Starting phenix.real_space_refine on Tue Aug 4 19:50:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9prc_71807/08_2026/9prc_71807.cif Found real_map, /net/cci-nas-00/data/ceres_data/9prc_71807/08_2026/9prc_71807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9prc_71807/08_2026/9prc_71807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9prc_71807/08_2026/9prc_71807.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9prc_71807/08_2026/9prc_71807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9prc_71807/08_2026/9prc_71807.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 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: 4 Type Number sf(0) Gaussians P 152 5.49 5 C 3543 2.51 5 N 1149 2.21 5 O 1649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s 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: 6493 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 422 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 422 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 412 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 48} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 412 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 48} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 412 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 48} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 756 Classifications: {'RNA': 36} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 18} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "K" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 840 Classifications: {'RNA': 40} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 20} Link IDs: {'rna3p': 39} Chain breaks: 1 Chain: "M" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 756 Classifications: {'RNA': 36} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 18} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "P" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 840 Classifications: {'RNA': 40} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 19, 'rna3p_pyr': 16} Link IDs: {'rna2p': 4, 'rna3p': 35} Chain breaks: 1 Time building chain proxies: 1.58, per 1000 atoms: 0.24 Number of scatterers: 6493 At special positions: 0 Unit cell: (120.285, 106.434, 85.293, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 152 15.00 O 1649 8.00 N 1149 7.00 C 3543 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: 0.50 Conformation dependent library (CDL) restraints added in 254.1 milliseconds 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 722 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 96.5% alpha, 0.0% beta 64 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 12 through 48 removed outlier: 3.881A pdb=" N VAL A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 removed outlier: 4.224A pdb=" N ASN A 53 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 48 Processing helix chain 'B' and resid 49 through 59 removed outlier: 4.133A pdb=" N ASN B 53 " --> pdb=" O PRO B 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 48 removed outlier: 3.651A pdb=" N HIS C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 60 removed outlier: 3.627A pdb=" N GLY C 52 " --> pdb=" O HIS C 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 48 Processing helix chain 'D' and resid 48 through 60 removed outlier: 3.792A pdb=" N GLY D 52 " --> pdb=" O HIS D 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 47 removed outlier: 4.222A pdb=" N GLU E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'F' and resid 13 through 47 removed outlier: 4.471A pdb=" N GLU F 47 " --> pdb=" O LYS F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 60 Processing helix chain 'G' and resid 13 through 48 Processing helix chain 'G' and resid 48 through 61 removed outlier: 3.626A pdb=" N GLY G 52 " --> pdb=" O HIS G 48 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS G 61 " --> pdb=" O ILE G 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 47 Processing helix chain 'H' and resid 48 through 60 removed outlier: 3.532A pdb=" N GLY H 52 " --> pdb=" O HIS H 48 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) 311 hydrogen bonds defined for protein. 933 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 128 hydrogen bonds 256 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.29: 729 1.29 - 1.38: 1447 1.38 - 1.46: 1511 1.46 - 1.54: 2899 1.54 - 1.62: 319 Bond restraints: 6905 Sorted by residual: bond pdb=" N9 A P 27 " pdb=" C4 A P 27 " ideal model delta sigma weight residual 1.374 1.361 0.013 6.00e-03 2.78e+04 4.65e+00 bond pdb=" N9 A K 25 " pdb=" C4 A K 25 " ideal model delta sigma weight residual 1.374 1.386 -0.012 6.00e-03 2.78e+04 4.13e+00 bond pdb=" C3' U P 32 " pdb=" O3' U P 32 " ideal model delta sigma weight residual 1.427 1.447 -0.020 1.20e-02 6.94e+03 2.75e+00 bond pdb=" N7 A M 15 " pdb=" C5 A M 15 " ideal model delta sigma weight residual 1.388 1.379 0.009 6.00e-03 2.78e+04 2.03e+00 bond pdb=" C5 A J 37 " pdb=" C6 A J 37 " ideal model delta sigma weight residual 1.406 1.393 0.013 9.00e-03 1.23e+04 2.02e+00 ... (remaining 6900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 9347 1.89 - 3.78: 556 3.78 - 5.67: 33 5.67 - 7.56: 9 7.56 - 9.45: 2 Bond angle restraints: 9947 Sorted by residual: angle pdb=" O5' U K 20 " pdb=" C5' U K 20 " pdb=" C4' U K 20 " ideal model delta sigma weight residual 109.40 114.01 -4.61 8.00e-01 1.56e+00 3.31e+01 angle pdb=" O2 U K 20 " pdb=" C2 U K 20 " pdb=" N3 U K 20 " ideal model delta sigma weight residual 122.20 118.37 3.83 7.00e-01 2.04e+00 2.99e+01 angle pdb=" C3' U P 32 " pdb=" O3' U P 32 " pdb=" P A P 33 " ideal model delta sigma weight residual 119.70 125.76 -6.06 1.20e+00 6.94e-01 2.55e+01 angle pdb=" O5' A P 31 " pdb=" C5' A P 31 " pdb=" C4' A P 31 " ideal model delta sigma weight residual 109.40 113.32 -3.92 8.00e-01 1.56e+00 2.39e+01 angle pdb=" N1 U P 26 " pdb=" C6 U P 26 " pdb=" C5 U P 26 " ideal model delta sigma weight residual 122.70 125.08 -2.38 5.00e-01 4.00e+00 2.28e+01 ... (remaining 9942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 3876 35.69 - 71.39: 301 71.39 - 107.08: 14 107.08 - 142.78: 1 142.78 - 178.47: 3 Dihedral angle restraints: 4195 sinusoidal: 3080 harmonic: 1115 Sorted by residual: dihedral pdb=" O4' U P 34 " pdb=" C1' U P 34 " pdb=" N1 U P 34 " pdb=" C2 U P 34 " ideal model delta sinusoidal sigma weight residual -160.00 18.47 -178.47 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U P 32 " pdb=" C1' U P 32 " pdb=" N1 U P 32 " pdb=" C2 U P 32 " ideal model delta sinusoidal sigma weight residual 232.00 66.49 165.51 1 1.70e+01 3.46e-03 6.54e+01 dihedral pdb=" O4' U P 26 " pdb=" C1' U P 26 " pdb=" N1 U P 26 " pdb=" C2 U P 26 " ideal model delta sinusoidal sigma weight residual -128.00 -24.01 -103.99 1 1.70e+01 3.46e-03 4.13e+01 ... (remaining 4192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 912 0.037 - 0.073: 135 0.073 - 0.110: 23 0.110 - 0.146: 152 0.146 - 0.183: 3 Chirality restraints: 1225 Sorted by residual: chirality pdb=" C1' A P 41 " pdb=" O4' A P 41 " pdb=" C2' A P 41 " pdb=" N9 A P 41 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" P A P 33 " pdb=" OP1 A P 33 " pdb=" OP2 A P 33 " pdb=" O5' A P 33 " both_signs ideal model delta sigma weight residual True 2.41 -2.56 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CB ILE H 54 " pdb=" CA ILE H 54 " pdb=" CG1 ILE H 54 " pdb=" CG2 ILE H 54 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 1222 not shown) Planarity restraints: 705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 28 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.22e+00 pdb=" CD GLU D 28 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU D 28 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU D 28 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 15 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" CD GLU D 15 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU D 15 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU D 15 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 28 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" CD GLU G 28 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU G 28 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU G 28 " 0.011 2.00e-02 2.50e+03 ... (remaining 702 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 838 2.75 - 3.29: 6294 3.29 - 3.82: 12980 3.82 - 4.36: 13699 4.36 - 4.90: 19686 Nonbonded interactions: 53497 Sorted by model distance: nonbonded pdb=" O4 U P 12 " pdb=" N6 A P 33 " model vdw 2.208 3.120 nonbonded pdb=" OD1 ASN D 53 " pdb=" O2' U J 32 " model vdw 2.212 3.040 nonbonded pdb=" OE2 GLU B 31 " pdb=" NH1 ARG B 35 " model vdw 2.246 3.120 nonbonded pdb=" OE2 GLU B 29 " pdb=" NH1 ARG B 32 " model vdw 2.287 3.120 nonbonded pdb=" O2 U P 10 " pdb=" N6 A P 35 " model vdw 2.302 3.120 ... (remaining 53492 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 12 through 60) selection = (chain 'B' and resid 12 through 60) selection = (chain 'C' and resid 12 through 60) selection = chain 'D' selection = (chain 'E' and resid 12 through 60) selection = chain 'F' selection = (chain 'G' and resid 12 through 60) selection = chain 'H' } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 5 through 44) selection = chain 'M' selection = (chain 'P' and resid 5 through 44) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 7.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.940 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 0.041 6905 Z= 0.250 Angle : 0.781 9.447 9947 Z= 0.589 Chirality : 0.053 0.183 1225 Planarity : 0.004 0.034 705 Dihedral : 19.631 178.472 3473 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.62 % Allowed : 37.21 % Favored : 60.17 % 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: 5.49 (0.40), residues: 385 helix: 3.77 (0.25), residues: 369 sheet: None (None), residues: 0 loop : -2.31 (1.03), residues: 16 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 32 TRP 0.016 0.002 TRP H 20 HIS 0.011 0.002 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.25 ( 6905) covalent geometry : angle 0.78071 / 0.59 ( 9947) hydrogen bonds : bond 0.07560 / 4.56 ( 439) hydrogen bonds : angle 3.57558 / 2.59 ( 1189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7302 (tm-30) REVERT: B 29 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7601 (mm-30) REVERT: E 45 GLU cc_start: 0.8032 (tp30) cc_final: 0.7684 (tm-30) REVERT: E 55 LYS cc_start: 0.6364 (tptm) cc_final: 0.5896 (tptm) REVERT: F 42 LYS cc_start: 0.8368 (tppt) cc_final: 0.8126 (mmtm) REVERT: G 46 ASP cc_start: 0.7738 (t0) cc_final: 0.7383 (t0) REVERT: H 18 GLU cc_start: 0.7717 (tp30) cc_final: 0.7216 (tp30) outliers start: 9 outliers final: 6 residues processed: 114 average time/residue: 0.1489 time to fit residues: 20.0629 Evaluate side-chains 110 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain H residue 51 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.0770 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 ASN F 53 ASN ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.123107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.099981 restraints weight = 18296.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.101757 restraints weight = 9402.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.102977 restraints weight = 6068.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.103794 restraints weight = 4612.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.104247 restraints weight = 3903.223| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.0613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6905 Z= 0.134 Angle : 0.484 6.637 9947 Z= 0.267 Chirality : 0.028 0.306 1225 Planarity : 0.003 0.028 705 Dihedral : 17.642 175.055 2543 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 3.78 % Allowed : 32.85 % Favored : 63.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.46 (0.39), residues: 385 helix: 3.74 (0.24), residues: 369 sheet: None (None), residues: 0 loop : -2.14 (1.05), residues: 16 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 32 TRP 0.012 0.001 TRP H 20 HIS 0.008 0.002 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 6905) covalent geometry : angle 0.48387 / 0.27 ( 9947) hydrogen bonds : bond 0.04936 / 3.31 ( 439) hydrogen bonds : angle 3.16618 / 2.32 ( 1189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7222 (tm-30) REVERT: B 48 HIS cc_start: 0.7946 (m90) cc_final: 0.7719 (m170) REVERT: D 13 ARG cc_start: 0.6244 (ttm170) cc_final: 0.5609 (ptm160) REVERT: E 45 GLU cc_start: 0.8001 (tp30) cc_final: 0.7721 (tm-30) REVERT: E 55 LYS cc_start: 0.6462 (tptm) cc_final: 0.5964 (tptm) REVERT: F 28 GLU cc_start: 0.6950 (tp30) cc_final: 0.6708 (tp30) REVERT: F 32 ARG cc_start: 0.7750 (mtm110) cc_final: 0.7520 (mtm110) REVERT: F 42 LYS cc_start: 0.8380 (tppt) cc_final: 0.8138 (mmtm) REVERT: G 46 ASP cc_start: 0.7907 (t0) cc_final: 0.7572 (t0) REVERT: H 18 GLU cc_start: 0.7808 (tp30) cc_final: 0.7259 (tp30) outliers start: 13 outliers final: 9 residues processed: 118 average time/residue: 0.1523 time to fit residues: 21.1659 Evaluate side-chains 113 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 51 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 32 optimal weight: 0.0050 chunk 14 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 0.0010 chunk 27 optimal weight: 0.0870 chunk 28 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 overall best weight: 0.1156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.126787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.104923 restraints weight = 19407.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.106755 restraints weight = 9731.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.107991 restraints weight = 6133.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.108805 restraints weight = 4575.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.109287 restraints weight = 3827.514| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6905 Z= 0.122 Angle : 0.455 7.071 9947 Z= 0.249 Chirality : 0.026 0.288 1225 Planarity : 0.003 0.032 705 Dihedral : 17.282 167.232 2539 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 4.36 % Allowed : 33.43 % Favored : 62.21 % 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: 5.71 (0.39), residues: 385 helix: 3.89 (0.24), residues: 369 sheet: None (None), residues: 0 loop : -1.97 (1.07), residues: 16 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 35 TRP 0.012 0.001 TRP H 20 HIS 0.012 0.002 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 6905) covalent geometry : angle 0.45457 / 0.25 ( 9947) hydrogen bonds : bond 0.04397 / 2.95 ( 439) hydrogen bonds : angle 2.97302 / 2.18 ( 1189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.179 Fit side-chains REVERT: B 28 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7155 (tm-30) REVERT: C 38 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8656 (mttm) REVERT: C 47 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.5941 (mp0) REVERT: C 58 LEU cc_start: 0.8909 (mt) cc_final: 0.8672 (mp) REVERT: E 45 GLU cc_start: 0.8015 (tp30) cc_final: 0.7794 (tm-30) REVERT: E 55 LYS cc_start: 0.6369 (tptm) cc_final: 0.5880 (tptm) REVERT: G 46 ASP cc_start: 0.7885 (t0) cc_final: 0.7586 (t0) REVERT: H 18 GLU cc_start: 0.7756 (tp30) cc_final: 0.7185 (tp30) outliers start: 15 outliers final: 8 residues processed: 125 average time/residue: 0.1444 time to fit residues: 21.3236 Evaluate side-chains 112 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain H residue 39 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 45 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.124541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.101385 restraints weight = 18695.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.103247 restraints weight = 9233.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.104550 restraints weight = 5806.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.105376 restraints weight = 4309.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.105825 restraints weight = 3633.505| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6905 Z= 0.138 Angle : 0.476 7.030 9947 Z= 0.258 Chirality : 0.028 0.298 1225 Planarity : 0.003 0.030 705 Dihedral : 17.226 165.896 2537 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 4.65 % Allowed : 35.47 % Favored : 59.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.63 (0.39), residues: 385 helix: 3.85 (0.24), residues: 369 sheet: None (None), residues: 0 loop : -2.08 (1.08), residues: 16 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 32 TRP 0.013 0.002 TRP F 50 HIS 0.007 0.002 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 6905) covalent geometry : angle 0.47559 / 0.26 ( 9947) hydrogen bonds : bond 0.04730 / 3.23 ( 439) hydrogen bonds : angle 3.08461 / 2.26 ( 1189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7258 (tm-30) REVERT: C 47 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.6021 (mp0) REVERT: E 55 LYS cc_start: 0.6378 (tptm) cc_final: 0.5824 (tptm) REVERT: F 42 LYS cc_start: 0.8386 (tppt) cc_final: 0.7930 (mmtm) REVERT: G 13 ARG cc_start: 0.7741 (ttt180) cc_final: 0.7299 (ttm-80) REVERT: G 46 ASP cc_start: 0.7848 (t0) cc_final: 0.7530 (t0) REVERT: H 18 GLU cc_start: 0.7753 (tp30) cc_final: 0.7199 (tp30) outliers start: 16 outliers final: 11 residues processed: 119 average time/residue: 0.1524 time to fit residues: 21.3296 Evaluate side-chains 117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain H residue 51 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 38 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 23 optimal weight: 0.0050 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.124605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.101337 restraints weight = 18764.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.103178 restraints weight = 9413.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.104459 restraints weight = 5983.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.105254 restraints weight = 4490.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.105654 restraints weight = 3807.122| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6905 Z= 0.127 Angle : 0.462 7.000 9947 Z= 0.253 Chirality : 0.027 0.292 1225 Planarity : 0.003 0.028 705 Dihedral : 17.206 164.310 2537 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 5.23 % Allowed : 34.30 % Favored : 60.47 % 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: 5.59 (0.39), residues: 385 helix: 3.83 (0.24), residues: 369 sheet: None (None), residues: 0 loop : -2.15 (1.09), residues: 16 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 24 TRP 0.011 0.001 TRP F 50 HIS 0.007 0.001 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 6905) covalent geometry : angle 0.46164 / 0.25 ( 9947) hydrogen bonds : bond 0.04627 / 3.15 ( 439) hydrogen bonds : angle 3.01479 / 2.22 ( 1189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.184 Fit side-chains REVERT: B 28 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7201 (tm-30) REVERT: C 38 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8667 (mttm) REVERT: C 47 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.6052 (mp0) REVERT: C 58 LEU cc_start: 0.8974 (mt) cc_final: 0.8716 (mp) REVERT: D 13 ARG cc_start: 0.6310 (ttm170) cc_final: 0.6052 (ptm160) REVERT: E 55 LYS cc_start: 0.6483 (tptm) cc_final: 0.5996 (tptm) REVERT: F 42 LYS cc_start: 0.8480 (tppt) cc_final: 0.8254 (mmtm) REVERT: G 13 ARG cc_start: 0.7842 (ttt180) cc_final: 0.7386 (ttm-80) REVERT: G 46 ASP cc_start: 0.7895 (t0) cc_final: 0.7587 (t0) REVERT: H 18 GLU cc_start: 0.7790 (tp30) cc_final: 0.7219 (tp30) outliers start: 18 outliers final: 13 residues processed: 117 average time/residue: 0.1559 time to fit residues: 21.4903 Evaluate side-chains 118 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 51 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 ASN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.124056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.100792 restraints weight = 18626.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.102593 restraints weight = 9443.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.103809 restraints weight = 6057.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.104356 restraints weight = 4594.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.104954 restraints weight = 3983.531| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6905 Z= 0.151 Angle : 0.496 8.466 9947 Z= 0.267 Chirality : 0.028 0.296 1225 Planarity : 0.003 0.026 705 Dihedral : 17.216 164.042 2537 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 5.23 % Allowed : 34.59 % Favored : 60.17 % 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: 5.49 (0.39), residues: 385 helix: 3.76 (0.24), residues: 369 sheet: None (None), residues: 0 loop : -2.29 (1.08), residues: 16 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 32 TRP 0.008 0.001 TRP B 20 HIS 0.006 0.001 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 6905) covalent geometry : angle 0.49588 / 0.27 ( 9947) hydrogen bonds : bond 0.05009 / 3.44 ( 439) hydrogen bonds : angle 3.05833 / 2.24 ( 1189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.229 Fit side-chains REVERT: B 28 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7232 (tm-30) REVERT: C 47 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.6057 (mp0) REVERT: E 55 LYS cc_start: 0.6485 (tptm) cc_final: 0.5999 (tptm) REVERT: F 42 LYS cc_start: 0.8423 (tppt) cc_final: 0.8213 (mmtm) REVERT: G 13 ARG cc_start: 0.7926 (ttt180) cc_final: 0.7457 (ttm-80) REVERT: G 46 ASP cc_start: 0.7940 (t0) cc_final: 0.7606 (t0) REVERT: H 18 GLU cc_start: 0.7822 (tp30) cc_final: 0.7247 (tp30) outliers start: 18 outliers final: 16 residues processed: 116 average time/residue: 0.1550 time to fit residues: 21.1954 Evaluate side-chains 119 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 51 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 31 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 9 optimal weight: 0.1980 chunk 45 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 8 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.125458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.103387 restraints weight = 19260.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.105229 restraints weight = 9713.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.106473 restraints weight = 6134.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.107139 restraints weight = 4606.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.107716 restraints weight = 3934.806| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6905 Z= 0.127 Angle : 0.476 7.761 9947 Z= 0.258 Chirality : 0.027 0.290 1225 Planarity : 0.004 0.046 705 Dihedral : 17.167 163.152 2537 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 4.36 % Allowed : 35.76 % Favored : 59.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.61 (0.39), residues: 385 helix: 3.84 (0.24), residues: 369 sheet: None (None), residues: 0 loop : -2.34 (1.08), residues: 16 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 32 TRP 0.010 0.001 TRP C 20 HIS 0.006 0.001 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 6905) covalent geometry : angle 0.47557 / 0.26 ( 9947) hydrogen bonds : bond 0.04692 / 3.21 ( 439) hydrogen bonds : angle 2.97233 / 2.19 ( 1189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.169 Fit side-chains REVERT: B 28 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7247 (tm-30) REVERT: C 38 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8681 (mttm) REVERT: C 47 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.6056 (mp0) REVERT: C 58 LEU cc_start: 0.8936 (mt) cc_final: 0.8687 (mp) REVERT: D 13 ARG cc_start: 0.6384 (OUTLIER) cc_final: 0.5994 (ptm160) REVERT: E 29 GLU cc_start: 0.7217 (tp30) cc_final: 0.6829 (tp30) REVERT: E 55 LYS cc_start: 0.6475 (tptm) cc_final: 0.5988 (tptm) REVERT: F 42 LYS cc_start: 0.8388 (tppt) cc_final: 0.8181 (mmtm) REVERT: G 46 ASP cc_start: 0.7920 (t0) cc_final: 0.7599 (t0) REVERT: H 18 GLU cc_start: 0.7802 (tp30) cc_final: 0.7244 (tp30) outliers start: 15 outliers final: 10 residues processed: 118 average time/residue: 0.1596 time to fit residues: 21.9810 Evaluate side-chains 114 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 57 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.125328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.103193 restraints weight = 19300.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.105035 restraints weight = 9724.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.106227 restraints weight = 6182.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.106886 restraints weight = 4693.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.107173 restraints weight = 4038.254| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6905 Z= 0.137 Angle : 0.507 9.213 9947 Z= 0.271 Chirality : 0.027 0.292 1225 Planarity : 0.004 0.031 705 Dihedral : 17.165 163.183 2537 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 5.23 % Allowed : 35.47 % Favored : 59.30 % 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: 5.58 (0.39), residues: 385 helix: 3.82 (0.24), residues: 369 sheet: None (None), residues: 0 loop : -2.36 (1.09), residues: 16 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 32 TRP 0.014 0.001 TRP C 50 HIS 0.007 0.001 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 6905) covalent geometry : angle 0.50699 / 0.27 ( 9947) hydrogen bonds : bond 0.04838 / 3.32 ( 439) hydrogen bonds : angle 3.00505 / 2.20 ( 1189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.167 Fit side-chains REVERT: C 38 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8694 (mttm) REVERT: C 47 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.6059 (mp0) REVERT: C 58 LEU cc_start: 0.8947 (mt) cc_final: 0.8684 (mp) REVERT: D 13 ARG cc_start: 0.6427 (OUTLIER) cc_final: 0.6097 (ptm160) REVERT: E 55 LYS cc_start: 0.6497 (tptm) cc_final: 0.6010 (tptm) REVERT: F 42 LYS cc_start: 0.8402 (tppt) cc_final: 0.8193 (mmtm) REVERT: G 46 ASP cc_start: 0.7907 (t0) cc_final: 0.7586 (t0) REVERT: H 18 GLU cc_start: 0.7804 (tp30) cc_final: 0.7229 (tp30) outliers start: 18 outliers final: 12 residues processed: 118 average time/residue: 0.1406 time to fit residues: 19.7418 Evaluate side-chains 118 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain H residue 58 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 8 optimal weight: 0.0670 chunk 44 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.125989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.103997 restraints weight = 19592.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.105838 restraints weight = 9799.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.107093 restraints weight = 6186.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.107802 restraints weight = 4623.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.108360 restraints weight = 3925.373| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6905 Z= 0.127 Angle : 0.518 8.311 9947 Z= 0.275 Chirality : 0.026 0.292 1225 Planarity : 0.004 0.043 705 Dihedral : 17.135 162.837 2537 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 4.36 % Allowed : 36.92 % Favored : 58.72 % 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: 5.59 (0.39), residues: 385 helix: 3.83 (0.24), residues: 369 sheet: None (None), residues: 0 loop : -2.37 (1.08), residues: 16 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 32 TRP 0.013 0.001 TRP H 20 HIS 0.007 0.001 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 6905) covalent geometry : angle 0.51801 / 0.27 ( 9947) hydrogen bonds : bond 0.04653 / 3.18 ( 439) hydrogen bonds : angle 2.96338 / 2.17 ( 1189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.120 Fit side-chains REVERT: C 38 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8673 (mttm) REVERT: C 47 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.6073 (mp0) REVERT: C 58 LEU cc_start: 0.8944 (mt) cc_final: 0.8702 (mp) REVERT: E 29 GLU cc_start: 0.6863 (tp30) cc_final: 0.6573 (tp30) REVERT: E 33 ASP cc_start: 0.7711 (m-30) cc_final: 0.7443 (m-30) REVERT: E 55 LYS cc_start: 0.6448 (tptm) cc_final: 0.5961 (tptm) REVERT: F 42 LYS cc_start: 0.8373 (tppt) cc_final: 0.8158 (mmtm) REVERT: G 46 ASP cc_start: 0.7921 (t0) cc_final: 0.7616 (t0) REVERT: H 18 GLU cc_start: 0.7788 (tp30) cc_final: 0.7213 (tp30) outliers start: 15 outliers final: 11 residues processed: 112 average time/residue: 0.1348 time to fit residues: 17.9393 Evaluate side-chains 114 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain H residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 21 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.123855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.100460 restraints weight = 18559.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.102268 restraints weight = 9388.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.103490 restraints weight = 6004.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.104195 restraints weight = 4565.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.104723 restraints weight = 3913.144| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6905 Z= 0.180 Angle : 0.563 9.072 9947 Z= 0.299 Chirality : 0.030 0.298 1225 Planarity : 0.004 0.050 705 Dihedral : 17.188 163.744 2537 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 4.36 % Allowed : 36.92 % Favored : 58.72 % 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: 5.40 (0.39), residues: 385 helix: 3.71 (0.24), residues: 369 sheet: None (None), residues: 0 loop : -2.46 (1.08), residues: 16 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 32 TRP 0.012 0.002 TRP C 50 HIS 0.004 0.001 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 ( 6905) covalent geometry : angle 0.56314 / 0.30 ( 9947) hydrogen bonds : bond 0.05468 / 3.78 ( 439) hydrogen bonds : angle 3.14725 / 2.31 ( 1189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.194 Fit side-chains REVERT: C 47 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6133 (mp0) REVERT: E 55 LYS cc_start: 0.6501 (tptm) cc_final: 0.6004 (tptm) REVERT: F 42 LYS cc_start: 0.8366 (tppt) cc_final: 0.8152 (mmtm) REVERT: G 46 ASP cc_start: 0.7868 (t0) cc_final: 0.7547 (t0) REVERT: H 18 GLU cc_start: 0.7781 (tp30) cc_final: 0.7228 (tp30) outliers start: 15 outliers final: 12 residues processed: 114 average time/residue: 0.1330 time to fit residues: 18.0352 Evaluate side-chains 114 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain H residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 ASN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.125078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.103026 restraints weight = 19238.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.104818 restraints weight = 9712.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.106057 restraints weight = 6214.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.106733 restraints weight = 4653.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.107329 restraints weight = 3969.679| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6905 Z= 0.141 Angle : 0.554 8.954 9947 Z= 0.291 Chirality : 0.028 0.290 1225 Planarity : 0.004 0.045 705 Dihedral : 17.129 162.910 2537 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 4.07 % Allowed : 36.92 % Favored : 59.01 % 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: 5.53 (0.39), residues: 385 helix: 3.79 (0.24), residues: 369 sheet: None (None), residues: 0 loop : -2.38 (1.09), residues: 16 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 32 TRP 0.013 0.001 TRP C 50 HIS 0.005 0.001 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6905) covalent geometry : angle 0.55371 / 0.29 ( 9947) hydrogen bonds : bond 0.04939 / 3.37 ( 439) hydrogen bonds : angle 3.06238 / 2.24 ( 1189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1401.76 seconds wall clock time: 24 minutes 53.10 seconds (1493.10 seconds total)