Starting phenix.real_space_refine on Tue Aug 4 12:24:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oip_70525/08_2026/9oip_70525.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oip_70525/08_2026/9oip_70525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oip_70525/08_2026/9oip_70525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oip_70525/08_2026/9oip_70525.map" model { file = "/net/cci-nas-00/data/ceres_data/9oip_70525/08_2026/9oip_70525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oip_70525/08_2026/9oip_70525.cif" } resolution = 2.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 1650 2.51 5 N 470 2.21 5 O 480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2620 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 262 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.57, per 1000 atoms: 0.22 Number of scatterers: 2620 At special positions: 0 Unit cell: (76.446, 66.582, 38.634, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 480 8.00 N 470 7.00 C 1650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 22 " distance=2.04 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 22 " distance=2.04 Simple disulfide: pdb=" SG CYS C 5 " - pdb=" SG CYS C 22 " distance=2.04 Simple disulfide: pdb=" SG CYS D 5 " - pdb=" SG CYS D 22 " distance=2.04 Simple disulfide: pdb=" SG CYS E 5 " - pdb=" SG CYS E 22 " distance=2.04 Simple disulfide: pdb=" SG CYS F 5 " - pdb=" SG CYS F 22 " distance=2.04 Simple disulfide: pdb=" SG CYS G 5 " - pdb=" SG CYS G 22 " distance=2.04 Simple disulfide: pdb=" SG CYS H 5 " - pdb=" SG CYS H 22 " distance=2.04 Simple disulfide: pdb=" SG CYS I 5 " - pdb=" SG CYS I 22 " distance=2.04 Simple disulfide: pdb=" SG CYS J 5 " - pdb=" SG CYS J 22 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 83.4 milliseconds 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 640 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 Processing sheet with id=AA2, first strand: chain 'E' and resid 17 through 22 removed outlier: 6.471A pdb=" N VAL C 17 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU G 20 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR C 19 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N CYS G 22 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE C 21 " --> pdb=" O CYS G 22 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 17 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU C 20 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR A 19 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N CYS C 22 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 21 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 25 through 26 removed outlier: 6.519A pdb=" N THR E 25 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR A 25 " --> pdb=" O VAL I 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 30 through 33 removed outlier: 6.229A pdb=" N ILE E 30 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLU G 33 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLU E 32 " --> pdb=" O GLU G 33 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 30 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLU I 33 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU A 32 " --> pdb=" O GLU I 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.850A pdb=" N PHE B 11 " --> pdb=" O GLU J 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 17 through 22 removed outlier: 6.472A pdb=" N VAL B 17 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU F 20 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR B 19 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N CYS F 22 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE B 21 " --> pdb=" O CYS F 22 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL H 17 " --> pdb=" O GLU J 18 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU J 20 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR H 19 " --> pdb=" O LEU J 20 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N CYS J 22 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE H 21 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 25 through 26 removed outlier: 6.516A pdb=" N THR D 25 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR B 25 " --> pdb=" O VAL J 26 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 30 through 33 removed outlier: 6.235A pdb=" N ILE D 30 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N GLU F 33 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU D 32 " --> pdb=" O GLU F 33 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE B 30 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N GLU J 33 " --> pdb=" O ILE B 30 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU B 32 " --> pdb=" O GLU J 33 " (cutoff:3.500A) 40 hydrogen bonds defined for protein. 120 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: 0.25 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 806 1.34 - 1.46: 533 1.46 - 1.58: 1291 1.58 - 1.71: 0 1.71 - 1.83: 20 Bond restraints: 2650 Sorted by residual: bond pdb=" CB GLU F 12 " pdb=" CG GLU F 12 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 4.03e+00 bond pdb=" CB GLU B 12 " pdb=" CG GLU B 12 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 4.03e+00 bond pdb=" CB GLU E 12 " pdb=" CG GLU E 12 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 3.99e+00 bond pdb=" CB GLU G 12 " pdb=" CG GLU G 12 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 3.98e+00 bond pdb=" CB GLU D 12 " pdb=" CG GLU D 12 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 3.98e+00 ... (remaining 2645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 3130 1.79 - 3.58: 319 3.58 - 5.37: 51 5.37 - 7.15: 20 7.15 - 8.94: 20 Bond angle restraints: 3540 Sorted by residual: angle pdb=" CA GLU F 12 " pdb=" CB GLU F 12 " pdb=" CG GLU F 12 " ideal model delta sigma weight residual 114.10 123.04 -8.94 2.00e+00 2.50e-01 2.00e+01 angle pdb=" CA GLU E 12 " pdb=" CB GLU E 12 " pdb=" CG GLU E 12 " ideal model delta sigma weight residual 114.10 123.04 -8.94 2.00e+00 2.50e-01 2.00e+01 angle pdb=" CA GLU H 12 " pdb=" CB GLU H 12 " pdb=" CG GLU H 12 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CA GLU I 12 " pdb=" CB GLU I 12 " pdb=" CG GLU I 12 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CA GLU J 12 " pdb=" CB GLU J 12 " pdb=" CG GLU J 12 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 ... (remaining 3535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.55: 1330 13.55 - 27.09: 190 27.09 - 40.64: 70 40.64 - 54.18: 60 54.18 - 67.73: 10 Dihedral angle restraints: 1660 sinusoidal: 710 harmonic: 950 Sorted by residual: dihedral pdb=" CB CYS F 5 " pdb=" SG CYS F 5 " pdb=" SG CYS F 22 " pdb=" CB CYS F 22 " ideal model delta sinusoidal sigma weight residual 93.00 25.27 67.73 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" CB CYS I 5 " pdb=" SG CYS I 5 " pdb=" SG CYS I 22 " pdb=" CB CYS I 22 " ideal model delta sinusoidal sigma weight residual 93.00 25.27 67.73 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" CB CYS D 5 " pdb=" SG CYS D 5 " pdb=" SG CYS D 22 " pdb=" CB CYS D 22 " ideal model delta sinusoidal sigma weight residual 93.00 25.28 67.72 1 1.00e+01 1.00e-02 5.96e+01 ... (remaining 1657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 179 0.035 - 0.070: 91 0.070 - 0.105: 68 0.105 - 0.139: 54 0.139 - 0.174: 18 Chirality restraints: 410 Sorted by residual: chirality pdb=" CA VAL J 17 " pdb=" N VAL J 17 " pdb=" C VAL J 17 " pdb=" CB VAL J 17 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA VAL G 17 " pdb=" N VAL G 17 " pdb=" C VAL G 17 " pdb=" CB VAL G 17 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CA VAL C 17 " pdb=" N VAL C 17 " pdb=" C VAL C 17 " pdb=" CB VAL C 17 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 407 not shown) Planarity restraints: 450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE I 15 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.00e+00 pdb=" C PHE I 15 " 0.046 2.00e-02 2.50e+03 pdb=" O PHE I 15 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA I 16 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 15 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" C PHE A 15 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE A 15 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 16 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 15 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C PHE F 15 " -0.045 2.00e-02 2.50e+03 pdb=" O PHE F 15 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA F 16 " 0.015 2.00e-02 2.50e+03 ... (remaining 447 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 1062 2.94 - 3.43: 2183 3.43 - 3.92: 4827 3.92 - 4.41: 5105 4.41 - 4.90: 10145 Nonbonded interactions: 23322 Sorted by model distance: nonbonded pdb=" OE2 GLU H 18 " pdb=" ND2 ASN J 13 " model vdw 2.446 3.120 nonbonded pdb=" ND2 ASN A 13 " pdb=" OE2 GLU I 18 " model vdw 2.449 3.120 nonbonded pdb=" ND2 ASN D 13 " pdb=" OE2 GLU F 18 " model vdw 2.454 3.120 nonbonded pdb=" ND2 ASN E 13 " pdb=" OE2 GLU G 18 " model vdw 2.455 3.120 nonbonded pdb=" OE2 GLU B 18 " pdb=" ND2 ASN F 13 " model vdw 2.463 3.120 ... (remaining 23317 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.550 Find NCS groups from input model: 0.010 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:5.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 0.060 2660 Z= 0.458 Angle : 1.395 8.943 3560 Z= 0.766 Chirality : 0.073 0.174 410 Planarity : 0.006 0.026 450 Dihedral : 17.048 48.463 990 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 9 PHE 0.020 0.005 PHE F 15 HIS 0.002 0.001 HIS J 10 Details of bonding type rmsd/Z covalent geometry : bond 0.01072 / 0.46 ( 2650) covalent geometry : angle 1.35455 / 0.75 ( 3540) SS BOND : bond 0.00478 / 0.31 ( 10) SS BOND : angle 4.64205 / 3.14 ( 20) hydrogen bonds : bond 0.15862 / 10.95 ( 40) hydrogen bonds : angle 10.00709 / 6.87 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.062 Fit side-chains REVERT: D 32 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8158 (mt-10) REVERT: E 32 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8142 (mt-10) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.5763 time to fit residues: 42.2780 Evaluate side-chains 59 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 13 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.186376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.165795 restraints weight = 2624.055| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 1.96 r_work: 0.4193 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4072 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2660 Z= 0.139 Angle : 0.543 6.499 3560 Z= 0.303 Chirality : 0.052 0.132 410 Planarity : 0.003 0.014 450 Dihedral : 6.347 20.044 330 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 6.00 % Allowed : 9.00 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.04 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 24 PHE 0.008 0.001 PHE A 11 HIS 0.003 0.001 HIS C 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 2650) covalent geometry : angle 0.53825 / 0.30 ( 3540) SS BOND : bond 0.00337 / 0.23 ( 10) SS BOND : angle 1.07935 / 0.74 ( 20) hydrogen bonds : bond 0.02376 / 1.61 ( 40) hydrogen bonds : angle 5.81047 / 4.15 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.118 Fit side-chains REVERT: E 18 GLU cc_start: 0.8228 (mp0) cc_final: 0.7940 (mt-10) REVERT: F 33 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8755 (mt-10) REVERT: G 33 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8724 (mt-10) REVERT: H 15 PHE cc_start: 0.7708 (t80) cc_final: 0.7250 (t80) REVERT: I 32 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8434 (mt-10) outliers start: 18 outliers final: 7 residues processed: 70 average time/residue: 0.5210 time to fit residues: 37.2908 Evaluate side-chains 60 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 CYS Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain D residue 5 CYS Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain G residue 5 CYS Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 HIS ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 ASN B 10 HIS ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 HIS D 13 ASN E 10 HIS F 10 HIS ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 HIS I 13 ASN ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.160522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.141642 restraints weight = 2586.508| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.75 r_work: 0.3873 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2660 Z= 0.273 Angle : 0.683 6.511 3560 Z= 0.391 Chirality : 0.057 0.151 410 Planarity : 0.003 0.012 450 Dihedral : 7.188 18.414 330 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 1.33 % Allowed : 23.00 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.75 (0.31), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.23), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG J 24 PHE 0.016 0.002 PHE G 11 HIS 0.003 0.001 HIS J 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.27 ( 2650) covalent geometry : angle 0.68180 / 0.39 ( 3540) SS BOND : bond 0.00222 / 0.14 ( 10) SS BOND : angle 0.87085 / 0.57 ( 20) hydrogen bonds : bond 0.02485 / 1.63 ( 40) hydrogen bonds : angle 5.92516 / 4.11 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.108 Fit side-chains REVERT: B 24 ARG cc_start: 0.8246 (ttt90) cc_final: 0.8010 (ttt90) REVERT: C 24 ARG cc_start: 0.8197 (ttt90) cc_final: 0.7963 (ttt90) REVERT: C 33 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8653 (mt-10) REVERT: F 24 ARG cc_start: 0.8157 (ttt90) cc_final: 0.7936 (ttt90) REVERT: F 33 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8830 (mt-10) REVERT: G 18 GLU cc_start: 0.8262 (mp0) cc_final: 0.8020 (mp0) REVERT: G 24 ARG cc_start: 0.8139 (ttt90) cc_final: 0.7921 (ttt90) REVERT: G 33 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8857 (mt-10) REVERT: J 24 ARG cc_start: 0.8159 (ttt90) cc_final: 0.7938 (ttt90) outliers start: 4 outliers final: 2 residues processed: 63 average time/residue: 0.8634 time to fit residues: 55.2313 Evaluate side-chains 63 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain I residue 28 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN C 13 ASN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 ASN ** H 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.167103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.147503 restraints weight = 2594.636| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 1.96 r_work: 0.4001 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2660 Z= 0.146 Angle : 0.531 6.000 3560 Z= 0.302 Chirality : 0.053 0.134 410 Planarity : 0.002 0.009 450 Dihedral : 6.164 16.199 330 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 2.33 % Allowed : 21.67 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.81 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 24 PHE 0.010 0.001 PHE F 11 HIS 0.001 0.000 HIS J 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 2650) covalent geometry : angle 0.53004 / 0.30 ( 3540) SS BOND : bond 0.00130 / 0.08 ( 10) SS BOND : angle 0.68469 / 0.45 ( 20) hydrogen bonds : bond 0.01975 / 1.27 ( 40) hydrogen bonds : angle 5.69246 / 4.05 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.133 Fit side-chains REVERT: A 28 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8576 (ptpt) REVERT: C 33 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8753 (mt-10) REVERT: E 18 GLU cc_start: 0.8307 (mp0) cc_final: 0.8031 (mt-10) REVERT: F 24 ARG cc_start: 0.8132 (ttt90) cc_final: 0.7929 (ttt90) REVERT: F 33 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8884 (mt-10) REVERT: G 33 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8856 (mt-10) REVERT: H 15 PHE cc_start: 0.7974 (t80) cc_final: 0.7753 (t80) REVERT: I 15 PHE cc_start: 0.8015 (t80) cc_final: 0.7788 (t80) REVERT: J 18 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8053 (mt-10) outliers start: 7 outliers final: 1 residues processed: 69 average time/residue: 0.6542 time to fit residues: 45.9559 Evaluate side-chains 68 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 18 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN B 13 ASN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 10 HIS H 13 ASN J 13 ASN J 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.167582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.148801 restraints weight = 2636.261| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 1.85 r_work: 0.4086 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3969 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2660 Z= 0.137 Angle : 0.517 5.715 3560 Z= 0.295 Chirality : 0.052 0.132 410 Planarity : 0.002 0.017 450 Dihedral : 6.096 20.136 330 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.00 % Allowed : 23.67 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.85 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 24 PHE 0.008 0.001 PHE G 11 HIS 0.001 0.000 HIS J 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 2650) covalent geometry : angle 0.51649 / 0.29 ( 3540) SS BOND : bond 0.00119 / 0.08 ( 10) SS BOND : angle 0.57853 / 0.38 ( 20) hydrogen bonds : bond 0.01898 / 1.19 ( 40) hydrogen bonds : angle 5.62579 / 4.03 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.106 Fit side-chains REVERT: F 33 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8784 (mt-10) REVERT: G 33 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8787 (mt-10) REVERT: H 15 PHE cc_start: 0.8047 (t80) cc_final: 0.7813 (t80) REVERT: I 15 PHE cc_start: 0.7999 (t80) cc_final: 0.7670 (t80) outliers start: 9 outliers final: 2 residues processed: 65 average time/residue: 0.5836 time to fit residues: 38.5909 Evaluate side-chains 63 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain I residue 28 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.162275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.143332 restraints weight = 2638.260| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 1.92 r_work: 0.4003 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3882 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2660 Z= 0.183 Angle : 0.567 5.787 3560 Z= 0.328 Chirality : 0.054 0.137 410 Planarity : 0.003 0.019 450 Dihedral : 6.328 18.660 330 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.00 % Allowed : 24.67 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.89 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 24 PHE 0.008 0.001 PHE F 11 HIS 0.002 0.001 HIS J 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 ( 2650) covalent geometry : angle 0.56642 / 0.33 ( 3540) SS BOND : bond 0.00158 / 0.10 ( 10) SS BOND : angle 0.67132 / 0.43 ( 20) hydrogen bonds : bond 0.02069 / 1.31 ( 40) hydrogen bonds : angle 5.64191 / 4.05 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.093 Fit side-chains REVERT: B 33 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8565 (mt-10) REVERT: E 18 GLU cc_start: 0.8358 (mp0) cc_final: 0.8101 (mt-10) REVERT: E 33 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8903 (mt-10) REVERT: F 33 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8818 (mt-10) REVERT: G 33 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8842 (mt-10) REVERT: I 15 PHE cc_start: 0.8074 (t80) cc_final: 0.7530 (t80) outliers start: 9 outliers final: 3 residues processed: 63 average time/residue: 0.6787 time to fit residues: 43.4576 Evaluate side-chains 65 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 28 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 13 ASN F 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.157024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.138168 restraints weight = 2669.685| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.95 r_work: 0.3946 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3824 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.6133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 2660 Z= 0.253 Angle : 0.643 5.800 3560 Z= 0.372 Chirality : 0.055 0.140 410 Planarity : 0.003 0.021 450 Dihedral : 6.711 20.039 330 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 3.67 % Allowed : 24.67 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.02 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 24 PHE 0.018 0.002 PHE H 15 HIS 0.003 0.001 HIS J 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.25 ( 2650) covalent geometry : angle 0.64283 / 0.37 ( 3540) SS BOND : bond 0.00236 / 0.15 ( 10) SS BOND : angle 0.68251 / 0.44 ( 20) hydrogen bonds : bond 0.02178 / 1.39 ( 40) hydrogen bonds : angle 5.81797 / 4.15 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.062 Fit side-chains REVERT: C 33 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8614 (mt-10) REVERT: E 33 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8896 (mt-10) REVERT: F 33 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8840 (mt-10) REVERT: G 33 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8818 (mt-10) outliers start: 11 outliers final: 2 residues processed: 66 average time/residue: 0.6478 time to fit residues: 43.3651 Evaluate side-chains 65 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain I residue 28 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.164581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.145182 restraints weight = 2666.125| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 1.95 r_work: 0.4041 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3922 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2660 Z= 0.148 Angle : 0.534 5.099 3560 Z= 0.309 Chirality : 0.053 0.135 410 Planarity : 0.003 0.022 450 Dihedral : 6.080 19.959 330 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.00 % Allowed : 26.00 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.97 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 24 PHE 0.011 0.001 PHE H 15 HIS 0.001 0.000 HIS J 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 2650) covalent geometry : angle 0.53317 / 0.31 ( 3540) SS BOND : bond 0.00116 / 0.08 ( 10) SS BOND : angle 0.68119 / 0.45 ( 20) hydrogen bonds : bond 0.02007 / 1.25 ( 40) hydrogen bonds : angle 5.70072 / 4.08 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.105 Fit side-chains REVERT: E 33 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8831 (mt-10) REVERT: F 9 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7572 (ttp80) REVERT: G 9 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7560 (ttp80) REVERT: G 33 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8856 (mt-10) REVERT: I 15 PHE cc_start: 0.8051 (t80) cc_final: 0.7647 (t80) outliers start: 9 outliers final: 3 residues processed: 68 average time/residue: 0.6118 time to fit residues: 42.3479 Evaluate side-chains 68 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 28 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.166943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.147211 restraints weight = 2655.461| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 1.96 r_work: 0.4067 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2660 Z= 0.112 Angle : 0.484 4.860 3560 Z= 0.278 Chirality : 0.051 0.132 410 Planarity : 0.003 0.024 450 Dihedral : 5.572 17.852 330 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.00 % Allowed : 27.33 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.90 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 24 PHE 0.013 0.001 PHE H 15 HIS 0.001 0.000 HIS J 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 2650) covalent geometry : angle 0.48301 / 0.28 ( 3540) SS BOND : bond 0.00085 / 0.05 ( 10) SS BOND : angle 0.64675 / 0.43 ( 20) hydrogen bonds : bond 0.01946 / 1.20 ( 40) hydrogen bonds : angle 5.66082 / 4.02 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.065 Fit side-chains REVERT: B 33 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8608 (mt-10) REVERT: E 33 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8823 (mt-10) REVERT: F 9 ARG cc_start: 0.7823 (ttp80) cc_final: 0.7595 (ttp80) REVERT: F 33 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8757 (mt-10) REVERT: G 9 ARG cc_start: 0.7860 (ttp80) cc_final: 0.7634 (ttp80) REVERT: G 33 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8785 (mt-10) REVERT: I 28 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8233 (mptt) outliers start: 6 outliers final: 0 residues processed: 68 average time/residue: 0.6969 time to fit residues: 48.0905 Evaluate side-chains 69 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain I residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.163923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.144768 restraints weight = 2677.089| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 1.92 r_work: 0.4037 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3918 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2660 Z= 0.163 Angle : 0.549 5.177 3560 Z= 0.317 Chirality : 0.053 0.136 410 Planarity : 0.003 0.039 450 Dihedral : 5.950 21.508 330 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.33 % Allowed : 29.67 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.98 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 24 PHE 0.009 0.001 PHE H 15 HIS 0.002 0.001 HIS J 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 2650) covalent geometry : angle 0.54926 / 0.32 ( 3540) SS BOND : bond 0.00131 / 0.09 ( 10) SS BOND : angle 0.57135 / 0.38 ( 20) hydrogen bonds : bond 0.02137 / 1.31 ( 40) hydrogen bonds : angle 5.77035 / 4.13 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.081 Fit side-chains REVERT: C 33 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8699 (mt-10) REVERT: E 33 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8911 (mt-10) REVERT: F 9 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7555 (ttp80) REVERT: G 9 ARG cc_start: 0.7851 (ttp80) cc_final: 0.7614 (ttp80) REVERT: G 33 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8824 (mt-10) outliers start: 4 outliers final: 1 residues processed: 64 average time/residue: 0.7295 time to fit residues: 47.4416 Evaluate side-chains 65 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain I residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.162725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.143794 restraints weight = 2637.690| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 1.88 r_work: 0.4032 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2660 Z= 0.169 Angle : 0.560 5.211 3560 Z= 0.323 Chirality : 0.053 0.136 410 Planarity : 0.004 0.035 450 Dihedral : 5.987 18.782 330 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 1.67 % Allowed : 28.33 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.04 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 24 PHE 0.012 0.001 PHE H 15 HIS 0.001 0.001 HIS J 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 2650) covalent geometry : angle 0.56008 / 0.32 ( 3540) SS BOND : bond 0.00134 / 0.09 ( 10) SS BOND : angle 0.58980 / 0.39 ( 20) hydrogen bonds : bond 0.02278 / 1.37 ( 40) hydrogen bonds : angle 5.77115 / 4.11 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1222.35 seconds wall clock time: 21 minutes 27.77 seconds (1287.77 seconds total)