Starting phenix.real_space_refine on Wed Aug 5 21:56:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k46_62048/08_2026/9k46_62048.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k46_62048/08_2026/9k46_62048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k46_62048/08_2026/9k46_62048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k46_62048/08_2026/9k46_62048.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k46_62048/08_2026/9k46_62048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k46_62048/08_2026/9k46_62048.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.051 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 6597 2.51 5 N 2172 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 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11844 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 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: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 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: 2.29, per 1000 atoms: 0.19 Number of scatterers: 11844 At special positions: 0 Unit cell: (123.28, 80.4, 115.776, 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 2172 7.00 C 6597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 207.3 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 72.4% alpha, 3.2% beta 144 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 1.62 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 131 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: 3.590A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 25 through 30 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 98 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 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.587A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 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 127 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.090A 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: 6.824A 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: 7.224A 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: 7.149A 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: 7.123A 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 87 408 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 346 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 1.13 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: 2001 1.33 - 1.45: 4263 1.45 - 1.57: 5784 1.57 - 1.69: 577 1.69 - 1.81: 26 Bond restraints: 12651 Sorted by residual: bond pdb=" O3' DG I -26 " pdb=" P DT I -25 " ideal model delta sigma weight residual 1.607 1.668 -0.061 1.20e-02 6.94e+03 2.56e+01 bond pdb=" O3' DT J -36 " pdb=" P DG J -35 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.20e-02 6.94e+03 1.84e+01 bond pdb=" O3' DC J -24 " pdb=" P DC J -23 " ideal model delta sigma weight residual 1.607 1.655 -0.048 1.20e-02 6.94e+03 1.63e+01 bond pdb=" O3' DA J 46 " pdb=" P DT J 47 " ideal model delta sigma weight residual 1.607 1.653 -0.046 1.20e-02 6.94e+03 1.45e+01 bond pdb=" C3' DA I -20 " pdb=" C2' DA I -20 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 ... (remaining 12646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 15888 1.03 - 2.07: 1732 2.07 - 3.10: 647 3.10 - 4.14: 47 4.14 - 5.17: 11 Bond angle restraints: 18325 Sorted by residual: angle pdb=" N3 DT I -11 " pdb=" C4 DT I -11 " pdb=" O4 DT I -11 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT I 22 " pdb=" C4 DT I 22 " pdb=" O4 DT I 22 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT I -53 " pdb=" C4 DT I -53 " pdb=" O4 DT I -53 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT I -33 " pdb=" C4 DT I -33 " pdb=" O4 DT I -33 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT I -69 " pdb=" C4 DT I -69 " pdb=" O4 DT I -69 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 ... (remaining 18320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.36: 4612 23.36 - 46.72: 1515 46.72 - 70.08: 789 70.08 - 93.44: 26 93.44 - 116.80: 1 Dihedral angle restraints: 6943 sinusoidal: 4791 harmonic: 2152 Sorted by residual: 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 -23.20 -116.80 1 3.50e+01 8.16e-04 1.14e+01 dihedral pdb=" CG ARG E 49 " pdb=" CD ARG E 49 " pdb=" NE ARG E 49 " pdb=" CZ ARG E 49 " ideal model delta sinusoidal sigma weight residual 180.00 137.26 42.74 2 1.50e+01 4.44e-03 9.83e+00 dihedral pdb=" CG ARG G 97 " pdb=" CD ARG G 97 " pdb=" NE ARG G 97 " pdb=" CZ ARG G 97 " ideal model delta sinusoidal sigma weight residual -180.00 -137.43 -42.57 2 1.50e+01 4.44e-03 9.76e+00 ... (remaining 6940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1129 0.031 - 0.061: 616 0.061 - 0.092: 218 0.092 - 0.122: 114 0.122 - 0.153: 12 Chirality restraints: 2089 Sorted by residual: chirality pdb=" P DC J 44 " pdb=" OP1 DC J 44 " pdb=" OP2 DC J 44 " pdb=" O5' DC J 44 " both_signs ideal model delta sigma weight residual True 2.34 -2.49 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" P DA I -8 " pdb=" OP1 DA I -8 " pdb=" OP2 DA I -8 " pdb=" O5' DA I -8 " both_signs ideal model delta sigma weight residual True 2.34 -2.49 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" P DT I 13 " pdb=" OP1 DT I 13 " pdb=" OP2 DT I 13 " pdb=" O5' DT I 13 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 2086 not shown) Planarity restraints: 1306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 59 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C LYS B 59 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS B 59 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE B 60 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C LYS F 59 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS F 59 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE F 60 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 52 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" CD GLU F 52 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU F 52 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU F 52 " -0.009 2.00e-02 2.50e+03 ... (remaining 1303 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 910 2.74 - 3.28: 10492 3.28 - 3.82: 23150 3.82 - 4.36: 28452 4.36 - 4.90: 40346 Nonbonded interactions: 103350 Sorted by model distance: nonbonded pdb=" NH2 ARG C 41 " pdb=" OE1 GLU D 58 " model vdw 2.198 3.120 nonbonded pdb=" O ASN G 82 " pdb=" ND2 ASN G 82 " model vdw 2.201 3.120 nonbonded pdb=" O ASN C 82 " pdb=" ND2 ASN C 82 " model vdw 2.203 3.120 nonbonded pdb=" OH TYR C 48 " pdb=" OE2 GLU D 94 " model vdw 2.216 3.040 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.250 3.040 ... (remaining 103345 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: 1.360 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: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.400 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 12651 Z= 0.507 Angle : 0.754 5.173 18325 Z= 0.688 Chirality : 0.045 0.153 2089 Planarity : 0.004 0.034 1306 Dihedral : 29.027 116.802 5555 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.80 % Allowed : 20.67 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.30), residues: 730 helix: 1.32 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.06 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 41 TYR 0.016 0.001 TYR H 63 PHE 0.006 0.001 PHE G 34 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.51 (12651) covalent geometry : angle 0.75397 / 0.69 (18325) hydrogen bonds : bond 0.12183 / 8.32 ( 754) hydrogen bonds : angle 5.19157 / 3.75 ( 1898) *********************** 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 183 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 178 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8470 (tt0) cc_final: 0.7793 (tt0) REVERT: C 121 ASN cc_start: 0.9122 (t0) cc_final: 0.8887 (t0) REVERT: D 56 ASN cc_start: 0.9292 (m-40) cc_final: 0.9029 (m-40) REVERT: D 91 ASP cc_start: 0.8784 (t0) cc_final: 0.8551 (t0) REVERT: E 73 GLU cc_start: 0.8338 (tt0) cc_final: 0.7702 (tt0) REVERT: F 27 GLN cc_start: 0.9224 (tp40) cc_final: 0.9007 (mp10) REVERT: G 121 ASN cc_start: 0.9198 (t0) cc_final: 0.8962 (t0) REVERT: H 91 ASP cc_start: 0.8689 (t0) cc_final: 0.8483 (t0) outliers start: 5 outliers final: 4 residues processed: 181 average time/residue: 0.6857 time to fit residues: 131.5059 Evaluate side-chains 147 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 143 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 82 ASN D 107 ASN D 132 HIS G 82 ASN H 56 ASN H 107 ASN H 132 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.066122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.044131 restraints weight = 40167.156| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.91 r_work: 0.2629 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12651 Z= 0.183 Angle : 0.685 8.812 18325 Z= 0.394 Chirality : 0.045 0.224 2089 Planarity : 0.005 0.041 1306 Dihedral : 31.635 123.866 4082 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.37 % Allowed : 23.24 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.30), residues: 730 helix: 2.16 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.10 (0.42), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 80 TYR 0.017 0.002 TYR F 51 PHE 0.007 0.001 PHE A 67 HIS 0.004 0.001 HIS H 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.18 (12651) covalent geometry : angle 0.68470 / 0.39 (18325) hydrogen bonds : bond 0.05514 / 3.72 ( 754) hydrogen bonds : angle 3.24487 / 2.34 ( 1898) *********************** 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 170 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8587 (pm20) cc_final: 0.8120 (pm20) REVERT: A 73 GLU cc_start: 0.8698 (tt0) cc_final: 0.8261 (tt0) REVERT: A 94 GLU cc_start: 0.8875 (tp30) cc_final: 0.8642 (tt0) REVERT: C 80 ARG cc_start: 0.9175 (ttm-80) cc_final: 0.8965 (ttp80) REVERT: C 82 ASN cc_start: 0.8885 (t0) cc_final: 0.8637 (t160) REVERT: C 99 ASP cc_start: 0.8810 (t0) cc_final: 0.8154 (t0) REVERT: C 104 LYS cc_start: 0.9566 (ttpt) cc_final: 0.9329 (ttmm) REVERT: C 121 ASN cc_start: 0.8860 (t0) cc_final: 0.8449 (t0) REVERT: D 56 ASN cc_start: 0.8969 (m-40) cc_final: 0.8661 (m-40) REVERT: D 91 ASP cc_start: 0.9244 (t0) cc_final: 0.8878 (t0) REVERT: E 73 GLU cc_start: 0.8660 (tt0) cc_final: 0.8356 (tt0) REVERT: F 27 GLN cc_start: 0.9479 (tp40) cc_final: 0.9113 (mp10) REVERT: G 99 ASP cc_start: 0.8761 (t0) cc_final: 0.8103 (t0) REVERT: G 121 ASN cc_start: 0.8906 (t0) cc_final: 0.8561 (t0) REVERT: H 128 GLU cc_start: 0.8538 (tp30) cc_final: 0.8287 (mm-30) outliers start: 21 outliers final: 4 residues processed: 159 average time/residue: 0.6393 time to fit residues: 107.8286 Evaluate side-chains 149 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 145 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 85 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 40.0000 chunk 28 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.063287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.041544 restraints weight = 41452.603| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.96 r_work: 0.2563 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12651 Z= 0.242 Angle : 0.693 9.095 18325 Z= 0.396 Chirality : 0.046 0.221 2089 Planarity : 0.005 0.038 1306 Dihedral : 31.909 126.587 4075 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.72 % Allowed : 23.88 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.30), residues: 730 helix: 2.54 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.19 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 80 TYR 0.014 0.003 TYR H 63 PHE 0.012 0.001 PHE E 67 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.24 (12651) covalent geometry : angle 0.69309 / 0.40 (18325) hydrogen bonds : bond 0.06562 / 4.48 ( 754) hydrogen bonds : angle 3.08763 / 2.23 ( 1898) *********************** 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 163 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8752 (pm20) cc_final: 0.8259 (pm20) REVERT: A 73 GLU cc_start: 0.8705 (tt0) cc_final: 0.8286 (tt0) REVERT: B 88 TYR cc_start: 0.9322 (m-10) cc_final: 0.9114 (m-10) REVERT: C 80 ARG cc_start: 0.9213 (ttm-80) cc_final: 0.8953 (ttp80) REVERT: C 82 ASN cc_start: 0.9034 (t0) cc_final: 0.8762 (t160) REVERT: C 99 ASP cc_start: 0.8965 (t0) cc_final: 0.8627 (t0) REVERT: C 104 LYS cc_start: 0.9584 (ttpt) cc_final: 0.9351 (ttmm) REVERT: C 121 ASN cc_start: 0.8878 (t0) cc_final: 0.8663 (t0) REVERT: D 56 ASN cc_start: 0.9078 (m-40) cc_final: 0.8777 (m-40) REVERT: D 91 ASP cc_start: 0.9338 (t0) cc_final: 0.8933 (t0) REVERT: D 116 GLU cc_start: 0.9051 (mp0) cc_final: 0.8639 (mp0) REVERT: E 59 GLU cc_start: 0.8794 (pm20) cc_final: 0.8446 (pm20) REVERT: E 73 GLU cc_start: 0.8784 (tt0) cc_final: 0.8310 (tt0) REVERT: E 94 GLU cc_start: 0.8786 (tt0) cc_final: 0.8574 (tt0) REVERT: F 27 GLN cc_start: 0.9446 (tp40) cc_final: 0.9151 (mp10) REVERT: F 35 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.7898 (ttm-80) REVERT: F 88 TYR cc_start: 0.9373 (m-10) cc_final: 0.9125 (m-10) REVERT: G 28 MET cc_start: 0.9141 (tmm) cc_final: 0.8877 (tmm) REVERT: G 29 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.9110 (mtpp) REVERT: G 65 GLU cc_start: 0.9332 (tt0) cc_final: 0.9114 (tt0) REVERT: G 80 ARG cc_start: 0.9207 (ttm-80) cc_final: 0.8948 (ttp80) REVERT: G 82 ASN cc_start: 0.8909 (t0) cc_final: 0.8641 (t160) REVERT: G 99 ASP cc_start: 0.8817 (t0) cc_final: 0.8172 (t0) REVERT: G 121 ASN cc_start: 0.8948 (t0) cc_final: 0.8601 (t0) REVERT: H 91 ASP cc_start: 0.9285 (t0) cc_final: 0.8860 (t0) REVERT: H 128 GLU cc_start: 0.8719 (tp30) cc_final: 0.8391 (mm-30) outliers start: 17 outliers final: 8 residues processed: 153 average time/residue: 0.6685 time to fit residues: 108.2194 Evaluate side-chains 153 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 104 LYS Chi-restraints excluded: chain H residue 85 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 44 optimal weight: 0.0370 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.063560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.042070 restraints weight = 41275.620| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 1.97 r_work: 0.2584 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12651 Z= 0.143 Angle : 0.628 8.221 18325 Z= 0.366 Chirality : 0.043 0.207 2089 Planarity : 0.004 0.038 1306 Dihedral : 31.768 130.102 4075 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.24 % Allowed : 24.04 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.31 (0.30), residues: 730 helix: 2.85 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.03 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 80 TYR 0.013 0.001 TYR H 63 PHE 0.009 0.001 PHE A 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (12651) covalent geometry : angle 0.62761 / 0.37 (18325) hydrogen bonds : bond 0.04250 / 2.94 ( 754) hydrogen bonds : angle 2.79216 / 2.01 ( 1898) *********************** 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 174 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8804 (pm20) cc_final: 0.7841 (pm20) REVERT: A 73 GLU cc_start: 0.8769 (tt0) cc_final: 0.8362 (tt0) REVERT: A 94 GLU cc_start: 0.8781 (tp30) cc_final: 0.8573 (tt0) REVERT: B 85 ASP cc_start: 0.9340 (m-30) cc_final: 0.9131 (m-30) REVERT: C 82 ASN cc_start: 0.9042 (t0) cc_final: 0.8790 (t160) REVERT: C 99 ASP cc_start: 0.8977 (t0) cc_final: 0.8628 (t0) REVERT: C 104 LYS cc_start: 0.9581 (ttpt) cc_final: 0.9347 (ttmm) REVERT: C 121 ASN cc_start: 0.8898 (t0) cc_final: 0.8490 (t0) REVERT: D 56 ASN cc_start: 0.9047 (m-40) cc_final: 0.8802 (m-40) REVERT: D 91 ASP cc_start: 0.9315 (t0) cc_final: 0.8902 (t0) REVERT: D 116 GLU cc_start: 0.8962 (mp0) cc_final: 0.8412 (mp0) REVERT: D 128 GLU cc_start: 0.8708 (tp30) cc_final: 0.8310 (mm-30) REVERT: E 59 GLU cc_start: 0.8616 (pm20) cc_final: 0.8258 (pm20) REVERT: E 73 GLU cc_start: 0.8823 (tt0) cc_final: 0.8424 (tt0) REVERT: E 131 ARG cc_start: 0.9357 (OUTLIER) cc_final: 0.9155 (mtp85) REVERT: F 27 GLN cc_start: 0.9482 (OUTLIER) cc_final: 0.9161 (mp10) REVERT: G 99 ASP cc_start: 0.8787 (t0) cc_final: 0.8060 (t0) REVERT: G 104 LYS cc_start: 0.9564 (ttpt) cc_final: 0.9322 (ttmm) REVERT: G 121 ASN cc_start: 0.8918 (t0) cc_final: 0.8387 (t0) REVERT: H 128 GLU cc_start: 0.8634 (tp30) cc_final: 0.8367 (mm-30) outliers start: 14 outliers final: 7 residues processed: 164 average time/residue: 0.6141 time to fit residues: 106.9488 Evaluate side-chains 155 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 85 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 86 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 87 optimal weight: 30.0000 chunk 51 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.063133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.041777 restraints weight = 41572.615| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 1.96 r_work: 0.2572 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12651 Z= 0.169 Angle : 0.641 11.313 18325 Z= 0.370 Chirality : 0.044 0.209 2089 Planarity : 0.004 0.043 1306 Dihedral : 31.758 130.513 4073 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.08 % Allowed : 24.84 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.41 (0.30), residues: 730 helix: 2.93 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.02 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 80 TYR 0.012 0.001 TYR H 63 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 (12651) covalent geometry : angle 0.64077 / 0.37 (18325) hydrogen bonds : bond 0.04602 / 3.16 ( 754) hydrogen bonds : angle 2.79335 / 2.01 ( 1898) *********************** 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 157 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8679 (pm20) cc_final: 0.8308 (pm20) REVERT: A 73 GLU cc_start: 0.8752 (tt0) cc_final: 0.8376 (tt0) REVERT: B 85 ASP cc_start: 0.9339 (m-30) cc_final: 0.9132 (m-30) REVERT: C 99 ASP cc_start: 0.8970 (t0) cc_final: 0.8636 (t0) REVERT: C 104 LYS cc_start: 0.9585 (ttpt) cc_final: 0.9353 (ttmm) REVERT: C 121 ASN cc_start: 0.8885 (t0) cc_final: 0.8599 (t0) REVERT: D 56 ASN cc_start: 0.9025 (m-40) cc_final: 0.8731 (m-40) REVERT: D 91 ASP cc_start: 0.9322 (t0) cc_final: 0.8912 (t0) REVERT: D 116 GLU cc_start: 0.8972 (mp0) cc_final: 0.8510 (mp0) REVERT: E 59 GLU cc_start: 0.8639 (pm20) cc_final: 0.8264 (pm20) REVERT: E 73 GLU cc_start: 0.8780 (tt0) cc_final: 0.8350 (tt0) REVERT: F 27 GLN cc_start: 0.9426 (tp40) cc_final: 0.9168 (mp10) REVERT: F 35 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8040 (ttm-80) REVERT: F 85 ASP cc_start: 0.9342 (m-30) cc_final: 0.9133 (m-30) REVERT: G 28 MET cc_start: 0.9175 (tmm) cc_final: 0.8902 (tmm) REVERT: G 99 ASP cc_start: 0.8751 (t0) cc_final: 0.8033 (t0) REVERT: G 104 LYS cc_start: 0.9556 (ttpt) cc_final: 0.9325 (ttmm) REVERT: G 121 ASN cc_start: 0.8876 (t0) cc_final: 0.8316 (t0) REVERT: H 128 GLU cc_start: 0.8621 (tp30) cc_final: 0.8375 (mm-30) outliers start: 13 outliers final: 10 residues processed: 151 average time/residue: 0.6837 time to fit residues: 109.3255 Evaluate side-chains 153 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 85 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 32 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 85 optimal weight: 40.0000 chunk 22 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.062112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.040732 restraints weight = 41890.789| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.02 r_work: 0.2547 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12651 Z= 0.199 Angle : 0.671 11.942 18325 Z= 0.379 Chirality : 0.045 0.214 2089 Planarity : 0.004 0.046 1306 Dihedral : 31.878 131.330 4073 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.72 % Allowed : 25.16 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.43 (0.30), residues: 730 helix: 2.96 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.08 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 80 TYR 0.013 0.002 TYR H 63 PHE 0.012 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 (12651) covalent geometry : angle 0.67118 / 0.38 (18325) hydrogen bonds : bond 0.05211 / 3.58 ( 754) hydrogen bonds : angle 2.86455 / 2.06 ( 1898) *********************** 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 160 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8660 (pm20) cc_final: 0.8215 (pm20) REVERT: A 73 GLU cc_start: 0.8796 (tt0) cc_final: 0.8402 (tt0) REVERT: C 99 ASP cc_start: 0.9005 (t0) cc_final: 0.8643 (t0) REVERT: C 104 LYS cc_start: 0.9577 (ttpt) cc_final: 0.9343 (ttmm) REVERT: C 121 ASN cc_start: 0.8897 (t0) cc_final: 0.8599 (t0) REVERT: D 56 ASN cc_start: 0.9072 (m-40) cc_final: 0.8362 (m-40) REVERT: D 91 ASP cc_start: 0.9351 (t0) cc_final: 0.8934 (t0) REVERT: D 116 GLU cc_start: 0.8993 (mp0) cc_final: 0.8515 (mp0) REVERT: E 59 GLU cc_start: 0.8653 (pm20) cc_final: 0.8253 (pm20) REVERT: E 73 GLU cc_start: 0.8932 (tt0) cc_final: 0.8635 (tt0) REVERT: F 27 GLN cc_start: 0.9413 (OUTLIER) cc_final: 0.9116 (mp10) REVERT: F 35 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8027 (ttm-80) REVERT: F 85 ASP cc_start: 0.9359 (m-30) cc_final: 0.9141 (m-30) REVERT: G 28 MET cc_start: 0.9264 (tmm) cc_final: 0.9010 (tmm) REVERT: G 99 ASP cc_start: 0.8720 (t0) cc_final: 0.7986 (t0) REVERT: G 121 ASN cc_start: 0.8892 (t0) cc_final: 0.8354 (t0) REVERT: H 116 GLU cc_start: 0.9016 (mp0) cc_final: 0.8397 (mp0) REVERT: H 128 GLU cc_start: 0.8645 (tp30) cc_final: 0.8326 (mm-30) outliers start: 17 outliers final: 9 residues processed: 149 average time/residue: 0.6569 time to fit residues: 103.6426 Evaluate side-chains 151 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 85 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 30.0000 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 97 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.062884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.041833 restraints weight = 41320.118| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.95 r_work: 0.2582 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12651 Z= 0.135 Angle : 0.632 12.985 18325 Z= 0.365 Chirality : 0.043 0.211 2089 Planarity : 0.004 0.040 1306 Dihedral : 31.745 132.685 4073 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.08 % Allowed : 27.56 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.54 (0.30), residues: 730 helix: 3.03 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.01 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 80 TYR 0.013 0.001 TYR H 63 PHE 0.011 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.14 (12651) covalent geometry : angle 0.63185 / 0.37 (18325) hydrogen bonds : bond 0.04066 / 2.81 ( 754) hydrogen bonds : angle 2.68481 / 1.94 ( 1898) *********************** 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 165 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8664 (pm20) cc_final: 0.8266 (pm20) REVERT: C 99 ASP cc_start: 0.8975 (t0) cc_final: 0.8640 (t0) REVERT: C 104 LYS cc_start: 0.9586 (ttpt) cc_final: 0.9350 (ttmm) REVERT: C 121 ASN cc_start: 0.8906 (t0) cc_final: 0.8586 (t0) REVERT: D 91 ASP cc_start: 0.9331 (t0) cc_final: 0.8888 (t0) REVERT: D 94 GLU cc_start: 0.9138 (tp30) cc_final: 0.8864 (tp30) REVERT: D 116 GLU cc_start: 0.8946 (mp0) cc_final: 0.8388 (mp0) REVERT: D 128 GLU cc_start: 0.8703 (tp30) cc_final: 0.8297 (mm-30) REVERT: E 59 GLU cc_start: 0.8663 (pm20) cc_final: 0.8288 (pm20) REVERT: F 27 GLN cc_start: 0.9438 (tp40) cc_final: 0.9031 (mp10) REVERT: F 35 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.7998 (ttm-80) REVERT: F 85 ASP cc_start: 0.9370 (m-30) cc_final: 0.9165 (m-30) REVERT: G 28 MET cc_start: 0.9247 (tmm) cc_final: 0.8892 (tmm) REVERT: G 99 ASP cc_start: 0.8700 (t0) cc_final: 0.7966 (t0) REVERT: G 101 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8609 (mt-10) REVERT: G 104 LYS cc_start: 0.9555 (ttpt) cc_final: 0.9320 (ttmm) REVERT: G 121 ASN cc_start: 0.8910 (t0) cc_final: 0.8339 (t0) REVERT: H 128 GLU cc_start: 0.8598 (tp30) cc_final: 0.8315 (mm-30) outliers start: 13 outliers final: 6 residues processed: 159 average time/residue: 0.6648 time to fit residues: 112.2001 Evaluate side-chains 151 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 85 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 83 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 chunk 95 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.062592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.041404 restraints weight = 41663.400| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 1.97 r_work: 0.2575 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12651 Z= 0.162 Angle : 0.653 13.437 18325 Z= 0.373 Chirality : 0.043 0.210 2089 Planarity : 0.004 0.039 1306 Dihedral : 31.720 132.978 4073 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.08 % Allowed : 28.69 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.48 (0.30), residues: 730 helix: 2.99 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.03 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 80 TYR 0.012 0.002 TYR H 63 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (12651) covalent geometry : angle 0.65273 / 0.37 (18325) hydrogen bonds : bond 0.04391 / 3.02 ( 754) hydrogen bonds : angle 2.72046 / 1.97 ( 1898) *********************** 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 158 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8633 (pm20) cc_final: 0.8235 (pm20) REVERT: C 99 ASP cc_start: 0.8992 (t0) cc_final: 0.8632 (t0) REVERT: C 104 LYS cc_start: 0.9592 (ttpt) cc_final: 0.9350 (ttmm) REVERT: C 121 ASN cc_start: 0.8898 (t0) cc_final: 0.8426 (t0) REVERT: D 91 ASP cc_start: 0.9344 (t0) cc_final: 0.8908 (t0) REVERT: D 94 GLU cc_start: 0.9127 (tp30) cc_final: 0.8857 (tp30) REVERT: D 116 GLU cc_start: 0.8964 (mp0) cc_final: 0.8539 (mp0) REVERT: D 128 GLU cc_start: 0.8756 (tp30) cc_final: 0.8307 (mm-30) REVERT: E 59 GLU cc_start: 0.8670 (pm20) cc_final: 0.7757 (pm20) REVERT: F 27 GLN cc_start: 0.9414 (OUTLIER) cc_final: 0.9116 (mp10) REVERT: F 35 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8019 (ttm-80) REVERT: G 28 MET cc_start: 0.9277 (tmm) cc_final: 0.9038 (tmm) REVERT: G 99 ASP cc_start: 0.8706 (t0) cc_final: 0.7936 (t0) REVERT: G 104 LYS cc_start: 0.9565 (ttpt) cc_final: 0.9328 (ttmm) REVERT: G 121 ASN cc_start: 0.8895 (t0) cc_final: 0.8345 (t0) REVERT: H 91 ASP cc_start: 0.9241 (t0) cc_final: 0.8818 (t0) REVERT: H 128 GLU cc_start: 0.8604 (tp30) cc_final: 0.8307 (mm-30) outliers start: 13 outliers final: 9 residues processed: 153 average time/residue: 0.7039 time to fit residues: 114.2307 Evaluate side-chains 153 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 85 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 87 optimal weight: 30.0000 chunk 41 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.062976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.041836 restraints weight = 41202.938| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 1.96 r_work: 0.2584 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12651 Z= 0.142 Angle : 0.642 13.654 18325 Z= 0.370 Chirality : 0.043 0.210 2089 Planarity : 0.004 0.044 1306 Dihedral : 31.648 133.511 4073 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.24 % Allowed : 29.01 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.30), residues: 730 helix: 3.00 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.03 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 80 TYR 0.012 0.002 TYR H 63 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (12651) covalent geometry : angle 0.64177 / 0.37 (18325) hydrogen bonds : bond 0.03982 / 2.75 ( 754) hydrogen bonds : angle 2.65693 / 1.93 ( 1898) *********************** 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 162 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8626 (pm20) cc_final: 0.8248 (pm20) REVERT: A 131 ARG cc_start: 0.9465 (OUTLIER) cc_final: 0.9207 (mtp85) REVERT: B 96 THR cc_start: 0.9646 (m) cc_final: 0.9124 (p) REVERT: C 99 ASP cc_start: 0.8980 (t0) cc_final: 0.8631 (t0) REVERT: C 104 LYS cc_start: 0.9590 (ttpt) cc_final: 0.9356 (ttmm) REVERT: C 121 ASN cc_start: 0.8887 (t0) cc_final: 0.8408 (t0) REVERT: D 91 ASP cc_start: 0.9347 (t0) cc_final: 0.8884 (t0) REVERT: D 94 GLU cc_start: 0.9121 (tp30) cc_final: 0.8857 (tp30) REVERT: D 116 GLU cc_start: 0.8966 (mp0) cc_final: 0.8409 (mp0) REVERT: D 128 GLU cc_start: 0.8695 (tp30) cc_final: 0.8299 (mm-30) REVERT: E 59 GLU cc_start: 0.8720 (pm20) cc_final: 0.8484 (pm20) REVERT: F 27 GLN cc_start: 0.9413 (OUTLIER) cc_final: 0.9097 (mp10) REVERT: G 28 MET cc_start: 0.9301 (tmm) cc_final: 0.9030 (tmm) REVERT: G 99 ASP cc_start: 0.8683 (t0) cc_final: 0.7922 (t0) REVERT: G 104 LYS cc_start: 0.9559 (ttpt) cc_final: 0.9319 (ttmm) REVERT: H 128 GLU cc_start: 0.8577 (tp30) cc_final: 0.8296 (mm-30) outliers start: 14 outliers final: 9 residues processed: 158 average time/residue: 0.6674 time to fit residues: 111.8091 Evaluate side-chains 154 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 85 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.062694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.041592 restraints weight = 41656.748| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.04 r_work: 0.2577 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12651 Z= 0.154 Angle : 0.655 14.860 18325 Z= 0.374 Chirality : 0.043 0.210 2089 Planarity : 0.004 0.043 1306 Dihedral : 31.619 133.675 4073 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.92 % Allowed : 29.17 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.44 (0.30), residues: 730 helix: 2.97 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.05 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 80 TYR 0.016 0.002 TYR B 88 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (12651) covalent geometry : angle 0.65481 / 0.37 (18325) hydrogen bonds : bond 0.04231 / 2.91 ( 754) hydrogen bonds : angle 2.70746 / 1.96 ( 1898) ********************** 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 155 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8605 (pm20) cc_final: 0.8214 (pm20) REVERT: A 131 ARG cc_start: 0.9453 (OUTLIER) cc_final: 0.9184 (mtp85) REVERT: C 99 ASP cc_start: 0.8979 (t0) cc_final: 0.8610 (t0) REVERT: C 104 LYS cc_start: 0.9592 (ttpt) cc_final: 0.9365 (ttmm) REVERT: C 121 ASN cc_start: 0.8857 (t0) cc_final: 0.8372 (t0) REVERT: C 122 SER cc_start: 0.9461 (p) cc_final: 0.9255 (t) REVERT: D 91 ASP cc_start: 0.9334 (t0) cc_final: 0.8887 (t0) REVERT: D 94 GLU cc_start: 0.9124 (tp30) cc_final: 0.8846 (tp30) REVERT: D 116 GLU cc_start: 0.8942 (mp0) cc_final: 0.8387 (mp0) REVERT: D 128 GLU cc_start: 0.8717 (tp30) cc_final: 0.8284 (mm-30) REVERT: E 59 GLU cc_start: 0.8648 (pm20) cc_final: 0.8212 (pm20) REVERT: F 27 GLN cc_start: 0.9415 (OUTLIER) cc_final: 0.9108 (mp10) REVERT: G 28 MET cc_start: 0.9339 (tmm) cc_final: 0.9067 (tmm) REVERT: G 99 ASP cc_start: 0.8662 (t0) cc_final: 0.7925 (t0) REVERT: G 104 LYS cc_start: 0.9560 (ttpt) cc_final: 0.9324 (ttmm) REVERT: H 91 ASP cc_start: 0.9252 (t0) cc_final: 0.8832 (t0) REVERT: H 128 GLU cc_start: 0.8597 (tp30) cc_final: 0.8304 (mm-30) outliers start: 12 outliers final: 8 residues processed: 150 average time/residue: 0.6577 time to fit residues: 104.6876 Evaluate side-chains 151 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 85 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.062249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.041137 restraints weight = 41728.149| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 1.98 r_work: 0.2572 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12651 Z= 0.172 Angle : 0.672 14.021 18325 Z= 0.378 Chirality : 0.043 0.214 2089 Planarity : 0.004 0.039 1306 Dihedral : 31.653 133.761 4073 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.60 % Allowed : 29.81 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.42 (0.30), residues: 730 helix: 2.96 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.12 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 80 TYR 0.017 0.002 TYR F 88 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (12651) covalent geometry : angle 0.67168 / 0.38 (18325) hydrogen bonds : bond 0.04396 / 3.02 ( 754) hydrogen bonds : angle 2.74213 / 1.99 ( 1898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3104.34 seconds wall clock time: 53 minutes 21.17 seconds (3201.17 seconds total)