Starting phenix.real_space_refine on Tue Jun 10 09:22:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k41_62038/06_2025/9k41_62038.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k41_62038/06_2025/9k41_62038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k41_62038/06_2025/9k41_62038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k41_62038/06_2025/9k41_62038.map" model { file = "/net/cci-nas-00/data/ceres_data/9k41_62038/06_2025/9k41_62038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k41_62038/06_2025/9k41_62038.cif" } resolution = 2.81 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= -0.002 sd= 0.052 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 289 5.49 5 S 14 5.16 5 C 6585 2.51 5 N 2168 2.21 5 O 2772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11828 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 785 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 785 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "I" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2950 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2992 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 6.91, per 1000 atoms: 0.58 Number of scatterers: 11828 At special positions: 0 Unit cell: (121.136, 75.04, 114.704, 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 14 16.00 P 289 15.00 O 2772 8.00 N 2168 7.00 C 6585 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: 2.67 Conformation dependent library (CDL) restraints added in 881.1 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: 1388 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 72.3% alpha, 3.2% beta 145 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 5.46 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.559A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) 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 removed outlier: 3.677A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.644A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 31 removed outlier: 3.546A pdb=" N ALA C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 46 Processing helix chain 'C' and resid 55 through 82 Processing helix chain 'C' and resid 88 through 99 Processing helix chain 'C' and resid 99 through 106 Processing helix chain 'D' and resid 60 through 72 Processing helix chain 'D' and resid 78 through 107 Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 127 through 147 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 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.687A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.598A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 31 Processing helix chain 'G' and resid 35 through 46 Processing helix chain 'G' and resid 55 through 82 Processing helix chain 'G' and resid 88 through 98 Processing helix chain 'G' and resid 99 through 106 Processing helix chain 'H' and resid 60 through 72 Processing helix chain 'H' and resid 78 through 107 Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 126 through 147 removed outlier: 3.528A pdb=" N ALA H 130 " --> pdb=" O PRO H 126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.044A 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: 6.439A pdb=" N THR B 96 " --> pdb=" O THR G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 52 removed outlier: 7.447A pdb=" N ARG C 51 " --> pdb=" O ILE D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AA6, first strand: chain 'C' and resid 109 through 111 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.111A 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 51 through 52 removed outlier: 7.241A pdb=" N ARG G 51 " --> pdb=" O ILE H 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 86 through 87 405 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 696 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2177 1.33 - 1.45: 4095 1.45 - 1.57: 5758 1.57 - 1.69: 577 1.69 - 1.81: 26 Bond restraints: 12633 Sorted by residual: bond pdb=" O3' DC J -26 " pdb=" P DA J -25 " ideal model delta sigma weight residual 1.607 1.653 -0.046 1.50e-02 4.44e+03 9.38e+00 bond pdb=" O3' DA I -9 " pdb=" P DA I -8 " ideal model delta sigma weight residual 1.607 1.642 -0.035 1.50e-02 4.44e+03 5.56e+00 bond pdb=" O3' DC I -6 " pdb=" P DA I -5 " ideal model delta sigma weight residual 1.607 1.640 -0.033 1.50e-02 4.44e+03 4.78e+00 bond pdb=" CA ILE F 26 " pdb=" CB ILE F 26 " ideal model delta sigma weight residual 1.538 1.553 -0.015 1.37e-02 5.33e+03 1.25e+00 bond pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.22e+00 ... (remaining 12628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 17094 1.03 - 2.07: 911 2.07 - 3.10: 261 3.10 - 4.13: 20 4.13 - 5.17: 13 Bond angle restraints: 18299 Sorted by residual: angle pdb=" N ASN B 25 " pdb=" CA ASN B 25 " pdb=" C ASN B 25 " ideal model delta sigma weight residual 113.20 109.14 4.06 1.21e+00 6.83e-01 1.12e+01 angle pdb=" N ASP F 24 " pdb=" CA ASP F 24 " pdb=" C ASP F 24 " ideal model delta sigma weight residual 111.17 115.78 -4.61 1.41e+00 5.03e-01 1.07e+01 angle pdb=" O3' DG J -27 " pdb=" C3' DG J -27 " pdb=" C2' DG J -27 " ideal model delta sigma weight residual 111.50 106.84 4.66 1.50e+00 4.44e-01 9.67e+00 angle pdb=" O3' DA I -8 " pdb=" C3' DA I -8 " pdb=" C2' DA I -8 " ideal model delta sigma weight residual 111.50 106.95 4.55 1.50e+00 4.44e-01 9.22e+00 angle pdb=" O3' DC J -26 " pdb=" C3' DC J -26 " pdb=" C2' DC J -26 " ideal model delta sigma weight residual 111.50 107.12 4.38 1.50e+00 4.44e-01 8.52e+00 ... (remaining 18294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.84: 4451 20.84 - 41.69: 1347 41.69 - 62.53: 1084 62.53 - 83.38: 50 83.38 - 104.22: 3 Dihedral angle restraints: 6935 sinusoidal: 4785 harmonic: 2150 Sorted by residual: dihedral pdb=" CA PRO H 126 " pdb=" C PRO H 126 " pdb=" N GLY H 127 " pdb=" CA GLY H 127 " ideal model delta harmonic sigma weight residual 180.00 163.93 16.07 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CG ARG A 49 " pdb=" CD ARG A 49 " pdb=" NE ARG A 49 " pdb=" CZ ARG A 49 " ideal model delta sinusoidal sigma weight residual 90.00 132.97 -42.97 2 1.50e+01 4.44e-03 9.91e+00 dihedral pdb=" C4' DG J -17 " pdb=" C3' DG J -17 " pdb=" O3' DG J -17 " pdb=" P DC J -16 " ideal model delta sinusoidal sigma weight residual -140.00 -35.78 -104.22 1 3.50e+01 8.16e-04 9.76e+00 ... (remaining 6932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1640 0.040 - 0.079: 364 0.079 - 0.119: 68 0.119 - 0.158: 11 0.158 - 0.198: 4 Chirality restraints: 2087 Sorted by residual: chirality pdb=" C3' DA I -8 " pdb=" C4' DA I -8 " pdb=" O3' DA I -8 " pdb=" C2' DA I -8 " both_signs ideal model delta sigma weight residual False -2.66 -2.86 0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" CA ASP F 24 " pdb=" N ASP F 24 " pdb=" C ASP F 24 " pdb=" CB ASP F 24 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" C3' DG J -27 " pdb=" C4' DG J -27 " pdb=" O3' DG J -27 " pdb=" C2' DG J -27 " both_signs ideal model delta sigma weight residual False -2.66 -2.85 0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 2084 not shown) Planarity restraints: 1304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 125 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO H 126 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 44 " 0.011 2.00e-02 2.50e+03 1.07e-02 2.60e+00 pdb=" N1 DC J 44 " -0.013 2.00e-02 2.50e+03 pdb=" C2 DC J 44 " 0.021 2.00e-02 2.50e+03 pdb=" O2 DC J 44 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DC J 44 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC J 44 " 0.008 2.00e-02 2.50e+03 pdb=" N4 DC J 44 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DC J 44 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DC J 44 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 125 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.29e+00 pdb=" N PRO D 126 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 126 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 126 " -0.021 5.00e-02 4.00e+02 ... (remaining 1301 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1308 2.75 - 3.29: 10382 3.29 - 3.82: 23519 3.82 - 4.36: 27964 4.36 - 4.90: 39816 Nonbonded interactions: 102989 Sorted by model distance: nonbonded pdb=" NZ LYS D 55 " pdb=" OP1 DT I -46 " model vdw 2.209 3.120 nonbonded pdb=" NH2 ARG G 41 " pdb=" OE1 GLU H 58 " model vdw 2.267 3.120 nonbonded pdb=" O SER G 85 " pdb=" OG SER G 85 " model vdw 2.303 3.040 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH1 ARG A 131 " model vdw 2.306 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.309 3.120 ... (remaining 102984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.100 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 31.740 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 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 : 0.004 0.046 12633 Z= 0.179 Angle : 0.561 5.167 18299 Z= 0.350 Chirality : 0.036 0.198 2087 Planarity : 0.004 0.041 1304 Dihedral : 28.881 104.221 5547 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.29 % Allowed : 22.99 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.93 (0.30), residues: 730 helix: 1.71 (0.22), residues: 548 sheet: None (None), residues: 0 loop : 0.08 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 113 PHE 0.006 0.001 PHE C 34 TYR 0.010 0.002 TYR B 98 ARG 0.004 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.12474 ( 753) hydrogen bonds : angle 4.65008 ( 1902) covalent geometry : bond 0.00384 (12633) covalent geometry : angle 0.56064 (18299) *********************** 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 152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.842 Fit side-chains REVERT: C 99 ASP cc_start: 0.8819 (t70) cc_final: 0.7585 (t0) REVERT: C 121 ASN cc_start: 0.9301 (t0) cc_final: 0.8789 (t0) REVERT: D 82 MET cc_start: 0.9307 (tpt) cc_final: 0.9096 (mmm) REVERT: D 91 ASP cc_start: 0.9111 (t70) cc_final: 0.8801 (t0) REVERT: G 81 ASP cc_start: 0.8985 (m-30) cc_final: 0.8775 (m-30) REVERT: G 99 ASP cc_start: 0.8900 (t70) cc_final: 0.8635 (t0) REVERT: G 121 ASN cc_start: 0.9264 (t0) cc_final: 0.8854 (t0) REVERT: H 58 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8145 (mm-30) REVERT: H 91 ASP cc_start: 0.9098 (t0) cc_final: 0.8782 (t0) REVERT: H 128 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8131 (tm-30) outliers start: 8 outliers final: 0 residues processed: 148 average time/residue: 1.6711 time to fit residues: 262.0524 Evaluate side-chains 110 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN A 113 HIS B 25 ASN B 27 GLN B 75 HIS C 33 GLN C 82 ASN D 56 ASN E 68 GLN E 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 33 GLN G 77 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.054460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.038214 restraints weight = 52631.507| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.90 r_work: 0.2757 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12633 Z= 0.160 Angle : 0.567 8.134 18299 Z= 0.344 Chirality : 0.033 0.128 2087 Planarity : 0.004 0.038 1304 Dihedral : 30.984 99.735 4071 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.77 % Allowed : 22.99 % Favored : 75.24 % 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: 2.90 (0.31), residues: 730 helix: 2.49 (0.22), residues: 556 sheet: None (None), residues: 0 loop : 0.03 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.006 0.001 PHE E 67 TYR 0.011 0.001 TYR H 63 ARG 0.007 0.001 ARG D 105 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 753) hydrogen bonds : angle 2.76197 ( 1902) covalent geometry : bond 0.00346 (12633) covalent geometry : angle 0.56723 (18299) *********************** 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 142 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: B 50 ILE cc_start: 0.9426 (mm) cc_final: 0.9176 (mp) REVERT: C 99 ASP cc_start: 0.8689 (t70) cc_final: 0.7715 (t70) REVERT: C 101 GLU cc_start: 0.8220 (pm20) cc_final: 0.7657 (pm20) REVERT: C 121 ASN cc_start: 0.9268 (OUTLIER) cc_final: 0.8680 (t0) REVERT: D 82 MET cc_start: 0.9410 (tpt) cc_final: 0.9146 (mmm) REVERT: D 91 ASP cc_start: 0.9346 (t70) cc_final: 0.8958 (t0) REVERT: D 94 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8721 (tp30) REVERT: D 128 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8261 (tp30) REVERT: G 81 ASP cc_start: 0.9181 (m-30) cc_final: 0.8924 (m-30) REVERT: G 99 ASP cc_start: 0.9181 (t70) cc_final: 0.8630 (t0) REVERT: G 121 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8679 (t0) REVERT: H 58 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8383 (mm-30) REVERT: H 91 ASP cc_start: 0.9273 (t0) cc_final: 0.8887 (t0) REVERT: H 94 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8463 (tm-30) REVERT: H 128 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8291 (tm-30) outliers start: 11 outliers final: 3 residues processed: 140 average time/residue: 1.5502 time to fit residues: 230.6444 Evaluate side-chains 120 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 62 optimal weight: 0.0370 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.3460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 ASN E 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.053538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.037528 restraints weight = 53205.745| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.91 r_work: 0.2728 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12633 Z= 0.165 Angle : 0.561 8.369 18299 Z= 0.339 Chirality : 0.033 0.122 2087 Planarity : 0.004 0.036 1304 Dihedral : 31.087 93.701 4071 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.77 % Allowed : 22.83 % Favored : 75.40 % 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: 3.29 (0.31), residues: 730 helix: 2.79 (0.22), residues: 556 sheet: None (None), residues: 0 loop : 0.10 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.006 0.001 PHE C 34 TYR 0.009 0.001 TYR H 63 ARG 0.007 0.000 ARG H 105 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 753) hydrogen bonds : angle 2.62099 ( 1902) covalent geometry : bond 0.00361 (12633) covalent geometry : angle 0.56077 (18299) *********************** 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 133 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 1.003 Fit side-chains REVERT: C 99 ASP cc_start: 0.8711 (t70) cc_final: 0.7806 (t70) REVERT: C 101 GLU cc_start: 0.8264 (pm20) cc_final: 0.7541 (pm20) REVERT: C 121 ASN cc_start: 0.9230 (OUTLIER) cc_final: 0.8694 (t0) REVERT: D 82 MET cc_start: 0.9492 (tpt) cc_final: 0.9159 (mmm) REVERT: D 91 ASP cc_start: 0.9359 (t70) cc_final: 0.8992 (t0) REVERT: D 94 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8552 (tm-30) REVERT: D 106 TYR cc_start: 0.8821 (m-10) cc_final: 0.8393 (m-80) REVERT: D 128 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8362 (tp30) REVERT: F 92 ARG cc_start: 0.9447 (OUTLIER) cc_final: 0.9207 (mtp-110) REVERT: G 99 ASP cc_start: 0.9196 (t70) cc_final: 0.8687 (t0) REVERT: G 121 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8631 (t0) REVERT: H 58 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8329 (mm-30) REVERT: H 91 ASP cc_start: 0.9304 (t0) cc_final: 0.8927 (t0) REVERT: H 94 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8474 (tm-30) REVERT: H 128 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8326 (tm-30) outliers start: 11 outliers final: 5 residues processed: 132 average time/residue: 1.7887 time to fit residues: 249.6715 Evaluate side-chains 119 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN D 107 ASN E 39 HIS F 25 ASN G 82 ASN H 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.049056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.033368 restraints weight = 53312.244| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 1.92 r_work: 0.2580 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 12633 Z= 0.315 Angle : 0.661 9.741 18299 Z= 0.387 Chirality : 0.038 0.133 2087 Planarity : 0.004 0.036 1304 Dihedral : 32.123 96.438 4071 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.09 % Allowed : 23.95 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.95 (0.32), residues: 730 helix: 2.56 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.08 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE D 65 TYR 0.011 0.002 TYR F 51 ARG 0.006 0.001 ARG D 105 Details of bonding type rmsd hydrogen bonds : bond 0.06158 ( 753) hydrogen bonds : angle 3.11330 ( 1902) covalent geometry : bond 0.00708 (12633) covalent geometry : angle 0.66106 (18299) *********************** 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 124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.973 Fit side-chains REVERT: A 115 LYS cc_start: 0.9538 (OUTLIER) cc_final: 0.9283 (mtpp) REVERT: C 99 ASP cc_start: 0.9019 (t70) cc_final: 0.7944 (t0) REVERT: C 101 GLU cc_start: 0.8313 (pm20) cc_final: 0.7663 (pm20) REVERT: C 121 ASN cc_start: 0.9338 (OUTLIER) cc_final: 0.8812 (t0) REVERT: D 82 MET cc_start: 0.9494 (tpt) cc_final: 0.9083 (mmm) REVERT: D 91 ASP cc_start: 0.9375 (t70) cc_final: 0.9027 (t0) REVERT: D 94 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8554 (tm-30) REVERT: D 106 TYR cc_start: 0.8811 (m-10) cc_final: 0.8413 (m-80) REVERT: D 128 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8506 (tp30) REVERT: E 115 LYS cc_start: 0.9537 (OUTLIER) cc_final: 0.9285 (mtpp) REVERT: G 99 ASP cc_start: 0.9222 (t70) cc_final: 0.8755 (t0) REVERT: G 121 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8696 (t0) REVERT: H 58 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8477 (mm-30) REVERT: H 91 ASP cc_start: 0.9349 (t0) cc_final: 0.8989 (t0) REVERT: H 94 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8562 (tm-30) REVERT: H 128 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8462 (tm-30) outliers start: 13 outliers final: 4 residues processed: 122 average time/residue: 1.8088 time to fit residues: 233.2673 Evaluate side-chains 113 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.050243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.034598 restraints weight = 52707.409| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.88 r_work: 0.2640 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12633 Z= 0.191 Angle : 0.592 9.176 18299 Z= 0.354 Chirality : 0.034 0.123 2087 Planarity : 0.004 0.036 1304 Dihedral : 31.471 95.888 4071 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.61 % Allowed : 24.12 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.21 (0.31), residues: 730 helix: 2.76 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.04 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 72 PHE 0.007 0.001 PHE A 67 TYR 0.009 0.001 TYR F 88 ARG 0.005 0.000 ARG D 105 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 753) hydrogen bonds : angle 2.67936 ( 1902) covalent geometry : bond 0.00426 (12633) covalent geometry : angle 0.59168 (18299) *********************** 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 124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: C 28 MET cc_start: 0.9221 (ptt) cc_final: 0.8903 (ppp) REVERT: C 99 ASP cc_start: 0.8849 (t70) cc_final: 0.7771 (t0) REVERT: C 101 GLU cc_start: 0.8253 (pm20) cc_final: 0.7712 (pm20) REVERT: C 121 ASN cc_start: 0.9259 (OUTLIER) cc_final: 0.8757 (t0) REVERT: D 82 MET cc_start: 0.9547 (tpt) cc_final: 0.9203 (mmm) REVERT: D 91 ASP cc_start: 0.9351 (t70) cc_final: 0.8983 (t0) REVERT: D 94 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8629 (tm-30) REVERT: D 106 TYR cc_start: 0.8771 (m-10) cc_final: 0.8347 (m-80) REVERT: D 128 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8417 (tp30) REVERT: E 80 THR cc_start: 0.9505 (m) cc_final: 0.9304 (p) REVERT: G 99 ASP cc_start: 0.9252 (t70) cc_final: 0.8773 (t0) REVERT: G 121 ASN cc_start: 0.9195 (OUTLIER) cc_final: 0.8690 (t0) REVERT: H 58 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8297 (mm-30) REVERT: H 91 ASP cc_start: 0.9312 (t0) cc_final: 0.8931 (t0) REVERT: H 94 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8548 (tm-30) REVERT: H 128 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8392 (tm-30) outliers start: 10 outliers final: 4 residues processed: 123 average time/residue: 1.7253 time to fit residues: 224.7048 Evaluate side-chains 116 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.051266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.035248 restraints weight = 53937.036| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.96 r_work: 0.2672 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12633 Z= 0.166 Angle : 0.587 10.936 18299 Z= 0.348 Chirality : 0.033 0.120 2087 Planarity : 0.004 0.035 1304 Dihedral : 31.168 92.855 4071 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.45 % Allowed : 25.24 % Favored : 73.31 % 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: 3.36 (0.31), residues: 730 helix: 2.86 (0.22), residues: 556 sheet: None (None), residues: 0 loop : 0.04 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.006 0.001 PHE A 67 TYR 0.009 0.001 TYR H 63 ARG 0.009 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 753) hydrogen bonds : angle 2.55545 ( 1902) covalent geometry : bond 0.00369 (12633) covalent geometry : angle 0.58687 (18299) *********************** 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 126 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: C 28 MET cc_start: 0.9198 (ptt) cc_final: 0.8927 (ppp) REVERT: C 99 ASP cc_start: 0.8809 (t70) cc_final: 0.7749 (t0) REVERT: C 101 GLU cc_start: 0.8175 (pm20) cc_final: 0.7730 (pm20) REVERT: C 121 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8726 (t0) REVERT: D 91 ASP cc_start: 0.9391 (t70) cc_final: 0.9023 (t0) REVERT: D 94 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8592 (tm-30) REVERT: D 106 TYR cc_start: 0.8796 (m-10) cc_final: 0.8397 (m-80) REVERT: D 128 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8366 (tp30) REVERT: E 122 LYS cc_start: 0.9191 (ptpp) cc_final: 0.8963 (ptmm) REVERT: G 99 ASP cc_start: 0.9224 (t70) cc_final: 0.8593 (t0) REVERT: G 121 ASN cc_start: 0.9135 (OUTLIER) cc_final: 0.8637 (t0) REVERT: H 58 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8346 (mm-30) REVERT: H 91 ASP cc_start: 0.9324 (t0) cc_final: 0.8950 (t0) REVERT: H 94 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8556 (tm-30) REVERT: H 128 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8378 (tm-30) outliers start: 9 outliers final: 3 residues processed: 125 average time/residue: 1.7932 time to fit residues: 237.1444 Evaluate side-chains 115 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.050261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.034181 restraints weight = 53868.003| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.95 r_work: 0.2633 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12633 Z= 0.207 Angle : 0.607 11.434 18299 Z= 0.357 Chirality : 0.034 0.151 2087 Planarity : 0.004 0.035 1304 Dihedral : 31.377 91.891 4071 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.45 % Allowed : 26.21 % Favored : 72.35 % 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: 3.28 (0.31), residues: 730 helix: 2.82 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.07 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE E 78 TYR 0.012 0.002 TYR B 88 ARG 0.007 0.000 ARG H 105 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 753) hydrogen bonds : angle 2.70515 ( 1902) covalent geometry : bond 0.00465 (12633) covalent geometry : angle 0.60738 (18299) *********************** 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 123 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASP cc_start: 0.8886 (t70) cc_final: 0.7775 (t0) REVERT: C 101 GLU cc_start: 0.8256 (pm20) cc_final: 0.7755 (pm20) REVERT: C 121 ASN cc_start: 0.9205 (OUTLIER) cc_final: 0.8734 (t0) REVERT: D 82 MET cc_start: 0.9547 (tpt) cc_final: 0.9070 (mmm) REVERT: D 91 ASP cc_start: 0.9391 (t70) cc_final: 0.9040 (t0) REVERT: D 94 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8610 (tm-30) REVERT: D 128 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8470 (tp30) REVERT: G 99 ASP cc_start: 0.9259 (t70) cc_final: 0.8841 (t0) REVERT: G 121 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.8660 (t0) REVERT: H 58 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8535 (mm-30) REVERT: H 91 ASP cc_start: 0.9338 (t0) cc_final: 0.8964 (t0) REVERT: H 94 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8579 (tm-30) REVERT: H 128 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8407 (tm-30) outliers start: 9 outliers final: 5 residues processed: 121 average time/residue: 2.5056 time to fit residues: 321.1751 Evaluate side-chains 118 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.049198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.033334 restraints weight = 54403.906| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 1.91 r_work: 0.2596 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 12633 Z= 0.251 Angle : 0.639 10.845 18299 Z= 0.372 Chirality : 0.036 0.144 2087 Planarity : 0.004 0.035 1304 Dihedral : 31.660 93.859 4071 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.77 % Allowed : 25.40 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.16 (0.31), residues: 730 helix: 2.76 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.20 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE G 34 TYR 0.014 0.002 TYR F 88 ARG 0.007 0.000 ARG C 80 Details of bonding type rmsd hydrogen bonds : bond 0.04847 ( 753) hydrogen bonds : angle 2.78055 ( 1902) covalent geometry : bond 0.00568 (12633) covalent geometry : angle 0.63883 (18299) *********************** 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 123 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: C 99 ASP cc_start: 0.8966 (t70) cc_final: 0.7871 (t0) REVERT: C 101 GLU cc_start: 0.8239 (pm20) cc_final: 0.7831 (pm20) REVERT: C 121 ASN cc_start: 0.9254 (OUTLIER) cc_final: 0.8739 (t0) REVERT: D 91 ASP cc_start: 0.9370 (t70) cc_final: 0.9005 (t0) REVERT: D 94 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8613 (tm-30) REVERT: D 106 TYR cc_start: 0.8817 (m-10) cc_final: 0.8354 (m-80) REVERT: D 128 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8487 (tp30) REVERT: G 99 ASP cc_start: 0.9240 (t70) cc_final: 0.8788 (t0) REVERT: G 121 ASN cc_start: 0.9223 (OUTLIER) cc_final: 0.8689 (t0) REVERT: H 58 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8528 (mm-30) REVERT: H 91 ASP cc_start: 0.9330 (t0) cc_final: 0.8966 (t0) REVERT: H 94 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8567 (tm-30) REVERT: H 106 TYR cc_start: 0.8753 (m-10) cc_final: 0.8449 (m-80) REVERT: H 128 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8434 (tm-30) outliers start: 11 outliers final: 6 residues processed: 121 average time/residue: 2.5919 time to fit residues: 333.8221 Evaluate side-chains 117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.048953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.033276 restraints weight = 54260.816| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 1.90 r_work: 0.2591 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 12633 Z= 0.250 Angle : 0.643 12.315 18299 Z= 0.374 Chirality : 0.036 0.146 2087 Planarity : 0.004 0.034 1304 Dihedral : 31.678 95.693 4071 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.77 % Allowed : 25.56 % Favored : 72.67 % 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: 3.19 (0.31), residues: 730 helix: 2.78 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.19 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE E 78 TYR 0.018 0.002 TYR F 88 ARG 0.007 0.000 ARG C 80 Details of bonding type rmsd hydrogen bonds : bond 0.04694 ( 753) hydrogen bonds : angle 2.75647 ( 1902) covalent geometry : bond 0.00565 (12633) covalent geometry : angle 0.64329 (18299) *********************** 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 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: C 99 ASP cc_start: 0.9009 (t70) cc_final: 0.7899 (t0) REVERT: C 101 GLU cc_start: 0.8255 (pm20) cc_final: 0.7747 (pm20) REVERT: C 121 ASN cc_start: 0.9256 (OUTLIER) cc_final: 0.8748 (t0) REVERT: D 91 ASP cc_start: 0.9356 (t70) cc_final: 0.9009 (t0) REVERT: D 94 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8618 (tm-30) REVERT: D 106 TYR cc_start: 0.8815 (m-10) cc_final: 0.8342 (m-80) REVERT: D 128 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8478 (tp30) REVERT: G 99 ASP cc_start: 0.9247 (t70) cc_final: 0.8818 (t0) REVERT: G 121 ASN cc_start: 0.9237 (OUTLIER) cc_final: 0.8685 (t0) REVERT: H 58 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8532 (mm-30) REVERT: H 91 ASP cc_start: 0.9338 (t0) cc_final: 0.8978 (t0) REVERT: H 94 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8566 (tm-30) REVERT: H 106 TYR cc_start: 0.8739 (m-10) cc_final: 0.8500 (m-80) REVERT: H 128 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8422 (tm-30) outliers start: 11 outliers final: 6 residues processed: 118 average time/residue: 1.6767 time to fit residues: 210.2447 Evaluate side-chains 114 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.049699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.034057 restraints weight = 53307.311| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.88 r_work: 0.2625 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12633 Z= 0.182 Angle : 0.625 12.297 18299 Z= 0.364 Chirality : 0.034 0.132 2087 Planarity : 0.004 0.035 1304 Dihedral : 31.452 95.093 4071 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.29 % Allowed : 26.05 % Favored : 72.67 % 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: 3.27 (0.31), residues: 730 helix: 2.84 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.17 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.007 0.001 PHE A 67 TYR 0.017 0.002 TYR F 88 ARG 0.008 0.000 ARG D 105 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 753) hydrogen bonds : angle 2.62244 ( 1902) covalent geometry : bond 0.00410 (12633) covalent geometry : angle 0.62452 (18299) ********************** 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 118 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 99 ASP cc_start: 0.8865 (t70) cc_final: 0.7827 (t0) REVERT: C 101 GLU cc_start: 0.8279 (pm20) cc_final: 0.7874 (pm20) REVERT: C 121 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.8746 (t0) REVERT: D 82 MET cc_start: 0.9489 (tpt) cc_final: 0.9232 (mmm) REVERT: D 91 ASP cc_start: 0.9345 (t70) cc_final: 0.8986 (t0) REVERT: D 94 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8594 (tm-30) REVERT: D 106 TYR cc_start: 0.8806 (m-10) cc_final: 0.8339 (m-80) REVERT: D 128 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8495 (tp30) REVERT: G 99 ASP cc_start: 0.9238 (t70) cc_final: 0.8834 (t0) REVERT: G 121 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.8691 (t0) REVERT: H 58 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8556 (mm-30) REVERT: H 91 ASP cc_start: 0.9309 (t0) cc_final: 0.8947 (t0) REVERT: H 94 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8566 (tm-30) REVERT: H 128 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8398 (tm-30) outliers start: 8 outliers final: 6 residues processed: 118 average time/residue: 1.7100 time to fit residues: 214.6124 Evaluate side-chains 116 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.049965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.034411 restraints weight = 53548.292| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.88 r_work: 0.2640 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12633 Z= 0.165 Angle : 0.622 13.326 18299 Z= 0.362 Chirality : 0.034 0.138 2087 Planarity : 0.004 0.035 1304 Dihedral : 31.418 94.905 4071 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.77 % Allowed : 25.72 % Favored : 72.51 % 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: 3.27 (0.31), residues: 730 helix: 2.83 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.13 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.007 0.001 PHE E 67 TYR 0.021 0.001 TYR B 88 ARG 0.007 0.000 ARG D 105 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 753) hydrogen bonds : angle 2.57695 ( 1902) covalent geometry : bond 0.00369 (12633) covalent geometry : angle 0.62217 (18299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7946.21 seconds wall clock time: 140 minutes 34.38 seconds (8434.38 seconds total)