Starting phenix.real_space_refine on Thu Jul 2 21:37:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xnp_33322/07_2026/7xnp_33322.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnp_33322/07_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_33322/07_2026/7xnp_33322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnp_33322/07_2026/7xnp_33322.map" model { file = "/net/cci-nas-00/data/ceres_data/7xnp_33322/07_2026/7xnp_33322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnp_33322/07_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-dev-6108/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: 2.38, per 1000 atoms: 0.22 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: 0.94 Conformation dependent library (CDL) restraints added in 227.9 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: 1.68 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: 1.73 Time building geometry restraints manager: 1.27 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: 15548 1.71 - 3.41: 1147 3.41 - 5.12: 53 5.12 - 6.82: 7 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.740 Find NCS groups from input model: 0.070 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:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.270 ------------------------------------------------------------------------------- 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 : 0.880 8.527 16762 Z= 0.731 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 0.88007 / 0.73 (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 : 0.293 Fit side-chains REVERT: A 118 THR cc_start: 0.8782 (m) cc_final: 0.8542 (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: 0.8834 time to fit residues: 98.6068 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 : 0.319 ------------------------------------------------------------------------------- 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: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.192940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.161643 restraints weight = 10612.989| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 0.68 r_work: 0.3561 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11633 Z= 0.141 Angle : 0.646 8.173 16762 Z= 0.380 Chirality : 0.049 0.220 1913 Planarity : 0.005 0.053 1271 Dihedral : 30.690 170.330 3504 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.62 % Allowed : 6.95 % Favored : 91.44 % 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: 0.86 (0.28), residues: 730 helix: 0.96 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 96 TYR 0.014 0.001 TYR G 57 PHE 0.008 0.001 PHE F 61 HIS 0.002 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.14 (11633) covalent geometry : angle 0.64572 / 0.38 (16762) hydrogen bonds : bond 0.05298 / 3.67 ( 713) hydrogen bonds : angle 3.16577 / 2.24 ( 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 : 0.296 Fit side-chains REVERT: A 118 THR cc_start: 0.8866 (m) cc_final: 0.8666 (m) REVERT: C 88 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6966 (mpt90) REVERT: C 95 LYS cc_start: 0.7411 (mmpt) cc_final: 0.7125 (mmpt) REVERT: C 101 THR cc_start: 0.7790 (m) cc_final: 0.7539 (m) REVERT: G 92 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7743 (mt-10) outliers start: 10 outliers final: 3 residues processed: 100 average time/residue: 0.8353 time to fit residues: 88.2703 Evaluate side-chains 99 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 83 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 73 optimal weight: 30.0000 chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 = 0.187169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.155382 restraints weight = 10628.580| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 0.71 r_work: 0.3479 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1105 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= 0.219 Angle : 0.712 8.477 16762 Z= 0.406 Chirality : 0.051 0.211 1913 Planarity : 0.006 0.050 1271 Dihedral : 31.000 171.430 3504 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.23 % Allowed : 8.40 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.29), residues: 730 helix: 1.27 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -0.50 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 131 TYR 0.016 0.002 TYR D 37 PHE 0.015 0.003 PHE H 67 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.22 (11633) covalent geometry : angle 0.71196 / 0.41 (16762) hydrogen bonds : bond 0.05897 / 4.04 ( 713) hydrogen bonds : angle 3.17120 / 2.23 ( 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: 20 poor density : 102 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 45 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8234 (m) REVERT: C 88 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.7089 (mmp80) REVERT: C 95 LYS cc_start: 0.7385 (mmpt) cc_final: 0.7053 (mmpt) REVERT: C 101 THR cc_start: 0.7806 (m) cc_final: 0.7570 (m) REVERT: E 64 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8104 (mptt) REVERT: E 76 GLN cc_start: 0.7907 (tt0) cc_final: 0.7537 (pt0) REVERT: E 120 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7637 (mtt) REVERT: F 91 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7828 (ttmm) REVERT: G 92 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: H 90 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6133 (mp0) outliers start: 20 outliers final: 8 residues processed: 105 average time/residue: 0.8300 time to fit residues: 91.9990 Evaluate side-chains 109 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR 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 F residue 91 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 20.0000 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.188668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.156396 restraints weight = 10653.898| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 0.69 r_work: 0.3493 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11633 Z= 0.153 Angle : 0.667 8.685 16762 Z= 0.385 Chirality : 0.049 0.214 1913 Planarity : 0.005 0.046 1271 Dihedral : 31.010 170.784 3504 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.07 % Allowed : 9.37 % 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: 1.71 (0.29), residues: 730 helix: 1.67 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.37 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 96 TYR 0.016 0.002 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 0.00278 / 0.15 (11633) covalent geometry : angle 0.66654 / 0.39 (16762) hydrogen bonds : bond 0.05261 / 3.61 ( 713) hydrogen bonds : angle 3.03605 / 2.13 ( 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 115 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: C 88 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.7111 (mmp80) REVERT: C 95 LYS cc_start: 0.7360 (mmpt) cc_final: 0.7019 (mmpt) REVERT: E 64 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8077 (mptt) REVERT: E 76 GLN cc_start: 0.7850 (tt0) cc_final: 0.7484 (pt0) REVERT: E 120 MET cc_start: 0.8005 (mtt) cc_final: 0.7591 (mtt) REVERT: F 91 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7990 (ttmm) REVERT: G 92 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: H 90 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6563 (mp0) outliers start: 19 outliers final: 10 residues processed: 100 average time/residue: 0.8009 time to fit residues: 84.7838 Evaluate side-chains 109 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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 F residue 60 VAL Chi-restraints excluded: chain F residue 91 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 62 optimal weight: 0.0000 chunk 41 optimal weight: 0.7980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.189425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.157010 restraints weight = 10607.910| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 0.69 r_work: 0.3515 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 11633 Z= 0.138 Angle : 0.644 8.050 16762 Z= 0.376 Chirality : 0.048 0.205 1913 Planarity : 0.004 0.044 1271 Dihedral : 31.008 170.229 3504 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.27 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: 1.87 (0.30), residues: 730 helix: 1.80 (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 0.020 0.001 ARG H 96 TYR 0.018 0.001 TYR G 57 PHE 0.011 0.002 PHE A 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.14 (11633) covalent geometry : angle 0.64430 / 0.38 (16762) hydrogen bonds : bond 0.05073 / 3.50 ( 713) hydrogen bonds : angle 2.99068 / 2.10 ( 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 114 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.288 Fit side-chains REVERT: C 88 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.7086 (mmp80) REVERT: C 95 LYS cc_start: 0.7310 (mmpt) cc_final: 0.6951 (mmpt) REVERT: E 64 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8021 (mptt) REVERT: E 76 GLN cc_start: 0.7836 (tt0) cc_final: 0.7438 (pt0) REVERT: E 120 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7525 (mtt) REVERT: F 91 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7821 (ttmm) REVERT: G 92 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: H 90 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6545 (mp0) outliers start: 16 outliers final: 6 residues processed: 100 average time/residue: 0.7314 time to fit residues: 77.5548 Evaluate side-chains 107 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 120 MET 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 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: 1.9990 chunk 69 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 89 ASN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.189076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.157007 restraints weight = 10637.514| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 0.68 r_work: 0.3509 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1169 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= 0.162 Angle : 0.647 8.217 16762 Z= 0.376 Chirality : 0.048 0.207 1913 Planarity : 0.004 0.045 1271 Dihedral : 31.016 169.594 3504 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.07 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: 1.99 (0.30), residues: 730 helix: 1.91 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 96 TYR 0.013 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 0.00305 / 0.16 (11633) covalent geometry : angle 0.64719 / 0.38 (16762) hydrogen bonds : bond 0.05058 / 3.49 ( 713) hydrogen bonds : angle 2.95558 / 2.08 ( 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: 16 poor density : 99 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7342 (mmpt) cc_final: 0.6968 (mmpt) REVERT: E 64 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8041 (mptt) REVERT: E 76 GLN cc_start: 0.7849 (tt0) cc_final: 0.7422 (pt0) REVERT: E 120 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7552 (mtt) REVERT: F 91 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7820 (ttmm) REVERT: G 92 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: H 90 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6172 (mp0) outliers start: 16 outliers final: 8 residues processed: 101 average time/residue: 0.8039 time to fit residues: 85.8341 Evaluate side-chains 109 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 91 LYS Chi-restraints excluded: chain G residue 62 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 93 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 95 optimal weight: 30.0000 chunk 17 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.189732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.157629 restraints weight = 10581.237| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 0.68 r_work: 0.3516 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11633 Z= 0.135 Angle : 0.630 7.995 16762 Z= 0.370 Chirality : 0.047 0.210 1913 Planarity : 0.004 0.044 1271 Dihedral : 31.011 169.713 3504 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.75 % Allowed : 11.31 % 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: 2.08 (0.30), residues: 730 helix: 1.98 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.34 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG H 96 TYR 0.016 0.001 TYR G 57 PHE 0.011 0.002 PHE F 61 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.14 (11633) covalent geometry : angle 0.63005 / 0.37 (16762) hydrogen bonds : bond 0.04933 / 3.40 ( 713) hydrogen bonds : angle 2.92210 / 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 114 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7325 (mmpt) cc_final: 0.6933 (mmpt) REVERT: E 64 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8037 (mptt) REVERT: E 76 GLN cc_start: 0.7821 (tt0) cc_final: 0.7413 (pt0) REVERT: E 120 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7509 (mtt) REVERT: F 91 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7982 (ttmm) REVERT: G 92 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: H 90 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6160 (mp0) outliers start: 17 outliers final: 8 residues processed: 100 average time/residue: 0.7251 time to fit residues: 76.8259 Evaluate side-chains 109 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 91 LYS Chi-restraints excluded: chain G residue 62 ILE 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: 0.0870 chunk 83 optimal weight: 30.0000 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 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: 1.4166 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.189895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.158126 restraints weight = 10623.292| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 0.69 r_work: 0.3523 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1273 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= 0.153 Angle : 0.621 7.815 16762 Z= 0.364 Chirality : 0.046 0.218 1913 Planarity : 0.004 0.044 1271 Dihedral : 31.009 170.094 3504 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.42 % Allowed : 12.44 % 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: 2.25 (0.30), residues: 730 helix: 2.11 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.32 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 96 TYR 0.015 0.001 TYR G 57 PHE 0.012 0.002 PHE F 61 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (11633) covalent geometry : angle 0.62116 / 0.36 (16762) hydrogen bonds : bond 0.04824 / 3.32 ( 713) hydrogen bonds : angle 2.84733 / 2.01 ( 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 115 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: B 52 GLU cc_start: 0.7422 (tp30) cc_final: 0.7000 (mp0) REVERT: C 88 ARG cc_start: 0.7570 (mmt180) cc_final: 0.7211 (mmt-90) REVERT: C 95 LYS cc_start: 0.7317 (mmpt) cc_final: 0.6941 (mmpt) REVERT: E 64 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8040 (mptt) REVERT: E 76 GLN cc_start: 0.7846 (tt0) cc_final: 0.7401 (pt0) REVERT: F 91 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7978 (ttmm) REVERT: G 92 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: H 90 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6204 (mp0) outliers start: 15 outliers final: 7 residues processed: 102 average time/residue: 0.7219 time to fit residues: 77.9656 Evaluate side-chains 107 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 91 LYS Chi-restraints excluded: chain G residue 62 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 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: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.189805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.157830 restraints weight = 10511.091| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 0.71 r_work: 0.3496 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11633 Z= 0.153 Angle : 0.621 7.819 16762 Z= 0.363 Chirality : 0.046 0.217 1913 Planarity : 0.004 0.044 1271 Dihedral : 31.041 169.765 3504 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.26 % Allowed : 12.60 % 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: 2.26 (0.30), residues: 730 helix: 2.14 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.42 (0.40), residues: 187 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 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (11633) covalent geometry : angle 0.62076 / 0.36 (16762) hydrogen bonds : bond 0.04823 / 3.32 ( 713) hydrogen bonds : angle 2.83016 / 1.99 ( 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 118 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: B 52 GLU cc_start: 0.7504 (tp30) cc_final: 0.7045 (mp0) REVERT: C 88 ARG cc_start: 0.7376 (mmt180) cc_final: 0.7059 (mmt-90) REVERT: C 95 LYS cc_start: 0.7257 (mmpt) cc_final: 0.6898 (mmpt) REVERT: E 64 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8054 (mptt) REVERT: E 76 GLN cc_start: 0.7910 (tt0) cc_final: 0.7461 (pt0) REVERT: F 91 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.8020 (ttmm) REVERT: G 92 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7865 (mt-10) outliers start: 14 outliers final: 7 residues processed: 108 average time/residue: 0.6886 time to fit residues: 78.6893 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 : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 91 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 44 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 78 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.190108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.158257 restraints weight = 10620.567| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 0.66 r_work: 0.3537 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11633 Z= 0.137 Angle : 0.615 7.737 16762 Z= 0.361 Chirality : 0.046 0.214 1913 Planarity : 0.004 0.044 1271 Dihedral : 31.038 169.744 3504 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.78 % Allowed : 13.73 % Favored : 84.49 % 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: 2.32 (0.30), residues: 730 helix: 2.19 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.39 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 96 TYR 0.016 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 0.00228 / 0.14 (11633) covalent geometry : angle 0.61501 / 0.36 (16762) hydrogen bonds : bond 0.04753 / 3.28 ( 713) hydrogen bonds : angle 2.81127 / 1.98 ( 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 109 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: B 52 GLU cc_start: 0.7416 (tp30) cc_final: 0.6997 (mp0) REVERT: C 88 ARG cc_start: 0.7354 (mmt180) cc_final: 0.7043 (mmt-90) REVERT: C 95 LYS cc_start: 0.7273 (mmpt) cc_final: 0.6878 (mmpt) REVERT: E 64 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8009 (mptt) REVERT: E 76 GLN cc_start: 0.7840 (tt0) cc_final: 0.7414 (pt0) REVERT: E 120 MET cc_start: 0.7967 (mtt) cc_final: 0.7646 (mtt) REVERT: F 91 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7983 (ttmm) REVERT: G 92 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7795 (mt-10) outliers start: 11 outliers final: 7 residues processed: 101 average time/residue: 0.7307 time to fit residues: 78.0339 Evaluate side-chains 107 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 91 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 44 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 91 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 76 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 overall best weight: 1.0282 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.190131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.157942 restraints weight = 10576.682| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 0.69 r_work: 0.3516 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11633 Z= 0.142 Angle : 0.615 8.022 16762 Z= 0.361 Chirality : 0.046 0.218 1913 Planarity : 0.004 0.044 1271 Dihedral : 31.038 169.740 3504 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.94 % Allowed : 13.73 % Favored : 84.33 % 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 are not related in a simple way. whole: 2.34 (0.30), residues: 730 helix: 2.20 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.39 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 96 TYR 0.016 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 0.00255 / 0.14 (11633) covalent geometry : angle 0.61537 / 0.36 (16762) hydrogen bonds : bond 0.04739 / 3.27 ( 713) hydrogen bonds : angle 2.80609 / 1.98 ( 1805) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3484.15 seconds wall clock time: 60 minutes 3.56 seconds (3603.56 seconds total)