633 Z= 0.154 Angle : 0.654 8.143 16762 Z= 0.377 Chirality : 0.048 0.232 1913 Planarity : 0.004 0.045 1271 Dihedral : 30.933 170.579 3504 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.91 % Allowed : 11.15 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.30), residues: 730 helix: 1.91 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.37 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 88 TYR 0.014 0.001 TYR G 57 PHE 0.012 0.002 PHE F 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (11633) covalent geometry : angle 0.65375 / 0.38 (16762) hydrogen bonds : bond 0.04992 / 3.44 ( 713) hydrogen bonds : angle 2.94207 / 2.06 ( 1805) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7327 (mmpt) cc_final: 0.6965 (mmpt) REVERT: E 64 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8043 (mptt) REVERT: E 76 GLN cc_start: 0.7842 (tt0) cc_final: 0.7442 (pt0) REVERT: E 120 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7502 (mtt) REVERT: F 91 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7910 (ttmm) REVERT: G 92 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: H 90 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6167 (mp0) outliers start: 18 outliers final: 9 residues processed: 99 average time/residue: 0.7464 time to fit residues: 78.1790 Evaluate side-chains 105 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 95 optimal weight: 30.0000 chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 89 ASN D 92 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.189738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.157440 restraints weight = 10585.182| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 0.68 r_work: 0.3508 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11633 Z= 0.136 Angle : 0.643 7.834 16762 Z= 0.372 Chirality : 0.047 0.225 1913 Planarity : 0.004 0.044 1271 Dihedral : 30.929 170.765 3504 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.26 % Allowed : 12.12 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.30), residues: 730 helix: 1.98 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.36 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG H 96 TYR 0.015 0.001 TYR G 57 PHE 0.011 0.001 PHE F 61 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.14 (11633) covalent geometry : angle 0.64253 / 0.37 (16762) hydrogen bonds : bond 0.04921 / 3.39 ( 713) hydrogen bonds : angle 2.92031 / 2.05 ( 1805) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7664 (pt0) cc_final: 0.7463 (pt0) REVERT: C 95 LYS cc_start: 0.7358 (mmpt) cc_final: 0.6966 (mmpt) REVERT: E 64 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8038 (mptt) REVERT: E 76 GLN cc_start: 0.7862 (tt0) cc_final: 0.7445 (pt0) REVERT: E 120 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7480 (mtt) REVERT: F 91 LYS cc_start: 0.8211 (ttpt) cc_final: 0.7816 (ttmm) REVERT: G 92 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: H 90 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6177 (mp0) outliers start: 14 outliers final: 9 residues processed: 98 average time/residue: 0.7187 time to fit residues: 74.6842 Evaluate side-chains 106 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 60 optimal weight: 0.7980 chunk 83 optimal weight: 30.0000 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN D 92 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.188509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.156375 restraints weight = 10623.652| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 0.66 r_work: 0.3511 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11633 Z= 0.177 Angle : 0.665 8.322 16762 Z= 0.381 Chirality : 0.049 0.233 1913 Planarity : 0.005 0.045 1271 Dihedral : 30.966 171.092 3504 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.91 % Allowed : 11.95 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.30), residues: 730 helix: 1.95 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.42 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 96 TYR 0.013 0.002 TYR G 57 PHE 0.013 0.002 PHE F 61 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (11633) covalent geometry : angle 0.66480 / 0.38 (16762) hydrogen bonds : bond 0.05119 / 3.51 ( 713) hydrogen bonds : angle 2.93687 / 2.06 ( 1805) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: B 52 GLU cc_start: 0.7407 (tp30) cc_final: 0.6948 (mp0) REVERT: C 95 LYS cc_start: 0.7289 (mmpt) cc_final: 0.6934 (mmpt) REVERT: D 90 GLU cc_start: 0.7296 (mp0) cc_final: 0.7092 (mp0) REVERT: E 64 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8049 (mptt) REVERT: E 76 GLN cc_start: 0.7872 (tt0) cc_final: 0.7422 (pt0) REVERT: F 91 LYS cc_start: 0.8230 (ttpt) cc_final: 0.7953 (ttmm) REVERT: G 64 GLU cc_start: 0.7711 (tp30) cc_final: 0.7416 (tp30) REVERT: G 92 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7807 (mt-10) REVERT: H 90 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6154 (mp0) outliers start: 18 outliers final: 10 residues processed: 105 average time/residue: 0.7427 time to fit residues: 82.6272 Evaluate side-chains 111 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 57 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN D 92 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.188892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.157114 restraints weight = 10508.760| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 0.64 r_work: 0.3522 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11633 Z= 0.145 Angle : 0.653 7.865 16762 Z= 0.376 Chirality : 0.048 0.227 1913 Planarity : 0.005 0.044 1271 Dihedral : 30.968 170.920 3504 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.10 % Allowed : 12.44 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.30), residues: 730 helix: 1.98 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.41 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 96 TYR 0.015 0.001 TYR G 57 PHE 0.013 0.002 PHE F 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.15 (11633) covalent geometry : angle 0.65290 / 0.38 (16762) hydrogen bonds : bond 0.05032 / 3.46 ( 713) hydrogen bonds : angle 2.91910 / 2.05 ( 1805) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: B 52 GLU cc_start: 0.7387 (tp30) cc_final: 0.6917 (mp0) REVERT: C 95 LYS cc_start: 0.7272 (mmpt) cc_final: 0.6914 (mmpt) REVERT: D 90 GLU cc_start: 0.7282 (mp0) cc_final: 0.7073 (mp0) REVERT: E 64 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8047 (mptt) REVERT: E 76 GLN cc_start: 0.7849 (tt0) cc_final: 0.7402 (pt0) REVERT: F 91 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7951 (ttmm) REVERT: G 64 GLU cc_start: 0.7701 (tp30) cc_final: 0.7408 (tp30) REVERT: G 92 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: H 90 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6138 (mp0) outliers start: 13 outliers final: 9 residues processed: 102 average time/residue: 0.7537 time to fit residues: 81.1297 Evaluate side-chains 108 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN D 92 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.189093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.157022 restraints weight = 10613.461| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 0.65 r_work: 0.3520 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11633 Z= 0.141 Angle : 0.650 8.256 16762 Z= 0.375 Chirality : 0.048 0.230 1913 Planarity : 0.004 0.044 1271 Dihedral : 30.968 171.004 3504 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.10 % Allowed : 12.76 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.30), residues: 730 helix: 2.03 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.40 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 96 TYR 0.015 0.001 TYR G 57 PHE 0.013 0.002 PHE F 61 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (11633) covalent geometry : angle 0.65047 / 0.37 (16762) hydrogen bonds : bond 0.04966 / 3.41 ( 713) hydrogen bonds : angle 2.91147 / 2.05 ( 1805) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: B 52 GLU cc_start: 0.7392 (tp30) cc_final: 0.6915 (mp0) REVERT: C 95 LYS cc_start: 0.7261 (mmpt) cc_final: 0.6898 (mmpt) REVERT: D 90 GLU cc_start: 0.7288 (mp0) cc_final: 0.7079 (mp0) REVERT: E 64 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8042 (mptt) REVERT: E 76 GLN cc_start: 0.7852 (tt0) cc_final: 0.7405 (pt0) REVERT: F 91 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7970 (ttmm) REVERT: G 64 GLU cc_start: 0.7711 (tp30) cc_final: 0.7415 (tp30) REVERT: G 92 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: H 90 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6144 (mp0) outliers start: 13 outliers final: 8 residues processed: 101 average time/residue: 0.7635 time to fit residues: 81.6445 Evaluate side-chains 108 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 91 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 27 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 76 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN D 92 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.189054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.157106 restraints weight = 10573.899| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 0.66 r_work: 0.3522 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11633 Z= 0.147 Angle : 0.648 7.983 16762 Z= 0.374 Chirality : 0.048 0.231 1913 Planarity : 0.004 0.044 1271 Dihedral : 30.966 170.976 3504 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.78 % Allowed : 13.09 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.30), residues: 730 helix: 2.02 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.40 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 96 TYR 0.015 0.001 TYR G 57 PHE 0.012 0.002 PHE F 61 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.15 (11633) covalent geometry : angle 0.64801 / 0.37 (16762) hydrogen bonds : bond 0.04978 / 3.42 ( 713) hydrogen bonds : angle 2.90580 / 2.04 ( 1805) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3468.14 seconds wall clock time: 59 minutes 47.59 seconds (3587.59 seconds total)