Starting phenix.real_space_refine on Wed Sep 17 04:59:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cqu_45823/09_2025/9cqu_45823.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cqu_45823/09_2025/9cqu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cqu_45823/09_2025/9cqu_45823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cqu_45823/09_2025/9cqu_45823.map" model { file = "/net/cci-nas-00/data/ceres_data/9cqu_45823/09_2025/9cqu_45823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cqu_45823/09_2025/9cqu_45823.cif" } 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-2.0-5805/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: 1.38, per 1000 atoms: 0.29 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: 0.48 Conformation dependent library (CDL) restraints added in 183.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.12 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: 0.54 Time building geometry restraints manager: 0.59 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=" 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 bond pdb=" N VAL B 98 " pdb=" CA VAL B 98 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.92e+00 bond pdb=" ND HEM C 201 " pdb="FE HEM C 201 " ideal model delta sigma weight residual 2.080 1.864 0.216 7.00e-02 2.04e+02 9.52e+00 ... (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: 4.010 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.760 Find NCS groups from input model: 0.080 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:9.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.140 ------------------------------------------------------------------------------- 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 : 0.011 0.409 4640 Z= 0.369 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 aren 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 0.00697 ( 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 : 0.115 Fit side-chains REVERT: A 60 LYS cc_start: 0.8511 (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: 0.9013 time to fit residues: 56.4746 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 : 0.155 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.158526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.134475 restraints weight = 4371.963| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.21 r_work: 0.3220 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 4640 Z= 0.128 Angle : 0.632 13.458 6358 Z= 0.256 Chirality : 0.038 0.126 688 Planarity : 0.005 0.049 794 Dihedral : 9.796 80.936 632 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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 aren 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 : 2.13 (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 0.00328 ( 4636) covalent geometry : angle 0.63151 ( 6358) hydrogen bonds : bond 0.03538 ( 336) hydrogen bonds : angle 4.12506 ( 957) Misc. bond : bond 0.11616 ( 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 : 0.171 Fit side-chains REVERT: A 16 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7346 (mptt) REVERT: A 60 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8043 (ttmt) REVERT: A 90 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7794 (ttpp) REVERT: B 26 GLU cc_start: 0.7793 (pt0) cc_final: 0.7323 (tt0) REVERT: B 59 LYS cc_start: 0.8466 (mttt) cc_final: 0.7664 (mtpt) REVERT: B 139 ASN cc_start: 0.8136 (m-40) cc_final: 0.6771 (t0) REVERT: D 68 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8095 (tp) REVERT: D 120 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7697 (ptpp) REVERT: D 121 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8561 (mt-10) REVERT: D 141 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7997 (mp) outliers start: 18 outliers final: 1 residues processed: 69 average time/residue: 0.7626 time to fit residues: 54.2494 Evaluate side-chains 56 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.122 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 141 LEU 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: 0.5980 chunk 48 optimal weight: 1.9990 chunk 28 optimal weight: 0.0370 chunk 27 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.158567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.135752 restraints weight = 4268.636| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.11 r_work: 0.3209 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 4640 Z= 0.129 Angle : 0.653 15.587 6358 Z= 0.257 Chirality : 0.038 0.131 688 Planarity : 0.005 0.048 794 Dihedral : 9.886 86.629 628 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 3.08 % Allowed : 16.52 % 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 aren not related in a simple way. whole: 3.76 (0.37), residues: 560 helix: 2.61 (0.25), residues: 436 sheet: None (None), residues: 0 loop : 2.24 (0.68), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 31 TYR 0.006 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 0.00332 ( 4636) covalent geometry : angle 0.65279 ( 6358) hydrogen bonds : bond 0.03479 ( 336) hydrogen bonds : angle 3.97143 ( 957) Misc. bond : bond 0.10107 ( 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 71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.196 Fit side-chains REVERT: A 60 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8001 (ttmt) REVERT: A 90 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7726 (ttpp) REVERT: B 26 GLU cc_start: 0.7806 (pt0) cc_final: 0.7261 (tt0) REVERT: B 59 LYS cc_start: 0.8440 (mttt) cc_final: 0.7604 (mtpt) REVERT: B 82 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7560 (mptt) REVERT: D 120 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7679 (tttt) REVERT: D 121 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8520 (mt-10) outliers start: 14 outliers final: 3 residues processed: 67 average time/residue: 0.7417 time to fit residues: 51.2726 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 : 0.182 ------------------------------------------------------------------------------- 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 120 LYS 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: 0.7980 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.156568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.133848 restraints weight = 4269.494| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.10 r_work: 0.3210 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 4640 Z= 0.128 Angle : 0.650 15.504 6358 Z= 0.256 Chirality : 0.038 0.134 688 Planarity : 0.005 0.047 794 Dihedral : 9.707 89.589 626 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.71 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 aren not related in a simple way. whole: 3.79 (0.37), residues: 560 helix: 2.67 (0.25), residues: 436 sheet: None (None), residues: 0 loop : 2.11 (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 0.013 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 0.00332 ( 4636) covalent geometry : angle 0.65005 ( 6358) hydrogen bonds : bond 0.03377 ( 336) hydrogen bonds : angle 3.91706 ( 957) Misc. bond : bond 0.09426 ( 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 65 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.180 Fit side-chains REVERT: A 60 LYS cc_start: 0.8413 (ttmm) cc_final: 0.7988 (ttmt) REVERT: A 90 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7730 (ttpp) REVERT: B 26 GLU cc_start: 0.7824 (pt0) cc_final: 0.7330 (tt0) REVERT: B 59 LYS cc_start: 0.8432 (mttt) cc_final: 0.7591 (mtpt) REVERT: D 68 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8012 (tp) REVERT: D 121 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8476 (mt-10) outliers start: 14 outliers final: 4 residues processed: 61 average time/residue: 0.7314 time to fit residues: 46.0235 Evaluate side-chains 56 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 68 LEU Chi-restraints excluded: chain D residue 91 LEU 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: 0.3980 chunk 35 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.150528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.125885 restraints weight = 4370.582| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.22 r_work: 0.3254 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.342 4640 Z= 0.180 Angle : 0.716 16.670 6358 Z= 0.287 Chirality : 0.041 0.144 688 Planarity : 0.006 0.047 794 Dihedral : 9.741 89.092 622 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 3.08 % Allowed : 17.18 % 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 aren not related in a simple way. whole: 3.38 (0.37), residues: 560 helix: 2.41 (0.25), residues: 434 sheet: None (None), residues: 0 loop : 1.85 (0.67), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 31 TYR 0.009 0.002 TYR A 24 PHE 0.015 0.002 PHE B 118 TRP 0.009 0.001 TRP A 14 HIS 0.008 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 4636) covalent geometry : angle 0.71599 ( 6358) hydrogen bonds : bond 0.04196 ( 336) hydrogen bonds : angle 4.15226 ( 957) Misc. bond : bond 0.22909 ( 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 67 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.189 Fit side-chains REVERT: A 60 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8110 (ttmt) REVERT: A 90 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7781 (ttpp) REVERT: B 26 GLU cc_start: 0.8017 (pt0) cc_final: 0.7364 (tt0) REVERT: B 59 LYS cc_start: 0.8560 (mttt) cc_final: 0.7868 (mtpt) REVERT: B 61 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7589 (mptm) REVERT: D 68 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8166 (tp) REVERT: D 121 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8564 (mt-10) outliers start: 14 outliers final: 4 residues processed: 60 average time/residue: 0.8248 time to fit residues: 50.9679 Evaluate side-chains 59 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.157741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.135065 restraints weight = 4376.528| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.11 r_work: 0.3206 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 4640 Z= 0.114 Angle : 0.643 16.030 6358 Z= 0.247 Chirality : 0.037 0.123 688 Planarity : 0.005 0.047 794 Dihedral : 9.338 89.267 622 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.20 % Allowed : 18.28 % 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 aren not related in a simple way. whole: 3.86 (0.37), residues: 560 helix: 2.72 (0.25), residues: 436 sheet: None (None), residues: 0 loop : 2.11 (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 0.008 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 0.00293 ( 4636) covalent geometry : angle 0.64346 ( 6358) hydrogen bonds : bond 0.03029 ( 336) hydrogen bonds : angle 3.83373 ( 957) Misc. bond : bond 0.12664 ( 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 : 0.207 Fit side-chains REVERT: A 60 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8030 (ttmt) REVERT: A 90 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7719 (ttpp) REVERT: B 26 GLU cc_start: 0.7850 (pt0) cc_final: 0.7381 (tt0) REVERT: B 59 LYS cc_start: 0.8428 (mttt) cc_final: 0.7680 (mtpt) REVERT: B 61 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7430 (mptm) REVERT: D 68 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7996 (tp) REVERT: D 120 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7821 (ptpp) REVERT: D 121 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8407 (mt-10) outliers start: 10 outliers final: 2 residues processed: 56 average time/residue: 0.7915 time to fit residues: 45.7250 Evaluate side-chains 56 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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=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: 0.9980 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.152604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.129417 restraints weight = 4334.622| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.14 r_work: 0.3145 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.495 4640 Z= 0.211 Angle : 0.741 16.912 6358 Z= 0.301 Chirality : 0.043 0.153 688 Planarity : 0.006 0.048 794 Dihedral : 9.817 89.286 622 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.71 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 aren not related in a simple way. whole: 3.30 (0.37), residues: 560 helix: 2.35 (0.25), residues: 434 sheet: None (None), residues: 0 loop : 1.81 (0.67), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 31 TYR 0.012 0.002 TYR A 24 PHE 0.014 0.002 PHE B 118 TRP 0.010 0.002 TRP A 14 HIS 0.008 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00536 ( 4636) covalent geometry : angle 0.74096 ( 6358) hydrogen bonds : bond 0.04494 ( 336) hydrogen bonds : angle 4.19872 ( 957) Misc. bond : bond 0.30987 ( 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 62 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.200 Fit side-chains REVERT: A 60 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8099 (ttmt) REVERT: A 90 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7749 (ttpp) REVERT: B 26 GLU cc_start: 0.8069 (pt0) cc_final: 0.7361 (tt0) REVERT: B 59 LYS cc_start: 0.8537 (mttt) cc_final: 0.7809 (mtpt) REVERT: B 61 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7504 (mptm) REVERT: B 101 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7400 (tp30) REVERT: D 68 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8151 (tp) REVERT: D 121 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8449 (mt-10) outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 0.8262 time to fit residues: 47.6942 Evaluate side-chains 59 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 B residue 101 GLU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 75 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: 0.3980 chunk 36 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 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: 5.9990 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN B 77 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.155646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.132485 restraints weight = 4347.594| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.14 r_work: 0.3190 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.323 4640 Z= 0.131 Angle : 0.673 16.475 6358 Z= 0.260 Chirality : 0.038 0.126 688 Planarity : 0.005 0.048 794 Dihedral : 9.543 89.865 622 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.20 % Allowed : 18.28 % 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 aren not related in a simple way. whole: 3.63 (0.37), residues: 560 helix: 2.62 (0.25), residues: 434 sheet: None (None), residues: 0 loop : 1.80 (0.66), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 31 TYR 0.010 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 0.00336 ( 4636) covalent geometry : angle 0.67286 ( 6358) hydrogen bonds : bond 0.03382 ( 336) hydrogen bonds : angle 3.92606 ( 957) Misc. bond : bond 0.19936 ( 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 62 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.124 Fit side-chains REVERT: A 60 LYS cc_start: 0.8452 (ttmm) cc_final: 0.8043 (ttmt) REVERT: A 90 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7713 (ttpp) REVERT: B 26 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: B 59 LYS cc_start: 0.8464 (mttt) cc_final: 0.7714 (mtpt) REVERT: B 61 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7543 (mptm) REVERT: D 68 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8056 (tp) REVERT: D 121 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8420 (mt-10) outliers start: 10 outliers final: 4 residues processed: 54 average time/residue: 0.8030 time to fit residues: 44.6280 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 : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain B residue 26 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 0.0670 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.154124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.130724 restraints weight = 4307.694| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.15 r_work: 0.3191 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.312 4640 Z= 0.134 Angle : 0.672 16.533 6358 Z= 0.261 Chirality : 0.038 0.130 688 Planarity : 0.005 0.049 794 Dihedral : 9.464 89.919 622 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.20 % Allowed : 18.50 % Favored : 79.30 % 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 aren not related in a simple way. whole: 3.67 (0.36), residues: 560 helix: 2.66 (0.25), residues: 434 sheet: None (None), residues: 0 loop : 1.76 (0.65), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 TYR 0.010 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 0.00346 ( 4636) covalent geometry : angle 0.67215 ( 6358) hydrogen bonds : bond 0.03437 ( 336) hydrogen bonds : angle 3.89572 ( 957) Misc. bond : bond 0.18895 ( 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: 10 poor density : 51 time to evaluate : 0.210 Fit side-chains REVERT: A 60 LYS cc_start: 0.8420 (ttmm) cc_final: 0.8003 (ttmt) REVERT: A 90 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7731 (ttpp) REVERT: B 26 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7358 (tt0) REVERT: B 59 LYS cc_start: 0.8439 (mttt) cc_final: 0.7666 (mtpt) REVERT: B 61 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7390 (mptm) REVERT: D 68 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8003 (tp) REVERT: D 121 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8394 (mt-10) outliers start: 10 outliers final: 3 residues processed: 55 average time/residue: 0.8369 time to fit residues: 47.4663 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 : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain B residue 26 GLU 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: 1.9990 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.154925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.131390 restraints weight = 4343.840| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.16 r_work: 0.3220 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.266 4640 Z= 0.124 Angle : 0.661 16.361 6358 Z= 0.256 Chirality : 0.037 0.127 688 Planarity : 0.005 0.050 794 Dihedral : 9.411 89.690 622 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.98 % Allowed : 18.72 % Favored : 79.30 % 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 aren not related in a simple way. whole: 3.77 (0.36), residues: 560 helix: 2.74 (0.25), residues: 434 sheet: None (None), residues: 0 loop : 1.76 (0.65), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 TYR 0.013 0.001 TYR A 24 PHE 0.008 0.001 PHE B 118 TRP 0.008 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 0.66091 ( 6358) hydrogen bonds : bond 0.03229 ( 336) hydrogen bonds : angle 3.84546 ( 957) Misc. bond : bond 0.16078 ( 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 61 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.197 Fit side-chains REVERT: A 60 LYS cc_start: 0.8436 (ttmm) cc_final: 0.8001 (ttmt) REVERT: A 90 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7755 (ttpp) REVERT: B 26 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7348 (tt0) REVERT: B 59 LYS cc_start: 0.8414 (mttt) cc_final: 0.7639 (mtpt) REVERT: B 61 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7387 (mptm) REVERT: D 68 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7971 (tp) REVERT: D 121 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8345 (mt-10) outliers start: 9 outliers final: 3 residues processed: 54 average time/residue: 0.8465 time to fit residues: 47.0574 Evaluate side-chains 57 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain B residue 26 GLU 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 43 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.156315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.135204 restraints weight = 4301.605| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.05 r_work: 0.3197 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.309 4640 Z= 0.142 Angle : 0.679 16.484 6358 Z= 0.266 Chirality : 0.038 0.133 688 Planarity : 0.005 0.049 794 Dihedral : 9.508 89.875 622 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.54 % Allowed : 18.72 % 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 aren not related in a simple way. whole: 3.65 (0.36), residues: 560 helix: 2.65 (0.24), residues: 434 sheet: None (None), residues: 0 loop : 1.71 (0.66), 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 0.00366 ( 4636) covalent geometry : angle 0.67926 ( 6358) hydrogen bonds : bond 0.03561 ( 336) hydrogen bonds : angle 3.92343 ( 957) Misc. bond : bond 0.18816 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1883.54 seconds wall clock time: 32 minutes 57.22 seconds (1977.22 seconds total)