Starting phenix.real_space_refine on Sat May 2 10:47:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cqu_45823/05_2026/9cqu_45823.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cqu_45823/05_2026/9cqu_45823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cqu_45823/05_2026/9cqu_45823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cqu_45823/05_2026/9cqu_45823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cqu_45823/05_2026/9cqu_45823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cqu_45823/05_2026/9cqu_45823.map" } resolution = 2.72 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= 0.021 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 Fe 4 7.16 5 S 12 5.16 5 C 2914 2.51 5 N 764 2.21 5 O 1013 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-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4707 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1050 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1110 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 137} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1050 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "D" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1110 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 137} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Time building chain proxies: 1.06, per 1000 atoms: 0.23 Number of scatterers: 4707 At special positions: 0 Unit cell: (77.91, 72.765, 65.415, 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) Fe 4 26.01 S 12 16.00 O 1013 8.00 N 764 7.00 C 2914 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 96.1 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 86.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 removed outlier: 3.535A pdb=" N GLY A 18 " --> pdb=" O TRP A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.643A pdb=" N THR A 41 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 94 through 113 removed outlier: 4.037A pdb=" N PHE A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 137 Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.967A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 36 through 46 removed outlier: 4.431A pdb=" N GLU B 43 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N SER B 44 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 57 through 77 Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 99 through 119 removed outlier: 3.997A pdb=" N PHE B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 142 Processing helix chain 'B' and resid 143 through 146 Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 removed outlier: 3.638A pdb=" N THR C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 95 through 113 removed outlier: 3.782A pdb=" N LYS C 99 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 137 Processing helix chain 'D' and resid 4 through 17 removed outlier: 3.908A pdb=" N LYS D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 36 through 46 removed outlier: 4.316A pdb=" N GLU D 43 " --> pdb=" O ARG D 40 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER D 44 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY D 46 " --> pdb=" O GLU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 Processing helix chain 'D' and resid 57 through 77 Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 85 through 95 Processing helix chain 'D' and resid 99 through 119 removed outlier: 4.115A pdb=" N PHE D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 123 through 142 336 hydrogen bonds defined for protein. 957 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.44 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 1859 1.38 - 1.57: 2743 1.57 - 1.75: 0 1.75 - 1.93: 19 1.93 - 2.11: 15 Bond restraints: 4636 Sorted by residual: bond pdb=" O1 OXY B 202 " pdb=" O2 OXY B 202 " ideal model delta sigma weight residual 1.109 1.208 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" O1 OXY A 202 " pdb=" O2 OXY A 202 " ideal model delta sigma weight residual 1.109 1.205 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" N THR B 123 " pdb=" CA THR B 123 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.62e+01 bond pdb=" C3B HEM C 201 " pdb=" CAB HEM C 201 " ideal model delta sigma weight residual 1.544 1.477 0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C3C HEM C 201 " pdb=" CAC HEM C 201 " ideal model delta sigma weight residual 1.544 1.479 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 4631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 6008 1.69 - 3.38: 278 3.38 - 5.07: 61 5.07 - 6.76: 8 6.76 - 8.45: 3 Bond angle restraints: 6358 Sorted by residual: angle pdb=" C PHE B 118 " pdb=" CA PHE B 118 " pdb=" CB PHE B 118 " ideal model delta sigma weight residual 110.79 119.24 -8.45 1.66e+00 3.63e-01 2.59e+01 angle pdb=" CA PHE D 118 " pdb=" CB PHE D 118 " pdb=" CG PHE D 118 " ideal model delta sigma weight residual 113.80 109.15 4.65 1.00e+00 1.00e+00 2.16e+01 angle pdb=" CA PHE B 118 " pdb=" CB PHE B 118 " pdb=" CG PHE B 118 " ideal model delta sigma weight residual 113.80 109.20 4.60 1.00e+00 1.00e+00 2.12e+01 angle pdb=" C PHE D 118 " pdb=" CA PHE D 118 " pdb=" CB PHE D 118 " ideal model delta sigma weight residual 110.79 117.75 -6.96 1.66e+00 3.63e-01 1.76e+01 angle pdb=" CA PHE B 118 " pdb=" C PHE B 118 " pdb=" O PHE B 118 " ideal model delta sigma weight residual 120.55 116.12 4.43 1.06e+00 8.90e-01 1.74e+01 ... (remaining 6353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 2240 17.24 - 34.48: 265 34.48 - 51.72: 88 51.72 - 68.96: 28 68.96 - 86.19: 5 Dihedral angle restraints: 2626 sinusoidal: 998 harmonic: 1628 Sorted by residual: dihedral pdb=" C2B HEM C 201 " pdb=" C3B HEM C 201 " pdb=" CAB HEM C 201 " pdb=" CBB HEM C 201 " ideal model delta sinusoidal sigma weight residual -0.00 -80.60 80.60 2 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" C2C HEM C 201 " pdb=" C3C HEM C 201 " pdb=" CAC HEM C 201 " pdb=" CBC HEM C 201 " ideal model delta sinusoidal sigma weight residual -0.00 -74.55 74.55 2 1.00e+01 1.00e-02 4.46e+01 dihedral pdb=" C PHE B 118 " pdb=" N PHE B 118 " pdb=" CA PHE B 118 " pdb=" CB PHE B 118 " ideal model delta harmonic sigma weight residual -122.60 -134.11 11.51 0 2.50e+00 1.60e-01 2.12e+01 ... (remaining 2623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 579 0.060 - 0.120: 90 0.120 - 0.181: 13 0.181 - 0.241: 4 0.241 - 0.301: 2 Chirality restraints: 688 Sorted by residual: chirality pdb=" CA PHE B 118 " pdb=" N PHE B 118 " pdb=" C PHE B 118 " pdb=" CB PHE B 118 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA PHE D 118 " pdb=" N PHE D 118 " pdb=" C PHE D 118 " pdb=" CB PHE D 118 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA PHE B 122 " pdb=" N PHE B 122 " pdb=" C PHE B 122 " pdb=" CB PHE B 122 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 685 not shown) Planarity restraints: 794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 94 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO A 95 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 122 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C PHE B 122 " -0.033 2.00e-02 2.50e+03 pdb=" O PHE B 122 " 0.012 2.00e-02 2.50e+03 pdb=" N THR B 123 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 118 " 0.016 2.00e-02 2.50e+03 1.34e-02 3.16e+00 pdb=" CG PHE D 118 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE D 118 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 118 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 118 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 118 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 118 " 0.002 2.00e-02 2.50e+03 ... (remaining 791 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 818 2.76 - 3.30: 4495 3.30 - 3.83: 8522 3.83 - 4.37: 10463 4.37 - 4.90: 17262 Nonbonded interactions: 41560 Sorted by model distance: nonbonded pdb=" NE2 HIS B 92 " pdb="FE HEM B 201 " model vdw 2.230 3.080 nonbonded pdb=" NE2 HIS A 87 " pdb="FE HEM A 201 " model vdw 2.249 3.080 nonbonded pdb=" O ASN B 80 " pdb=" OG1 THR B 84 " model vdw 2.267 3.040 nonbonded pdb=" O TYR D 35 " pdb=" OG1 THR D 38 " model vdw 2.274 3.040 nonbonded pdb=" O ASN D 80 " pdb=" OG1 THR D 84 " model vdw 2.279 3.040 ... (remaining 41555 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 2 through 201) selection = chain 'C' } ncs_group { reference = (chain 'B' and resid 2 through 201) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.550 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.012 0.409 4640 Z= 0.383 Angle : 0.822 8.449 6358 Z= 0.516 Chirality : 0.050 0.301 688 Planarity : 0.005 0.049 794 Dihedral : 17.922 86.195 1574 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.76 % Allowed : 18.50 % Favored : 79.74 % Cbeta Deviations : 0.38 % 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: 3.57 (0.36), residues: 560 helix: 2.63 (0.25), residues: 430 sheet: None (None), residues: 0 loop : 1.56 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 40 TYR 0.019 0.002 TYR A 24 PHE 0.031 0.003 PHE D 118 TRP 0.003 0.001 TRP C 14 HIS 0.006 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00726 ( 4636) covalent geometry : angle 0.82192 ( 6358) hydrogen bonds : bond 0.11062 ( 336) hydrogen bonds : angle 4.62266 ( 957) Misc. bond : bond 0.30499 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.092 Fit side-chains REVERT: A 60 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8180 (ttmt) REVERT: B 26 GLU cc_start: 0.7977 (pt0) cc_final: 0.7125 (tt0) REVERT: B 59 LYS cc_start: 0.8488 (mttt) cc_final: 0.7688 (mtpt) REVERT: B 139 ASN cc_start: 0.8178 (m-40) cc_final: 0.6848 (t0) REVERT: D 120 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7528 (mmmm) REVERT: D 121 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8560 (mt-10) outliers start: 8 outliers final: 3 residues processed: 61 average time/residue: 0.5155 time to fit residues: 32.4255 Evaluate side-chains 58 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 120 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS C 9 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.159715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.137912 restraints weight = 4352.982| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.01 r_work: 0.3271 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 4640 Z= 0.129 Angle : 0.635 13.717 6358 Z= 0.256 Chirality : 0.038 0.126 688 Planarity : 0.005 0.049 794 Dihedral : 9.827 81.219 632 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.96 % Allowed : 15.20 % Favored : 80.84 % 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: 3.75 (0.37), residues: 560 helix: 2.64 (0.25), residues: 434 sheet: None (None), residues: 0 loop : 2.12 (0.67), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 31 TYR 0.009 0.001 TYR A 24 PHE 0.015 0.002 PHE B 118 TRP 0.006 0.001 TRP A 14 HIS 0.004 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4636) covalent geometry : angle 0.63527 ( 6358) hydrogen bonds : bond 0.03580 ( 336) hydrogen bonds : angle 4.13072 ( 957) Misc. bond : bond 0.09882 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.097 Fit side-chains REVERT: A 16 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7400 (mptt) REVERT: A 60 LYS cc_start: 0.8547 (ttmm) cc_final: 0.8179 (ttmt) REVERT: A 90 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7780 (ttpp) REVERT: B 26 GLU cc_start: 0.7832 (pt0) cc_final: 0.7410 (tt0) REVERT: B 59 LYS cc_start: 0.8554 (mttt) cc_final: 0.7857 (mtpt) REVERT: B 139 ASN cc_start: 0.8250 (m-40) cc_final: 0.7012 (t0) REVERT: D 68 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8247 (tp) REVERT: D 120 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7778 (ptpp) REVERT: D 121 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8641 (mt-10) outliers start: 18 outliers final: 1 residues processed: 69 average time/residue: 0.4603 time to fit residues: 32.7327 Evaluate side-chains 55 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 120 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.158256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.135457 restraints weight = 4272.565| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.12 r_work: 0.3218 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.234 4640 Z= 0.134 Angle : 0.661 15.906 6358 Z= 0.259 Chirality : 0.038 0.131 688 Planarity : 0.005 0.048 794 Dihedral : 9.923 86.984 628 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 3.08 % Allowed : 16.74 % Favored : 80.18 % 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: 3.72 (0.37), residues: 560 helix: 2.59 (0.25), residues: 436 sheet: None (None), residues: 0 loop : 2.21 (0.68), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 TYR 0.007 0.001 TYR A 24 PHE 0.015 0.002 PHE B 118 TRP 0.007 0.001 TRP A 14 HIS 0.005 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 4636) covalent geometry : angle 0.66101 ( 6358) hydrogen bonds : bond 0.03550 ( 336) hydrogen bonds : angle 3.99613 ( 957) Misc. bond : bond 0.15830 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.111 Fit side-chains REVERT: A 60 LYS cc_start: 0.8474 (ttmm) cc_final: 0.8064 (ttmt) REVERT: A 90 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7713 (ttpp) REVERT: B 26 GLU cc_start: 0.7850 (pt0) cc_final: 0.7316 (tt0) REVERT: B 59 LYS cc_start: 0.8483 (mttt) cc_final: 0.7684 (mtpt) REVERT: B 82 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7597 (mptt) REVERT: D 68 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8071 (tp) REVERT: D 121 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8523 (mt-10) outliers start: 14 outliers final: 3 residues processed: 65 average time/residue: 0.4137 time to fit residues: 27.8029 Evaluate side-chains 60 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 132 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.159725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.137581 restraints weight = 4225.206| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.07 r_work: 0.3230 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.164 4640 Z= 0.124 Angle : 0.647 15.638 6358 Z= 0.253 Chirality : 0.038 0.132 688 Planarity : 0.005 0.047 794 Dihedral : 9.523 89.209 624 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.64 % Allowed : 16.96 % Favored : 80.40 % 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: 3.80 (0.37), residues: 560 helix: 2.67 (0.25), residues: 436 sheet: None (None), residues: 0 loop : 2.14 (0.66), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 TYR 0.007 0.001 TYR B 130 PHE 0.012 0.001 PHE B 118 TRP 0.007 0.001 TRP A 14 HIS 0.005 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4636) covalent geometry : angle 0.64687 ( 6358) hydrogen bonds : bond 0.03287 ( 336) hydrogen bonds : angle 3.89524 ( 957) Misc. bond : bond 0.11738 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.111 Fit side-chains REVERT: A 60 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8005 (ttmt) REVERT: A 90 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7713 (ttpp) REVERT: B 26 GLU cc_start: 0.7778 (pt0) cc_final: 0.7320 (tt0) REVERT: B 59 LYS cc_start: 0.8431 (mttt) cc_final: 0.7597 (mtpt) REVERT: B 139 ASN cc_start: 0.8033 (m-40) cc_final: 0.6708 (t0) REVERT: D 121 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8533 (mt-10) outliers start: 12 outliers final: 5 residues processed: 60 average time/residue: 0.4392 time to fit residues: 27.2256 Evaluate side-chains 55 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 132 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.153129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.129910 restraints weight = 4336.728| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.13 r_work: 0.3162 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.298 4640 Z= 0.150 Angle : 0.689 16.667 6358 Z= 0.270 Chirality : 0.039 0.136 688 Planarity : 0.005 0.046 794 Dihedral : 9.566 89.544 622 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.86 % Allowed : 17.40 % Favored : 79.74 % 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: 3.59 (0.37), residues: 560 helix: 2.57 (0.25), residues: 434 sheet: None (None), residues: 0 loop : 1.88 (0.66), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 TYR 0.008 0.002 TYR A 24 PHE 0.013 0.002 PHE B 118 TRP 0.009 0.001 TRP A 14 HIS 0.007 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 4636) covalent geometry : angle 0.68851 ( 6358) hydrogen bonds : bond 0.03774 ( 336) hydrogen bonds : angle 4.01539 ( 957) Misc. bond : bond 0.20557 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.112 Fit side-chains REVERT: A 60 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8024 (ttmt) REVERT: A 90 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7728 (ttpp) REVERT: B 26 GLU cc_start: 0.7948 (pt0) cc_final: 0.7388 (tt0) REVERT: B 59 LYS cc_start: 0.8483 (mttt) cc_final: 0.7737 (mtpt) REVERT: B 61 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7483 (mptm) REVERT: D 68 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8091 (tp) REVERT: D 120 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7794 (ptpp) REVERT: D 121 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8487 (mt-10) outliers start: 13 outliers final: 4 residues processed: 59 average time/residue: 0.4196 time to fit residues: 25.5717 Evaluate side-chains 60 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 120 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.159106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.135703 restraints weight = 4342.378| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.15 r_work: 0.3195 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.202 4640 Z= 0.118 Angle : 0.648 16.157 6358 Z= 0.248 Chirality : 0.037 0.127 688 Planarity : 0.005 0.046 794 Dihedral : 9.305 89.657 622 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.20 % Allowed : 18.06 % Favored : 79.74 % 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: 3.88 (0.37), residues: 560 helix: 2.74 (0.25), residues: 436 sheet: None (None), residues: 0 loop : 2.13 (0.67), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 TYR 0.007 0.001 TYR B 130 PHE 0.009 0.001 PHE B 118 TRP 0.008 0.001 TRP C 14 HIS 0.004 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4636) covalent geometry : angle 0.64827 ( 6358) hydrogen bonds : bond 0.03136 ( 336) hydrogen bonds : angle 3.84042 ( 957) Misc. bond : bond 0.14031 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.091 Fit side-chains REVERT: A 60 LYS cc_start: 0.8443 (ttmm) cc_final: 0.8013 (ttmt) REVERT: A 90 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7717 (ttpp) REVERT: B 26 GLU cc_start: 0.7874 (pt0) cc_final: 0.7370 (tt0) REVERT: B 59 LYS cc_start: 0.8425 (mttt) cc_final: 0.7669 (mtpt) REVERT: B 61 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7417 (mptm) REVERT: D 68 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8009 (tp) REVERT: D 120 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7827 (ptpp) REVERT: D 121 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8438 (mt-10) outliers start: 10 outliers final: 4 residues processed: 57 average time/residue: 0.4219 time to fit residues: 24.8192 Evaluate side-chains 60 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 132 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.153457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.129731 restraints weight = 4344.181| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.17 r_work: 0.3160 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.319 4640 Z= 0.161 Angle : 0.696 16.622 6358 Z= 0.274 Chirality : 0.040 0.139 688 Planarity : 0.005 0.046 794 Dihedral : 9.539 89.862 622 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.42 % Allowed : 17.62 % Favored : 79.96 % 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: 3.59 (0.36), residues: 560 helix: 2.56 (0.24), residues: 434 sheet: None (None), residues: 0 loop : 1.90 (0.66), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 TYR 0.008 0.002 TYR A 24 PHE 0.012 0.002 PHE B 118 TRP 0.009 0.001 TRP A 14 HIS 0.007 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 4636) covalent geometry : angle 0.69634 ( 6358) hydrogen bonds : bond 0.03873 ( 336) hydrogen bonds : angle 4.01251 ( 957) Misc. bond : bond 0.21833 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.111 Fit side-chains REVERT: A 60 LYS cc_start: 0.8458 (ttmm) cc_final: 0.8060 (ttmt) REVERT: A 90 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7698 (ttpp) REVERT: B 26 GLU cc_start: 0.8021 (pt0) cc_final: 0.7421 (tt0) REVERT: B 59 LYS cc_start: 0.8498 (mttt) cc_final: 0.7746 (mtpt) REVERT: B 61 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7474 (mptm) REVERT: D 68 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8085 (tp) REVERT: D 121 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8431 (mt-10) outliers start: 11 outliers final: 4 residues processed: 59 average time/residue: 0.4132 time to fit residues: 25.1944 Evaluate side-chains 58 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 120 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 0.5980 chunk 36 optimal weight: 0.0010 chunk 46 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.157102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.134533 restraints weight = 4344.333| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.10 r_work: 0.3213 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.223 4640 Z= 0.120 Angle : 0.654 16.216 6358 Z= 0.251 Chirality : 0.037 0.125 688 Planarity : 0.005 0.047 794 Dihedral : 9.307 89.681 622 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.98 % Allowed : 18.50 % Favored : 79.52 % 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: 3.87 (0.37), residues: 560 helix: 2.73 (0.25), residues: 436 sheet: None (None), residues: 0 loop : 2.12 (0.67), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 TYR 0.009 0.001 TYR A 24 PHE 0.008 0.001 PHE B 118 TRP 0.008 0.001 TRP C 14 HIS 0.005 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4636) covalent geometry : angle 0.65393 ( 6358) hydrogen bonds : bond 0.03134 ( 336) hydrogen bonds : angle 3.82448 ( 957) Misc. bond : bond 0.14963 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.094 Fit side-chains REVERT: A 60 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8057 (ttmt) REVERT: A 90 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7683 (ttpp) REVERT: B 26 GLU cc_start: 0.7892 (pt0) cc_final: 0.7430 (tt0) REVERT: B 59 LYS cc_start: 0.8450 (mttt) cc_final: 0.7737 (mtpt) REVERT: B 61 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7476 (mptm) REVERT: D 68 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8054 (tp) REVERT: D 121 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8421 (mt-10) outliers start: 9 outliers final: 3 residues processed: 55 average time/residue: 0.4183 time to fit residues: 23.7567 Evaluate side-chains 57 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 120 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 chunk 43 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.155268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.131809 restraints weight = 4301.032| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.15 r_work: 0.3191 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.231 4640 Z= 0.124 Angle : 0.659 16.230 6358 Z= 0.254 Chirality : 0.037 0.128 688 Planarity : 0.005 0.047 794 Dihedral : 9.335 89.908 622 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.98 % Allowed : 18.28 % Favored : 79.74 % 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: 3.86 (0.37), residues: 560 helix: 2.73 (0.25), residues: 436 sheet: None (None), residues: 0 loop : 2.08 (0.67), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 TYR 0.011 0.001 TYR A 24 PHE 0.009 0.001 PHE B 118 TRP 0.009 0.001 TRP A 14 HIS 0.005 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4636) covalent geometry : angle 0.65865 ( 6358) hydrogen bonds : bond 0.03256 ( 336) hydrogen bonds : angle 3.82865 ( 957) Misc. bond : bond 0.15541 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.100 Fit side-chains REVERT: A 60 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8031 (ttmt) REVERT: A 90 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7719 (ttpp) REVERT: B 26 GLU cc_start: 0.7935 (pt0) cc_final: 0.7399 (tt0) REVERT: B 59 LYS cc_start: 0.8450 (mttt) cc_final: 0.7708 (mtpt) REVERT: B 61 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7449 (mptm) REVERT: D 68 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8025 (tp) REVERT: D 121 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8410 (mt-10) outliers start: 9 outliers final: 4 residues processed: 55 average time/residue: 0.4277 time to fit residues: 24.3274 Evaluate side-chains 58 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 120 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.155058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.131940 restraints weight = 4322.634| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.14 r_work: 0.3175 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.284 4640 Z= 0.147 Angle : 0.684 16.435 6358 Z= 0.269 Chirality : 0.039 0.135 688 Planarity : 0.005 0.048 794 Dihedral : 9.523 89.970 622 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.98 % Allowed : 18.28 % Favored : 79.74 % 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: 3.68 (0.36), residues: 560 helix: 2.65 (0.24), residues: 434 sheet: None (None), residues: 0 loop : 1.82 (0.66), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 TYR 0.018 0.002 TYR A 24 PHE 0.011 0.002 PHE B 118 TRP 0.010 0.001 TRP A 14 HIS 0.006 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 4636) covalent geometry : angle 0.68416 ( 6358) hydrogen bonds : bond 0.03638 ( 336) hydrogen bonds : angle 3.93218 ( 957) Misc. bond : bond 0.19297 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.097 Fit side-chains REVERT: A 60 LYS cc_start: 0.8465 (ttmm) cc_final: 0.8066 (ttmt) REVERT: A 90 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7679 (ttpp) REVERT: B 26 GLU cc_start: 0.7982 (pt0) cc_final: 0.7400 (tt0) REVERT: B 59 LYS cc_start: 0.8488 (mttt) cc_final: 0.7751 (mtpt) REVERT: B 61 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7507 (mptm) REVERT: D 68 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8096 (tp) REVERT: D 121 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8429 (mt-10) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 0.4413 time to fit residues: 27.2823 Evaluate side-chains 61 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 120 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.155479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.133001 restraints weight = 4323.055| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.10 r_work: 0.3199 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.284 4640 Z= 0.138 Angle : 0.675 16.483 6358 Z= 0.264 Chirality : 0.038 0.131 688 Planarity : 0.005 0.048 794 Dihedral : 9.489 89.716 622 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.76 % Allowed : 18.72 % Favored : 79.52 % 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: 3.75 (0.36), residues: 560 helix: 2.71 (0.24), residues: 434 sheet: None (None), residues: 0 loop : 1.82 (0.65), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 TYR 0.016 0.002 TYR A 24 PHE 0.009 0.001 PHE B 118 TRP 0.009 0.001 TRP A 14 HIS 0.006 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4636) covalent geometry : angle 0.67548 ( 6358) hydrogen bonds : bond 0.03490 ( 336) hydrogen bonds : angle 3.91193 ( 957) Misc. bond : bond 0.18759 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1038.09 seconds wall clock time: 24 minutes 45.41 seconds (1485.41 seconds total)