Starting phenix.real_space_refine on Thu Jun 12 16:29:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8g_29850/06_2025/8g8g_29850.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8g_29850/06_2025/8g8g_29850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g8g_29850/06_2025/8g8g_29850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8g_29850/06_2025/8g8g_29850.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8g_29850/06_2025/8g8g_29850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8g_29850/06_2025/8g8g_29850.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 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 348 5.49 5 S 17 5.16 5 C 8089 2.51 5 N 2711 2.21 5 O 3393 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14558 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 895 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" 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: "D" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 756 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 915 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 3539 Classifications: {'DNA': 174} Link IDs: {'rna3p': 173} Chain: "J" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 3595 Classifications: {'DNA': 174} Link IDs: {'rna3p': 173} Chain: "X" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1152 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Time building chain proxies: 9.17, per 1000 atoms: 0.63 Number of scatterers: 14558 At special positions: 0 Unit cell: (97.52, 116.6, 189.74, 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 17 16.00 P 348 15.00 O 3393 8.00 N 2711 7.00 C 8089 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: 3.06 Conformation dependent library (CDL) restraints added in 1.0 seconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1752 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 10 sheets defined 71.5% alpha, 2.6% beta 157 base pairs and 325 stacking pairs defined. Time for finding SS restraints: 7.37 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 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.335A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.572A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 122 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 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 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.220A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.537A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 122 Processing helix chain 'X' and resid 141 through 161 Processing helix chain 'X' and resid 163 through 176 Processing helix chain 'X' and resid 180 through 189 removed outlier: 3.554A pdb=" N ILE X 184 " --> pdb=" O SER X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 193 through 211 Proline residue: X 202 - end of helix Processing helix chain 'X' and resid 215 through 220 Processing helix chain 'X' and resid 238 through 249 Processing helix chain 'X' and resid 256 through 268 removed outlier: 3.681A pdb=" N HIS X 262 " --> pdb=" O GLN X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 288 removed outlier: 4.058A pdb=" N SER X 288 " --> pdb=" O LYS X 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.873A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.630A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.964A 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: 6.919A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.035A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 493 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 379 hydrogen bonds 758 hydrogen bond angles 0 basepair planarities 157 basepair parallelities 325 stacking parallelities Total time for adding SS restraints: 7.08 Time building geometry restraints manager: 3.76 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: 2787 1.33 - 1.45: 5064 1.45 - 1.57: 6948 1.57 - 1.69: 694 1.69 - 1.81: 28 Bond restraints: 15521 Sorted by residual: bond pdb=" C LEU G 116 " pdb=" N PRO G 117 " ideal model delta sigma weight residual 1.332 1.213 0.119 1.34e-02 5.57e+03 7.87e+01 bond pdb=" C LEU F 22 " pdb=" N ARG F 23 " ideal model delta sigma weight residual 1.330 1.384 -0.054 1.22e-02 6.72e+03 1.98e+01 bond pdb=" N ASN B 25 " pdb=" CA ASN B 25 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.35e+00 bond pdb=" N ILE B 26 " pdb=" CA ILE B 26 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.24e-02 6.50e+03 6.55e+00 bond pdb=" C ARG A 40 " pdb=" N TYR A 41 " ideal model delta sigma weight residual 1.329 1.356 -0.027 1.43e-02 4.89e+03 3.66e+00 ... (remaining 15516 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 22312 2.38 - 4.76: 108 4.76 - 7.14: 12 7.14 - 9.52: 2 9.52 - 11.90: 1 Bond angle restraints: 22435 Sorted by residual: angle pdb=" CB MET X 197 " pdb=" CG MET X 197 " pdb=" SD MET X 197 " ideal model delta sigma weight residual 112.70 124.60 -11.90 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CA GLU X 238 " pdb=" CB GLU X 238 " pdb=" CG GLU X 238 " ideal model delta sigma weight residual 114.10 120.63 -6.53 2.00e+00 2.50e-01 1.07e+01 angle pdb=" O3' DA I 74 " pdb=" C3' DA I 74 " pdb=" C2' DA I 74 " ideal model delta sigma weight residual 111.50 116.28 -4.78 1.50e+00 4.44e-01 1.02e+01 angle pdb=" CB LYS A 37 " pdb=" CG LYS A 37 " pdb=" CD LYS A 37 " ideal model delta sigma weight residual 111.30 117.84 -6.54 2.30e+00 1.89e-01 8.09e+00 angle pdb=" C3' DT J -88 " pdb=" C2' DT J -88 " pdb=" C1' DT J -88 " ideal model delta sigma weight residual 101.60 97.56 4.04 1.50e+00 4.44e-01 7.25e+00 ... (remaining 22430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 6918 35.91 - 71.82: 1652 71.82 - 107.73: 18 107.73 - 143.64: 2 143.64 - 179.55: 1 Dihedral angle restraints: 8591 sinusoidal: 5887 harmonic: 2704 Sorted by residual: dihedral pdb=" C4' DC I 20 " pdb=" C3' DC I 20 " pdb=" O3' DC I 20 " pdb=" P DT I 21 " ideal model delta sinusoidal sigma weight residual 220.00 40.45 179.55 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J -93 " pdb=" C3' DG J -93 " pdb=" O3' DG J -93 " pdb=" P DG J -92 " ideal model delta sinusoidal sigma weight residual 220.00 81.86 138.14 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" C4' DA I 52 " pdb=" C3' DA I 52 " pdb=" O3' DA I 52 " pdb=" P DA I 53 " ideal model delta sinusoidal sigma weight residual 220.00 84.27 135.73 1 3.50e+01 8.16e-04 1.34e+01 ... (remaining 8588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2008 0.038 - 0.076: 454 0.076 - 0.114: 74 0.114 - 0.152: 12 0.152 - 0.190: 2 Chirality restraints: 2550 Sorted by residual: chirality pdb=" CA ILE B 26 " pdb=" N ILE B 26 " pdb=" C ILE B 26 " pdb=" CB ILE B 26 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CG LEU X 190 " pdb=" CB LEU X 190 " pdb=" CD1 LEU X 190 " pdb=" CD2 LEU X 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA LEU X 267 " pdb=" N LEU X 267 " pdb=" C LEU X 267 " pdb=" CB LEU X 267 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 2547 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 22 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.00e+01 pdb=" C LEU F 22 " -0.077 2.00e-02 2.50e+03 pdb=" O LEU F 22 " 0.030 2.00e-02 2.50e+03 pdb=" N ARG F 23 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.98e+00 pdb=" N PRO E 43 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 40 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C ARG A 40 " -0.031 2.00e-02 2.50e+03 pdb=" O ARG A 40 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 41 " 0.010 2.00e-02 2.50e+03 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 7 2.28 - 2.93: 5418 2.93 - 3.59: 21629 3.59 - 4.24: 41392 4.24 - 4.90: 59753 Nonbonded interactions: 128199 Sorted by model distance: nonbonded pdb=" O SER G 123 " pdb=" OP1 DG J -75 " model vdw 1.622 3.040 nonbonded pdb=" CD LYS G 124 " pdb=" O3' DA J -76 " model vdw 1.932 3.440 nonbonded pdb=" C SER G 123 " pdb=" OP1 DG J -75 " model vdw 2.057 3.270 nonbonded pdb=" NH1 ARG A 26 " pdb=" OP1 DA J 2 " model vdw 2.165 3.120 nonbonded pdb=" O HIS F 75 " pdb=" NH2 ARG H 89 " model vdw 2.238 3.120 ... (remaining 128194 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 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and resid 28 through 122) 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=0.00 max=1.00 mean=0.99 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: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 41.690 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4882 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 : 0.005 0.119 15521 Z= 0.230 Angle : 0.593 11.899 22435 Z= 0.354 Chirality : 0.033 0.190 2550 Planarity : 0.004 0.050 1630 Dihedral : 27.409 179.553 6839 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.64 % Allowed : 14.27 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 911 helix: 0.14 (0.19), residues: 648 sheet: None (None), residues: 0 loop : -1.29 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP X 277 HIS 0.004 0.001 HIS D 106 PHE 0.011 0.001 PHE X 187 TYR 0.009 0.001 TYR G 57 ARG 0.004 0.001 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.20972 ( 872) hydrogen bonds : angle 6.94673 ( 2216) covalent geometry : bond 0.00491 (15521) covalent geometry : angle 0.59320 (22435) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 271 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.5202 (mt) cc_final: 0.4916 (mt) REVERT: F 19 ARG cc_start: 0.7805 (mtt-85) cc_final: 0.7445 (ptp-170) REVERT: F 20 LYS cc_start: 0.7435 (tppt) cc_final: 0.7206 (tppt) outliers start: 5 outliers final: 0 residues processed: 273 average time/residue: 0.3101 time to fit residues: 116.4516 Evaluate side-chains 135 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.0270 chunk 71 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 24 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 76 GLN H 46 HIS H 81 ASN ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.083934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.058893 restraints weight = 98119.933| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.52 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 15521 Z= 0.217 Angle : 0.707 7.875 22435 Z= 0.412 Chirality : 0.039 0.187 2550 Planarity : 0.006 0.056 1630 Dihedral : 30.720 178.006 4949 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.68 % Allowed : 20.64 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.27), residues: 911 helix: 1.57 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.22 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 277 HIS 0.007 0.001 HIS B 75 PHE 0.014 0.001 PHE D 67 TYR 0.021 0.002 TYR A 54 ARG 0.011 0.001 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.05035 ( 872) hydrogen bonds : angle 3.52830 ( 2216) covalent geometry : bond 0.00480 (15521) covalent geometry : angle 0.70718 (22435) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.7282 (mt) cc_final: 0.6958 (mp) REVERT: B 88 TYR cc_start: 0.7952 (m-10) cc_final: 0.7646 (m-80) REVERT: E 126 LEU cc_start: 0.8272 (tp) cc_final: 0.7992 (tp) REVERT: F 19 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7454 (ptp-170) REVERT: G 118 LYS cc_start: 0.7038 (mmpt) cc_final: 0.5922 (tptp) REVERT: H 90 GLU cc_start: 0.8900 (mp0) cc_final: 0.8185 (mp0) outliers start: 21 outliers final: 8 residues processed: 164 average time/residue: 0.3821 time to fit residues: 92.1297 Evaluate side-chains 125 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 chunk 108 optimal weight: 10.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 40.0000 chunk 18 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 0.0970 chunk 91 optimal weight: 30.0000 chunk 6 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.082799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.057210 restraints weight = 96623.749| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.66 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15521 Z= 0.162 Angle : 0.613 6.065 22435 Z= 0.366 Chirality : 0.034 0.252 2550 Planarity : 0.004 0.048 1630 Dihedral : 30.392 179.922 4949 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.40 % Allowed : 22.04 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.27), residues: 911 helix: 1.81 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -1.15 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 277 HIS 0.007 0.001 HIS A 113 PHE 0.040 0.002 PHE B 61 TYR 0.021 0.001 TYR H 37 ARG 0.003 0.000 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 872) hydrogen bonds : angle 3.23258 ( 2216) covalent geometry : bond 0.00353 (15521) covalent geometry : angle 0.61302 (22435) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.7954 (mt) cc_final: 0.7753 (mp) REVERT: B 88 TYR cc_start: 0.8111 (m-10) cc_final: 0.7853 (m-10) REVERT: E 90 MET cc_start: 0.8799 (mmm) cc_final: 0.8585 (mmt) REVERT: E 126 LEU cc_start: 0.8541 (tp) cc_final: 0.8269 (tp) REVERT: F 19 ARG cc_start: 0.7905 (mtt-85) cc_final: 0.7361 (ptp-170) REVERT: F 79 LYS cc_start: 0.8524 (mppt) cc_final: 0.8070 (mtmm) REVERT: G 64 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8286 (tm-30) REVERT: G 118 LYS cc_start: 0.7294 (mmpt) cc_final: 0.6237 (tptp) REVERT: H 56 MET cc_start: 0.7999 (mmm) cc_final: 0.7758 (mmm) REVERT: H 86 ILE cc_start: 0.8872 (mt) cc_final: 0.8638 (mt) REVERT: H 90 GLU cc_start: 0.8948 (mp0) cc_final: 0.8149 (mp0) outliers start: 11 outliers final: 6 residues processed: 133 average time/residue: 0.3522 time to fit residues: 69.6629 Evaluate side-chains 121 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 65 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.079174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.054027 restraints weight = 94430.845| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.45 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15521 Z= 0.156 Angle : 0.588 6.172 22435 Z= 0.353 Chirality : 0.034 0.216 2550 Planarity : 0.004 0.043 1630 Dihedral : 30.285 176.656 4949 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.91 % Allowed : 22.04 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.28), residues: 911 helix: 2.07 (0.20), residues: 665 sheet: None (None), residues: 0 loop : -1.15 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 277 HIS 0.011 0.001 HIS B 75 PHE 0.015 0.001 PHE X 194 TYR 0.015 0.001 TYR H 37 ARG 0.007 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 872) hydrogen bonds : angle 3.10652 ( 2216) covalent geometry : bond 0.00330 (15521) covalent geometry : angle 0.58759 (22435) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.9203 (OUTLIER) cc_final: 0.8706 (p) REVERT: B 88 TYR cc_start: 0.8251 (m-10) cc_final: 0.7969 (m-10) REVERT: D 98 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8844 (mm) REVERT: E 59 GLU cc_start: 0.7644 (pm20) cc_final: 0.7315 (pm20) REVERT: E 126 LEU cc_start: 0.8803 (tp) cc_final: 0.8435 (tp) REVERT: F 19 ARG cc_start: 0.7804 (mtt-85) cc_final: 0.7281 (ptp-170) REVERT: G 64 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8230 (tm-30) REVERT: H 37 TYR cc_start: 0.8840 (m-80) cc_final: 0.8636 (m-10) REVERT: H 56 MET cc_start: 0.8331 (mmm) cc_final: 0.8001 (mmm) REVERT: H 90 GLU cc_start: 0.8942 (mp0) cc_final: 0.8235 (mp0) REVERT: X 197 MET cc_start: 0.7656 (tpp) cc_final: 0.7265 (tpp) outliers start: 15 outliers final: 5 residues processed: 142 average time/residue: 0.2678 time to fit residues: 56.8446 Evaluate side-chains 120 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 89 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 57 optimal weight: 0.0270 chunk 6 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS H 81 ASN ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.075128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.048665 restraints weight = 93000.678| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.47 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.7322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15521 Z= 0.166 Angle : 0.617 10.938 22435 Z= 0.365 Chirality : 0.034 0.153 2550 Planarity : 0.004 0.041 1630 Dihedral : 30.222 177.713 4949 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.04 % Allowed : 22.29 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.27), residues: 911 helix: 2.21 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.16 (0.33), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 277 HIS 0.004 0.001 HIS D 106 PHE 0.018 0.001 PHE D 67 TYR 0.012 0.001 TYR H 34 ARG 0.007 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 872) hydrogen bonds : angle 3.09372 ( 2216) covalent geometry : bond 0.00364 (15521) covalent geometry : angle 0.61700 (22435) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.9504 (OUTLIER) cc_final: 0.9026 (p) REVERT: B 88 TYR cc_start: 0.8416 (m-10) cc_final: 0.8091 (m-10) REVERT: D 91 ILE cc_start: 0.9417 (mt) cc_final: 0.9148 (mm) REVERT: E 59 GLU cc_start: 0.7613 (pm20) cc_final: 0.7277 (pm20) REVERT: E 62 ILE cc_start: 0.9207 (tp) cc_final: 0.9003 (tt) REVERT: E 65 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9141 (mp) REVERT: E 123 ASP cc_start: 0.8213 (m-30) cc_final: 0.7973 (t70) REVERT: F 19 ARG cc_start: 0.7595 (mtt-85) cc_final: 0.7156 (ptp-170) REVERT: F 20 LYS cc_start: 0.7745 (tppt) cc_final: 0.7530 (tppt) REVERT: F 63 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8371 (mt-10) REVERT: F 79 LYS cc_start: 0.8737 (mptt) cc_final: 0.8514 (mppt) REVERT: G 64 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8152 (tm-30) REVERT: G 73 ASN cc_start: 0.7609 (m-40) cc_final: 0.7389 (m-40) REVERT: H 56 MET cc_start: 0.8623 (mmm) cc_final: 0.8324 (mmm) REVERT: X 197 MET cc_start: 0.7843 (tpp) cc_final: 0.7374 (tpp) outliers start: 16 outliers final: 5 residues processed: 142 average time/residue: 0.2866 time to fit residues: 58.7520 Evaluate side-chains 119 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 51 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.065701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.038358 restraints weight = 94428.551| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.89 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 1.0600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 15521 Z= 0.237 Angle : 0.716 10.967 22435 Z= 0.419 Chirality : 0.039 0.190 2550 Planarity : 0.005 0.047 1630 Dihedral : 30.982 176.257 4949 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.44 % Allowed : 21.15 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.27), residues: 911 helix: 1.82 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.53 (0.33), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 277 HIS 0.006 0.002 HIS F 75 PHE 0.017 0.002 PHE X 194 TYR 0.021 0.002 TYR H 37 ARG 0.009 0.001 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.05669 ( 872) hydrogen bonds : angle 3.53285 ( 2216) covalent geometry : bond 0.00535 (15521) covalent geometry : angle 0.71625 (22435) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8863 (m-10) cc_final: 0.8465 (m-10) REVERT: D 31 LYS cc_start: 0.9020 (ttmm) cc_final: 0.8682 (ptpp) REVERT: D 98 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9204 (mm) REVERT: E 59 GLU cc_start: 0.7997 (pm20) cc_final: 0.7658 (pm20) REVERT: F 20 LYS cc_start: 0.7986 (tppt) cc_final: 0.7778 (tppt) REVERT: F 53 GLU cc_start: 0.8833 (tp30) cc_final: 0.8615 (tp30) REVERT: F 59 LYS cc_start: 0.9448 (OUTLIER) cc_final: 0.9111 (ttmm) REVERT: G 64 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7726 (tm-30) REVERT: G 92 GLU cc_start: 0.8850 (mp0) cc_final: 0.8354 (mp0) REVERT: X 197 MET cc_start: 0.7765 (tpp) cc_final: 0.7436 (tpp) outliers start: 27 outliers final: 9 residues processed: 149 average time/residue: 0.3242 time to fit residues: 66.9242 Evaluate side-chains 107 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain X residue 166 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 18 optimal weight: 4.9990 chunk 114 optimal weight: 0.4980 chunk 91 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS H 92 GLN ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.061737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.034969 restraints weight = 94758.448| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.78 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 1.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 15521 Z= 0.299 Angle : 0.725 11.559 22435 Z= 0.422 Chirality : 0.040 0.163 2550 Planarity : 0.005 0.047 1630 Dihedral : 31.380 177.103 4949 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.66 % Allowed : 23.57 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.27), residues: 911 helix: 1.88 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.40 (0.32), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP X 207 HIS 0.006 0.002 HIS F 75 PHE 0.016 0.002 PHE A 67 TYR 0.011 0.001 TYR A 41 ARG 0.008 0.001 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.05297 ( 872) hydrogen bonds : angle 3.53029 ( 2216) covalent geometry : bond 0.00659 (15521) covalent geometry : angle 0.72526 (22435) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9361 (mttp) cc_final: 0.8998 (mtmt) REVERT: B 84 MET cc_start: 0.9133 (mmm) cc_final: 0.8903 (mmm) REVERT: B 88 TYR cc_start: 0.9033 (m-10) cc_final: 0.8657 (m-10) REVERT: D 31 LYS cc_start: 0.9057 (ttmm) cc_final: 0.8838 (ptpp) REVERT: E 59 GLU cc_start: 0.8263 (pm20) cc_final: 0.7915 (pm20) REVERT: E 76 GLN cc_start: 0.8702 (tt0) cc_final: 0.8497 (mt0) REVERT: F 59 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9146 (ttmm) REVERT: F 63 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8394 (mt-10) REVERT: G 64 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7792 (tm-30) REVERT: G 92 GLU cc_start: 0.8601 (mp0) cc_final: 0.8192 (mp0) REVERT: H 90 GLU cc_start: 0.9095 (mp0) cc_final: 0.8278 (mp0) REVERT: X 197 MET cc_start: 0.7431 (tpp) cc_final: 0.7126 (tpp) outliers start: 13 outliers final: 3 residues processed: 124 average time/residue: 0.2901 time to fit residues: 51.6558 Evaluate side-chains 102 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain F residue 59 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN F 93 GLN ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.063444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.035862 restraints weight = 92285.672| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.77 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 1.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15521 Z= 0.161 Angle : 0.634 9.685 22435 Z= 0.371 Chirality : 0.035 0.156 2550 Planarity : 0.004 0.038 1630 Dihedral : 30.954 174.761 4949 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.02 % Allowed : 25.61 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.27), residues: 911 helix: 2.16 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.27 (0.33), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP X 207 HIS 0.010 0.001 HIS B 75 PHE 0.010 0.001 PHE D 67 TYR 0.015 0.001 TYR H 37 ARG 0.004 0.000 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 872) hydrogen bonds : angle 3.06435 ( 2216) covalent geometry : bond 0.00352 (15521) covalent geometry : angle 0.63442 (22435) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8148 (mp0) REVERT: B 74 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8196 (mp0) REVERT: B 88 TYR cc_start: 0.8964 (m-10) cc_final: 0.8536 (m-10) REVERT: D 31 LYS cc_start: 0.9023 (ttmm) cc_final: 0.8710 (ptpp) REVERT: E 59 GLU cc_start: 0.8120 (pm20) cc_final: 0.7908 (pm20) REVERT: F 59 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.9062 (ttmm) REVERT: G 64 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7688 (tm-30) REVERT: G 92 GLU cc_start: 0.8664 (mp0) cc_final: 0.8223 (mp0) REVERT: H 54 LYS cc_start: 0.9116 (mtpp) cc_final: 0.8853 (mmmm) REVERT: H 90 GLU cc_start: 0.9077 (mp0) cc_final: 0.8279 (mp0) REVERT: X 140 LYS cc_start: 0.7387 (pptt) cc_final: 0.7155 (mttp) REVERT: X 197 MET cc_start: 0.7740 (tpp) cc_final: 0.7357 (tpp) outliers start: 8 outliers final: 3 residues processed: 121 average time/residue: 0.2735 time to fit residues: 48.1365 Evaluate side-chains 112 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 111 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.061158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.034104 restraints weight = 93342.723| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.80 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 1.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 15521 Z= 0.258 Angle : 0.674 9.525 22435 Z= 0.393 Chirality : 0.037 0.164 2550 Planarity : 0.005 0.071 1630 Dihedral : 31.230 175.449 4949 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.89 % Allowed : 25.61 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.28), residues: 911 helix: 2.11 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -1.34 (0.32), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP X 277 HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE G 25 TYR 0.014 0.001 TYR H 37 ARG 0.005 0.001 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.04931 ( 872) hydrogen bonds : angle 3.34956 ( 2216) covalent geometry : bond 0.00582 (15521) covalent geometry : angle 0.67371 (22435) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8113 (mp0) REVERT: B 88 TYR cc_start: 0.9047 (m-10) cc_final: 0.8562 (m-10) REVERT: B 93 GLN cc_start: 0.8991 (tp40) cc_final: 0.8774 (tp40) REVERT: D 31 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8819 (ptpp) REVERT: F 59 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9043 (ttmm) REVERT: F 63 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8040 (mt-10) REVERT: G 64 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7727 (tm-30) REVERT: G 92 GLU cc_start: 0.8654 (mp0) cc_final: 0.8278 (mp0) REVERT: H 90 GLU cc_start: 0.9061 (mp0) cc_final: 0.8072 (mp0) REVERT: X 140 LYS cc_start: 0.7073 (pptt) cc_final: 0.6787 (mttp) REVERT: X 197 MET cc_start: 0.7524 (tpp) cc_final: 0.7223 (tpp) outliers start: 7 outliers final: 3 residues processed: 115 average time/residue: 0.2983 time to fit residues: 49.0473 Evaluate side-chains 107 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 31 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 119 optimal weight: 0.6980 chunk 121 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 218 GLN ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.061382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.034135 restraints weight = 91415.428| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.51 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 1.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15521 Z= 0.211 Angle : 0.655 13.715 22435 Z= 0.381 Chirality : 0.036 0.260 2550 Planarity : 0.005 0.081 1630 Dihedral : 30.947 174.564 4949 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.89 % Allowed : 25.86 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.27), residues: 911 helix: 2.12 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.40 (0.32), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP X 207 HIS 0.006 0.001 HIS B 75 PHE 0.009 0.001 PHE D 67 TYR 0.013 0.001 TYR H 37 ARG 0.004 0.000 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 872) hydrogen bonds : angle 3.18844 ( 2216) covalent geometry : bond 0.00469 (15521) covalent geometry : angle 0.65489 (22435) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9036 (m-10) cc_final: 0.8494 (m-10) REVERT: B 93 GLN cc_start: 0.8980 (tp40) cc_final: 0.8695 (tp40) REVERT: D 31 LYS cc_start: 0.9034 (ttmm) cc_final: 0.8716 (ptpp) REVERT: F 59 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.9053 (ttmm) REVERT: G 64 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7699 (tm-30) REVERT: G 92 GLU cc_start: 0.8611 (mp0) cc_final: 0.8230 (mp0) REVERT: H 73 GLU cc_start: 0.8957 (tp30) cc_final: 0.8537 (mm-30) REVERT: H 90 GLU cc_start: 0.9021 (mp0) cc_final: 0.8243 (mp0) REVERT: X 197 MET cc_start: 0.7686 (tpp) cc_final: 0.7288 (tpp) outliers start: 7 outliers final: 5 residues processed: 110 average time/residue: 0.3400 time to fit residues: 54.3791 Evaluate side-chains 110 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 31 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 51 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.061213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.034028 restraints weight = 91728.358| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.49 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 1.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15521 Z= 0.200 Angle : 0.641 9.546 22435 Z= 0.375 Chirality : 0.035 0.248 2550 Planarity : 0.005 0.065 1630 Dihedral : 30.870 174.452 4949 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.02 % Allowed : 25.22 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.28), residues: 911 helix: 2.18 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -1.39 (0.32), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP X 277 HIS 0.006 0.001 HIS B 75 PHE 0.008 0.001 PHE D 67 TYR 0.015 0.001 TYR H 37 ARG 0.004 0.000 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 872) hydrogen bonds : angle 3.19226 ( 2216) covalent geometry : bond 0.00445 (15521) covalent geometry : angle 0.64099 (22435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7360.06 seconds wall clock time: 128 minutes 59.68 seconds (7739.68 seconds total)