Starting phenix.real_space_refine on Sat May 10 02:17:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cqu_45823/05_2025/9cqu_45823.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cqu_45823/05_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_45823/05_2025/9cqu_45823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cqu_45823/05_2025/9cqu_45823.map" model { file = "/net/cci-nas-00/data/ceres_data/9cqu_45823/05_2025/9cqu_45823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cqu_45823/05_2025/9cqu_45823.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.55, per 1000 atoms: 0.97 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: 1.31 Conformation dependent library (CDL) restraints added in 577.5 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: 0.47 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: 1.19 Time building geometry restraints manager: 1.47 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 140 or resid 201)) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 2 through 146 or resid 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: 2.540 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 16.370 Find NCS groups from input model: 0.190 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:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.550 ------------------------------------------------------------------------------- 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 : 6.17 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (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 TRP 0.003 0.001 TRP C 14 HIS 0.006 0.001 HIS B 116 PHE 0.031 0.003 PHE D 118 TYR 0.019 0.002 TYR A 24 ARG 0.003 0.000 ARG D 40 Details of bonding type rmsd hydrogen bonds : bond 0.11062 ( 336) hydrogen bonds : angle 4.62266 ( 957) covalent geometry : bond 0.00697 ( 4636) covalent geometry : angle 0.82192 ( 6358) 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 : 0.449 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: 1.6479 time to fit residues: 103.6648 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 : 0.510 ------------------------------------------------------------------------------- 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 45 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.157082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.133250 restraints weight = 4317.019| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.19 r_work: 0.3206 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.217 4640 Z= 0.144 Angle : 0.660 14.451 6358 Z= 0.267 Chirality : 0.039 0.130 688 Planarity : 0.005 0.049 794 Dihedral : 9.947 83.331 632 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 3.74 % Allowed : 15.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.63 (0.37), residues: 560 helix: 2.55 (0.25), residues: 434 sheet: None (None), residues: 0 loop : 2.11 (0.67), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 14 HIS 0.005 0.001 HIS B 117 PHE 0.018 0.002 PHE B 118 TYR 0.010 0.002 TYR A 24 ARG 0.002 0.000 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 336) hydrogen bonds : angle 4.20109 ( 957) covalent geometry : bond 0.00367 ( 4636) covalent geometry : angle 0.65994 ( 6358) Misc. bond : bond 0.14374 ( 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: 17 poor density : 56 time to evaluate : 0.475 Fit side-chains REVERT: A 60 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8057 (ttmt) REVERT: A 90 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7807 (ttpp) REVERT: B 26 GLU cc_start: 0.7818 (pt0) cc_final: 0.7308 (tt0) REVERT: B 59 LYS cc_start: 0.8475 (mttt) cc_final: 0.7669 (mtpt) REVERT: B 139 ASN cc_start: 0.8147 (m-40) cc_final: 0.6790 (t0) REVERT: D 68 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8121 (tp) REVERT: D 120 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7712 (ptpp) REVERT: D 121 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8547 (mt-10) REVERT: D 141 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8031 (mp) outliers start: 17 outliers final: 1 residues processed: 69 average time/residue: 1.4529 time to fit residues: 103.6567 Evaluate side-chains 54 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.159075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.136917 restraints weight = 4235.979| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.08 r_work: 0.3241 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 4640 Z= 0.137 Angle : 0.663 15.547 6358 Z= 0.262 Chirality : 0.038 0.133 688 Planarity : 0.005 0.048 794 Dihedral : 9.969 87.098 628 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 3.30 % Allowed : 16.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.37), residues: 560 helix: 2.58 (0.25), residues: 434 sheet: None (None), residues: 0 loop : 2.05 (0.68), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 14 HIS 0.005 0.001 HIS B 116 PHE 0.016 0.002 PHE B 118 TYR 0.007 0.001 TYR A 24 ARG 0.002 0.000 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 336) hydrogen bonds : angle 4.02529 ( 957) covalent geometry : bond 0.00351 ( 4636) covalent geometry : angle 0.66336 ( 6358) Misc. bond : bond 0.09514 ( 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 68 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.529 Fit side-chains REVERT: A 60 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8140 (ttmt) REVERT: A 90 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7748 (ttpp) REVERT: B 26 GLU cc_start: 0.7887 (pt0) cc_final: 0.7355 (tt0) REVERT: B 59 LYS cc_start: 0.8517 (mttt) cc_final: 0.7765 (mtpt) REVERT: B 82 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7624 (mptt) REVERT: D 121 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8543 (mt-10) outliers start: 15 outliers final: 2 residues processed: 64 average time/residue: 1.4668 time to fit residues: 97.1988 Evaluate side-chains 56 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.154884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.132227 restraints weight = 4284.070| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.10 r_work: 0.3183 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 4640 Z= 0.147 Angle : 0.674 15.754 6358 Z= 0.269 Chirality : 0.039 0.137 688 Planarity : 0.005 0.046 794 Dihedral : 9.580 89.890 622 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.52 % Allowed : 16.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.58 (0.37), residues: 560 helix: 2.55 (0.25), residues: 434 sheet: None (None), residues: 0 loop : 1.91 (0.67), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 14 HIS 0.006 0.001 HIS B 116 PHE 0.013 0.002 PHE B 118 TYR 0.007 0.002 TYR A 24 ARG 0.002 0.000 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 336) hydrogen bonds : angle 4.03221 ( 957) covalent geometry : bond 0.00378 ( 4636) covalent geometry : angle 0.67435 ( 6358) Misc. bond : bond 0.12771 ( 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 70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.509 Fit side-chains REVERT: A 60 LYS cc_start: 0.8406 (ttmm) cc_final: 0.7991 (ttmt) REVERT: A 90 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7738 (ttpp) REVERT: B 26 GLU cc_start: 0.7903 (pt0) cc_final: 0.7304 (tt0) REVERT: B 59 LYS cc_start: 0.8457 (mttt) cc_final: 0.7604 (mtpt) REVERT: D 68 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8027 (tp) REVERT: D 121 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8497 (mt-10) REVERT: D 132 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8154 (mttm) outliers start: 16 outliers final: 4 residues processed: 65 average time/residue: 1.5622 time to fit residues: 104.8638 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 : 0.515 ------------------------------------------------------------------------------- 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 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: 0.2980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 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 = 0.3715 r_free = 0.3715 target = 0.157689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.136482 restraints weight = 4288.787| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 0.95 r_work: 0.3198 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.232 4640 Z= 0.136 Angle : 0.665 16.219 6358 Z= 0.259 Chirality : 0.038 0.132 688 Planarity : 0.005 0.047 794 Dihedral : 9.487 89.781 622 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.42 % Allowed : 17.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.37), residues: 560 helix: 2.62 (0.25), residues: 434 sheet: None (None), residues: 0 loop : 1.91 (0.66), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 14 HIS 0.005 0.001 HIS B 116 PHE 0.011 0.001 PHE B 118 TYR 0.007 0.001 TYR A 24 ARG 0.001 0.000 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 336) hydrogen bonds : angle 3.92536 ( 957) covalent geometry : bond 0.00352 ( 4636) covalent geometry : angle 0.66456 ( 6358) Misc. bond : bond 0.15564 ( 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 62 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.531 Fit side-chains REVERT: A 60 LYS cc_start: 0.8522 (ttmm) cc_final: 0.8154 (ttmt) REVERT: A 90 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7715 (ttpp) REVERT: B 26 GLU cc_start: 0.7932 (pt0) cc_final: 0.7462 (tt0) REVERT: B 59 LYS cc_start: 0.8520 (mttt) cc_final: 0.7855 (mtpt) REVERT: B 61 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7627 (mptm) REVERT: D 68 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8157 (tp) REVERT: D 120 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7852 (ptpp) REVERT: D 121 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8481 (mt-10) REVERT: D 132 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8282 (mttm) outliers start: 11 outliers final: 3 residues processed: 57 average time/residue: 1.5256 time to fit residues: 89.9578 Evaluate side-chains 58 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.156164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.133624 restraints weight = 4275.675| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.09 r_work: 0.3194 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.261 4640 Z= 0.133 Angle : 0.664 16.348 6358 Z= 0.259 Chirality : 0.038 0.130 688 Planarity : 0.005 0.046 794 Dihedral : 9.420 89.831 622 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.42 % Allowed : 17.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.37), residues: 560 helix: 2.66 (0.25), residues: 434 sheet: None (None), residues: 0 loop : 1.91 (0.66), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 14 HIS 0.005 0.001 HIS B 116 PHE 0.010 0.001 PHE B 118 TYR 0.007 0.001 TYR A 24 ARG 0.001 0.000 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 336) hydrogen bonds : angle 3.90304 ( 957) covalent geometry : bond 0.00342 ( 4636) covalent geometry : angle 0.66444 ( 6358) Misc. bond : bond 0.16354 ( 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 63 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.447 Fit side-chains REVERT: A 60 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8034 (ttmt) REVERT: A 90 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7725 (ttpp) REVERT: B 26 GLU cc_start: 0.7899 (pt0) cc_final: 0.7341 (tt0) REVERT: B 59 LYS cc_start: 0.8444 (mttt) cc_final: 0.7680 (mtpt) REVERT: B 61 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7459 (mptm) REVERT: D 68 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8023 (tp) REVERT: D 121 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8380 (mt-10) REVERT: D 132 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8145 (mttm) outliers start: 11 outliers final: 4 residues processed: 58 average time/residue: 1.5454 time to fit residues: 92.6445 Evaluate side-chains 59 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 5 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.156866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.134413 restraints weight = 4265.366| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.09 r_work: 0.3206 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.244 4640 Z= 0.125 Angle : 0.654 16.204 6358 Z= 0.253 Chirality : 0.037 0.127 688 Planarity : 0.005 0.046 794 Dihedral : 9.367 89.695 622 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.64 % Allowed : 17.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.37), residues: 560 helix: 2.70 (0.25), residues: 436 sheet: None (None), residues: 0 loop : 2.04 (0.66), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 14 HIS 0.005 0.001 HIS B 116 PHE 0.009 0.001 PHE B 118 TYR 0.007 0.001 TYR A 24 ARG 0.001 0.000 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 336) hydrogen bonds : angle 3.84368 ( 957) covalent geometry : bond 0.00322 ( 4636) covalent geometry : angle 0.65363 ( 6358) Misc. bond : bond 0.14979 ( 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: 12 poor density : 50 time to evaluate : 0.489 Fit side-chains REVERT: A 60 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8017 (ttmt) REVERT: A 90 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7709 (ttpp) REVERT: B 26 GLU cc_start: 0.7877 (pt0) cc_final: 0.7345 (tt0) REVERT: B 59 LYS cc_start: 0.8421 (mttt) cc_final: 0.7660 (mtpt) REVERT: B 61 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7459 (mptm) REVERT: D 68 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8016 (tp) REVERT: D 121 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8382 (mt-10) REVERT: D 132 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8146 (mttm) outliers start: 12 outliers final: 4 residues processed: 56 average time/residue: 1.5269 time to fit residues: 88.4760 Evaluate side-chains 57 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 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 = 0.3713 r_free = 0.3713 target = 0.157416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.136338 restraints weight = 4247.352| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.04 r_work: 0.3210 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.269 4640 Z= 0.130 Angle : 0.660 16.205 6358 Z= 0.257 Chirality : 0.038 0.129 688 Planarity : 0.005 0.046 794 Dihedral : 9.371 89.815 622 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.37), residues: 560 helix: 2.68 (0.25), residues: 436 sheet: None (None), residues: 0 loop : 2.01 (0.67), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.005 0.001 HIS B 116 PHE 0.009 0.001 PHE B 118 TYR 0.009 0.001 TYR A 24 ARG 0.001 0.000 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 336) hydrogen bonds : angle 3.85953 ( 957) covalent geometry : bond 0.00334 ( 4636) covalent geometry : angle 0.66013 ( 6358) Misc. bond : bond 0.16271 ( 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: 10 poor density : 50 time to evaluate : 0.461 Fit side-chains REVERT: A 60 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8151 (ttmt) REVERT: A 90 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7671 (ttpp) REVERT: B 26 GLU cc_start: 0.7961 (pt0) cc_final: 0.7468 (tt0) REVERT: B 59 LYS cc_start: 0.8517 (mttt) cc_final: 0.7847 (mtpt) REVERT: B 61 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7625 (mptm) REVERT: D 68 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8157 (tp) REVERT: D 121 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8457 (mt-10) REVERT: D 132 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8279 (mttm) outliers start: 10 outliers final: 4 residues processed: 55 average time/residue: 1.4289 time to fit residues: 81.3748 Evaluate side-chains 58 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.157701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.136811 restraints weight = 4262.391| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.03 r_work: 0.3217 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.268 4640 Z= 0.129 Angle : 0.661 16.211 6358 Z= 0.257 Chirality : 0.038 0.129 688 Planarity : 0.005 0.047 794 Dihedral : 9.418 89.649 622 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.36), residues: 560 helix: 2.69 (0.24), residues: 436 sheet: None (None), residues: 0 loop : 1.97 (0.66), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.005 0.001 HIS B 116 PHE 0.009 0.001 PHE B 118 TYR 0.012 0.001 TYR A 24 ARG 0.001 0.000 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 336) hydrogen bonds : angle 3.84909 ( 957) covalent geometry : bond 0.00335 ( 4636) covalent geometry : angle 0.66096 ( 6358) Misc. bond : bond 0.16166 ( 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 57 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.508 Fit side-chains REVERT: A 60 LYS cc_start: 0.8494 (ttmm) cc_final: 0.8089 (ttmt) REVERT: A 90 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7635 (ttpp) REVERT: B 26 GLU cc_start: 0.7920 (pt0) cc_final: 0.7415 (tt0) REVERT: B 59 LYS cc_start: 0.8473 (mttt) cc_final: 0.7771 (mtpt) REVERT: B 61 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7531 (mptm) REVERT: D 68 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8086 (tp) REVERT: D 121 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8382 (mt-10) REVERT: D 132 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8218 (mttm) outliers start: 9 outliers final: 4 residues processed: 52 average time/residue: 1.5500 time to fit residues: 83.4189 Evaluate side-chains 56 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.156815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.135845 restraints weight = 4262.960| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.04 r_work: 0.3192 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.294 4640 Z= 0.136 Angle : 0.671 16.363 6358 Z= 0.262 Chirality : 0.038 0.131 688 Planarity : 0.005 0.047 794 Dihedral : 9.474 89.791 622 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.36), residues: 560 helix: 2.65 (0.24), residues: 436 sheet: None (None), residues: 0 loop : 1.90 (0.65), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.005 0.001 HIS B 116 PHE 0.010 0.001 PHE B 118 TYR 0.015 0.002 TYR A 24 ARG 0.001 0.000 ARG D 104 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 336) hydrogen bonds : angle 3.88979 ( 957) covalent geometry : bond 0.00350 ( 4636) covalent geometry : angle 0.67104 ( 6358) Misc. bond : bond 0.17780 ( 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 57 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.469 Fit side-chains REVERT: A 60 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8169 (ttmt) REVERT: A 90 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7650 (ttpp) REVERT: B 26 GLU cc_start: 0.7969 (pt0) cc_final: 0.7484 (tt0) REVERT: B 59 LYS cc_start: 0.8525 (mttt) cc_final: 0.7863 (mtpt) REVERT: B 61 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7616 (mptm) REVERT: D 68 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8167 (tp) REVERT: D 121 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8369 (mt-10) REVERT: D 132 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8270 (mttm) outliers start: 9 outliers final: 5 residues processed: 53 average time/residue: 1.5679 time to fit residues: 86.0451 Evaluate side-chains 56 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 132 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 3 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.155510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.134293 restraints weight = 4270.070| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 0.96 r_work: 0.3191 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.357 4640 Z= 0.158 Angle : 0.694 16.702 6358 Z= 0.274 Chirality : 0.039 0.138 688 Planarity : 0.005 0.047 794 Dihedral : 9.624 89.994 622 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.36), residues: 560 helix: 2.57 (0.24), residues: 434 sheet: None (None), residues: 0 loop : 1.72 (0.65), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 14 HIS 0.006 0.001 HIS B 116 PHE 0.011 0.002 PHE B 118 TYR 0.019 0.002 TYR A 24 ARG 0.001 0.000 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 336) hydrogen bonds : angle 3.98312 ( 957) covalent geometry : bond 0.00405 ( 4636) covalent geometry : angle 0.69365 ( 6358) Misc. bond : bond 0.21951 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3312.34 seconds wall clock time: 58 minutes 1.69 seconds (3481.69 seconds total)