Starting phenix.real_space_refine on Tue Aug 4 12:27:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oid_70521/08_2026/9oid_70521.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oid_70521/08_2026/9oid_70521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oid_70521/08_2026/9oid_70521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oid_70521/08_2026/9oid_70521.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oid_70521/08_2026/9oid_70521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oid_70521/08_2026/9oid_70521.map" } resolution = 3.0 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= 0.001 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 1710 2.51 5 N 460 2.21 5 O 470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2660 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 266 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.41, per 1000 atoms: 0.15 Number of scatterers: 2660 At special positions: 0 Unit cell: (74.802, 64.938, 37.812, 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 470 8.00 N 460 7.00 C 1710 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=2.02 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 22 " distance=2.02 Simple disulfide: pdb=" SG CYS C 5 " - pdb=" SG CYS C 22 " distance=2.02 Simple disulfide: pdb=" SG CYS D 5 " - pdb=" SG CYS D 22 " distance=2.02 Simple disulfide: pdb=" SG CYS E 5 " - pdb=" SG CYS E 22 " distance=2.02 Simple disulfide: pdb=" SG CYS F 5 " - pdb=" SG CYS F 22 " distance=2.02 Simple disulfide: pdb=" SG CYS G 5 " - pdb=" SG CYS G 22 " distance=2.02 Simple disulfide: pdb=" SG CYS H 5 " - pdb=" SG CYS H 22 " distance=2.02 Simple disulfide: pdb=" SG CYS I 5 " - pdb=" SG CYS I 22 " distance=2.02 Simple disulfide: pdb=" SG CYS J 5 " - pdb=" SG CYS J 22 " distance=2.02 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: 0.11 Conformation dependent library (CDL) restraints added in 52.4 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, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 removed outlier: 6.672A pdb=" N LEU A 20 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE C 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.590A pdb=" N PHE A 26 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE C 26 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE E 26 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE G 26 " --> pdb=" O LEU I 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA5, first strand: chain 'B' and resid 20 through 21 removed outlier: 6.672A pdb=" N LEU B 20 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE D 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.590A pdb=" N PHE B 26 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE D 26 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE F 26 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE H 26 " --> pdb=" O LEU J 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 14 removed outlier: 6.227A pdb=" N ASN C 13 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASN E 13 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN G 13 " --> pdb=" O LYS I 14 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 12 through 14 removed outlier: 6.227A pdb=" N ASN D 13 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASN F 13 " --> pdb=" O LYS H 14 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASN H 13 " --> pdb=" O LYS J 14 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 26 hydrogen bonds defined for protein. 78 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: 0.20 Time building geometry restraints manager: 0.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 860 1.34 - 1.45: 460 1.45 - 1.57: 1380 1.57 - 1.68: 0 1.68 - 1.80: 20 Bond restraints: 2720 Sorted by residual: bond pdb=" N ALA J 2 " pdb=" CA ALA J 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N ALA A 2 " pdb=" CA ALA A 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N ALA F 2 " pdb=" CA ALA F 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N ALA I 2 " pdb=" CA ALA I 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N ALA C 2 " pdb=" CA ALA C 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 ... (remaining 2715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 3196 1.30 - 2.61: 331 2.61 - 3.91: 84 3.91 - 5.21: 29 5.21 - 6.51: 10 Bond angle restraints: 3650 Sorted by residual: angle pdb=" N ASN C 24 " pdb=" CA ASN C 24 " pdb=" C ASN C 24 " ideal model delta sigma weight residual 109.81 105.58 4.23 1.53e+00 4.27e-01 7.66e+00 angle pdb=" N ASN F 24 " pdb=" CA ASN F 24 " pdb=" C ASN F 24 " ideal model delta sigma weight residual 109.81 105.63 4.18 1.53e+00 4.27e-01 7.48e+00 angle pdb=" N ASN I 24 " pdb=" CA ASN I 24 " pdb=" C ASN I 24 " ideal model delta sigma weight residual 109.81 105.64 4.17 1.53e+00 4.27e-01 7.42e+00 angle pdb=" N ASN G 24 " pdb=" CA ASN G 24 " pdb=" C ASN G 24 " ideal model delta sigma weight residual 109.81 105.64 4.17 1.53e+00 4.27e-01 7.42e+00 angle pdb=" N ASN E 24 " pdb=" CA ASN E 24 " pdb=" C ASN E 24 " ideal model delta sigma weight residual 109.81 105.65 4.16 1.53e+00 4.27e-01 7.39e+00 ... (remaining 3645 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 17.88: 1430 17.88 - 35.75: 140 35.75 - 53.62: 40 53.62 - 71.49: 0 71.49 - 89.35: 10 Dihedral angle restraints: 1620 sinusoidal: 670 harmonic: 950 Sorted by residual: dihedral pdb=" CA ASN A 4 " pdb=" C ASN A 4 " pdb=" N CYS A 5 " pdb=" CA CYS A 5 " ideal model delta harmonic sigma weight residual 180.00 163.93 16.07 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA ASN D 4 " pdb=" C ASN D 4 " pdb=" N CYS D 5 " pdb=" CA CYS D 5 " ideal model delta harmonic sigma weight residual 180.00 163.94 16.06 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA ASN F 4 " pdb=" C ASN F 4 " pdb=" N CYS F 5 " pdb=" CA CYS F 5 " ideal model delta harmonic sigma weight residual 180.00 163.97 16.03 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 1617 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.026: 140 0.026 - 0.051: 98 0.051 - 0.075: 78 0.075 - 0.100: 49 0.100 - 0.125: 25 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA ILE J 8 " pdb=" N ILE J 8 " pdb=" C ILE J 8 " pdb=" CB ILE J 8 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE D 8 " pdb=" N ILE D 8 " pdb=" C ILE D 8 " pdb=" CB ILE D 8 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE A 8 " pdb=" N ILE A 8 " pdb=" C ILE A 8 " pdb=" CB ILE A 8 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 387 not shown) Planarity restraints: 480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 26 " -0.001 2.00e-02 2.50e+03 1.64e-02 4.70e+00 pdb=" CG PHE F 26 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE F 26 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE F 26 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE F 26 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE F 26 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE F 26 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 26 " -0.001 2.00e-02 2.50e+03 1.64e-02 4.69e+00 pdb=" CG PHE C 26 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE C 26 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE C 26 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE C 26 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE C 26 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 26 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 26 " 0.000 2.00e-02 2.50e+03 1.63e-02 4.68e+00 pdb=" CG PHE D 26 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE D 26 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE D 26 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE D 26 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE D 26 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 26 " 0.003 2.00e-02 2.50e+03 ... (remaining 477 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1454 2.99 - 3.47: 2468 3.47 - 3.94: 4496 3.94 - 4.42: 4940 4.42 - 4.90: 9952 Nonbonded interactions: 23310 Sorted by model distance: nonbonded pdb=" OE1 GLU A 18 " pdb=" OG SER B 29 " model vdw 2.512 3.040 nonbonded pdb=" N PHE G 26 " pdb=" O LEU I 25 " model vdw 2.520 3.120 nonbonded pdb=" N PHE H 26 " pdb=" O LEU J 25 " model vdw 2.521 3.120 nonbonded pdb=" OE1 GLU C 18 " pdb=" OG SER D 29 " model vdw 2.527 3.040 nonbonded pdb=" OE1 GLU E 18 " pdb=" OG SER F 29 " model vdw 2.533 3.040 ... (remaining 23305 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: 1.290 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: 0.000 Set scattering table: 0.010 Process input model: 3.020 Find NCS groups from input model: 0.020 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:5.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 : 0.006 0.039 2730 Z= 0.299 Angle : 1.045 6.512 3670 Z= 0.616 Chirality : 0.054 0.125 390 Planarity : 0.011 0.072 480 Dihedral : 16.946 89.355 950 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % 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: -4.58 (0.31), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.24), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 9 PHE 0.027 0.005 PHE C 26 HIS 0.006 0.003 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.30 ( 2720) covalent geometry : angle 1.03956 / 0.61 ( 3650) SS BOND : bond 0.00819 / 0.54 ( 10) SS BOND : angle 1.82733 / 1.25 ( 20) hydrogen bonds : bond 0.27986 / 18.67 ( 26) hydrogen bonds : angle 12.85854 / 8.79 ( 78) *********************** 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 76 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.059 Fit side-chains REVERT: A 9 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7384 (mtm180) REVERT: A 32 LYS cc_start: 0.7959 (mptp) cc_final: 0.7703 (mmtp) REVERT: B 9 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7258 (mtm-85) REVERT: B 32 LYS cc_start: 0.7956 (mptp) cc_final: 0.7723 (mmtp) REVERT: C 9 ARG cc_start: 0.7555 (mtm-85) cc_final: 0.7291 (mtm-85) REVERT: C 30 GLN cc_start: 0.7139 (mt0) cc_final: 0.6684 (mt0) REVERT: D 9 ARG cc_start: 0.7535 (mtm-85) cc_final: 0.7241 (mtm-85) REVERT: D 30 GLN cc_start: 0.7169 (mt0) cc_final: 0.6709 (mt0) REVERT: E 9 ARG cc_start: 0.7642 (mtm-85) cc_final: 0.7074 (mtm-85) REVERT: E 30 GLN cc_start: 0.7199 (mt0) cc_final: 0.6940 (mt0) REVERT: F 9 ARG cc_start: 0.7634 (mtm-85) cc_final: 0.7092 (mtm-85) REVERT: F 30 GLN cc_start: 0.7219 (mt0) cc_final: 0.6953 (mt0) REVERT: G 9 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.6963 (mtm-85) REVERT: G 14 LYS cc_start: 0.7778 (mttm) cc_final: 0.7279 (mtmm) REVERT: G 30 GLN cc_start: 0.6993 (mt0) cc_final: 0.6253 (mt0) REVERT: H 9 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.6934 (mtm-85) REVERT: H 14 LYS cc_start: 0.7802 (mttm) cc_final: 0.7311 (mtmm) REVERT: H 30 GLN cc_start: 0.7037 (mt0) cc_final: 0.6339 (mt0) REVERT: I 9 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.6846 (mmt-90) REVERT: I 30 GLN cc_start: 0.7199 (mt0) cc_final: 0.6068 (mt0) REVERT: I 32 LYS cc_start: 0.8396 (mptp) cc_final: 0.6211 (pmtt) REVERT: J 9 ARG cc_start: 0.7563 (mtm-85) cc_final: 0.6852 (mmt-90) REVERT: J 30 GLN cc_start: 0.7151 (mt0) cc_final: 0.6539 (pt0) REVERT: J 32 LYS cc_start: 0.8411 (mptp) cc_final: 0.6297 (pmtt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.4529 time to fit residues: 35.0766 Evaluate side-chains 52 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.058 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.0770 chunk 28 optimal weight: 0.0770 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 ASN E 13 ASN F 13 ASN G 13 ASN H 13 ASN I 13 ASN J 13 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.191450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.175439 restraints weight = 3189.479| |-----------------------------------------------------------------------------| r_work (start): 0.4571 rms_B_bonded: 2.31 r_work: 0.4473 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4365 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2730 Z= 0.118 Angle : 0.615 6.052 3670 Z= 0.350 Chirality : 0.045 0.127 390 Planarity : 0.002 0.013 480 Dihedral : 14.691 86.892 330 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.14 % Allowed : 10.69 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.35 (0.32), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.24), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG G 9 PHE 0.011 0.001 PHE A 11 HIS 0.002 0.000 HIS I 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 2720) covalent geometry : angle 0.61592 / 0.35 ( 3650) SS BOND : bond 0.00467 / 0.33 ( 10) SS BOND : angle 0.49118 / 0.31 ( 20) hydrogen bonds : bond 0.07273 / 4.98 ( 26) hydrogen bonds : angle 9.37013 / 6.13 ( 78) *********************** 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 79 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7808 (ttm-80) REVERT: A 10 HIS cc_start: 0.8684 (m-70) cc_final: 0.8111 (m-70) REVERT: B 9 ARG cc_start: 0.8148 (mtm-85) cc_final: 0.7826 (ttm-80) REVERT: B 10 HIS cc_start: 0.8667 (m-70) cc_final: 0.8118 (m-70) REVERT: B 28 ASN cc_start: 0.7019 (t0) cc_final: 0.6650 (t0) REVERT: C 9 ARG cc_start: 0.8044 (mtm-85) cc_final: 0.7800 (mtm-85) REVERT: C 14 LYS cc_start: 0.8272 (mttt) cc_final: 0.7860 (mtmm) REVERT: C 30 GLN cc_start: 0.7838 (mt0) cc_final: 0.7340 (mt0) REVERT: D 9 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.7752 (mtm-85) REVERT: D 14 LYS cc_start: 0.8284 (mttt) cc_final: 0.7879 (mtmm) REVERT: D 30 GLN cc_start: 0.7939 (mt0) cc_final: 0.7350 (mt0) REVERT: E 9 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7596 (mtm-85) REVERT: F 9 ARG cc_start: 0.7910 (mtm-85) cc_final: 0.7527 (mtm-85) REVERT: G 9 ARG cc_start: 0.8171 (mtm-85) cc_final: 0.7655 (mtm-85) REVERT: G 14 LYS cc_start: 0.8069 (mttm) cc_final: 0.7737 (mtmm) REVERT: H 9 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7625 (mtm-85) REVERT: H 14 LYS cc_start: 0.8095 (mttm) cc_final: 0.7783 (mtmm) REVERT: I 9 ARG cc_start: 0.8305 (mtm-85) cc_final: 0.7354 (mmt-90) REVERT: I 18 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7506 (mp0) REVERT: I 30 GLN cc_start: 0.7992 (mt0) cc_final: 0.7614 (mt0) REVERT: I 32 LYS cc_start: 0.8673 (mptp) cc_final: 0.6779 (pttm) REVERT: J 9 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7374 (mmt-90) REVERT: J 18 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7476 (mp0) REVERT: J 30 GLN cc_start: 0.8023 (mt0) cc_final: 0.7736 (mt0) REVERT: J 32 LYS cc_start: 0.8634 (mptp) cc_final: 0.6724 (pttm) outliers start: 12 outliers final: 0 residues processed: 73 average time/residue: 0.6108 time to fit residues: 45.2994 Evaluate side-chains 62 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** 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 = 0.4512 r_free = 0.4512 target = 0.179344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.162334 restraints weight = 3173.319| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 2.30 r_work: 0.4264 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4147 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2730 Z= 0.195 Angle : 0.642 6.620 3670 Z= 0.354 Chirality : 0.048 0.116 390 Planarity : 0.002 0.014 480 Dihedral : 13.294 82.205 330 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 6.21 % Allowed : 14.14 % Favored : 79.66 % 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: -4.14 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 9 PHE 0.032 0.002 PHE E 23 HIS 0.002 0.001 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.19 ( 2720) covalent geometry : angle 0.64175 / 0.35 ( 3650) SS BOND : bond 0.00997 / 0.63 ( 10) SS BOND : angle 0.67677 / 0.43 ( 20) hydrogen bonds : bond 0.07474 / 5.13 ( 26) hydrogen bonds : angle 10.25792 / 6.72 ( 78) *********************** 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 74 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.058 Fit side-chains REVERT: A 9 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.7808 (ttm-80) REVERT: A 30 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7890 (mt0) REVERT: B 9 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.7811 (ttm-80) REVERT: B 10 HIS cc_start: 0.8667 (m-70) cc_final: 0.8184 (m-70) REVERT: C 9 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7770 (mtm-85) REVERT: D 9 ARG cc_start: 0.8177 (mtm-85) cc_final: 0.7799 (mtm-85) REVERT: E 9 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7453 (mtm-85) REVERT: E 14 LYS cc_start: 0.8323 (mtmm) cc_final: 0.8089 (mtpp) REVERT: E 30 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7938 (mt0) REVERT: F 9 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7514 (mtm-85) REVERT: F 14 LYS cc_start: 0.8353 (mtmm) cc_final: 0.8117 (mtpp) REVERT: F 30 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7924 (mt0) REVERT: G 9 ARG cc_start: 0.8280 (mtm-85) cc_final: 0.7477 (mtm-85) REVERT: G 12 GLU cc_start: 0.8182 (tt0) cc_final: 0.7824 (tt0) REVERT: G 14 LYS cc_start: 0.8068 (mttm) cc_final: 0.7694 (mtmt) REVERT: H 9 ARG cc_start: 0.8286 (mtm-85) cc_final: 0.7486 (mtm-85) REVERT: H 12 GLU cc_start: 0.8200 (tt0) cc_final: 0.7833 (tt0) REVERT: H 14 LYS cc_start: 0.8024 (mttm) cc_final: 0.7658 (mtmt) REVERT: I 9 ARG cc_start: 0.8354 (mtm-85) cc_final: 0.7311 (mmt-90) REVERT: I 14 LYS cc_start: 0.8109 (mttm) cc_final: 0.7636 (mtmm) REVERT: I 18 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7461 (mp0) REVERT: I 32 LYS cc_start: 0.8539 (mptp) cc_final: 0.6315 (pttm) REVERT: J 9 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.7386 (mmt-90) REVERT: J 14 LYS cc_start: 0.8134 (mttm) cc_final: 0.7670 (mtmm) REVERT: J 18 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7439 (mp0) REVERT: J 32 LYS cc_start: 0.8551 (mptp) cc_final: 0.6318 (pttm) outliers start: 18 outliers final: 4 residues processed: 70 average time/residue: 0.5290 time to fit residues: 37.7095 Evaluate side-chains 61 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain J residue 22 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** 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 = 0.4555 r_free = 0.4555 target = 0.182888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.166379 restraints weight = 3147.758| |-----------------------------------------------------------------------------| r_work (start): 0.4421 rms_B_bonded: 2.21 r_work: 0.4311 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4196 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2730 Z= 0.140 Angle : 0.559 6.302 3670 Z= 0.320 Chirality : 0.045 0.114 390 Planarity : 0.002 0.013 480 Dihedral : 11.943 74.201 330 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.52 % Allowed : 19.31 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.86 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 9 PHE 0.029 0.002 PHE G 23 HIS 0.001 0.000 HIS A 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 2720) covalent geometry : angle 0.56025 / 0.32 ( 3650) SS BOND : bond 0.00605 / 0.41 ( 10) SS BOND : angle 0.39524 / 0.25 ( 20) hydrogen bonds : bond 0.07159 / 4.91 ( 26) hydrogen bonds : angle 9.83887 / 6.45 ( 78) *********************** 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 64 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.063 Fit side-chains REVERT: A 9 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.7789 (ttm-80) REVERT: A 10 HIS cc_start: 0.8700 (m-70) cc_final: 0.8235 (m-70) REVERT: A 30 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: B 9 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.7820 (ttm-80) REVERT: B 10 HIS cc_start: 0.8662 (m-70) cc_final: 0.8176 (m-70) REVERT: C 9 ARG cc_start: 0.8174 (mtm-85) cc_final: 0.7782 (mtm-85) REVERT: C 14 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7973 (mtpm) REVERT: D 9 ARG cc_start: 0.8228 (mtm-85) cc_final: 0.7826 (mtm-85) REVERT: D 14 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7791 (mtmm) REVERT: E 9 ARG cc_start: 0.8153 (mtm-85) cc_final: 0.7547 (mtm-85) REVERT: E 14 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8014 (mtpp) REVERT: F 9 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7552 (mtm-85) REVERT: F 14 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8027 (mtpp) REVERT: G 9 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.7574 (mtm-85) REVERT: G 14 LYS cc_start: 0.7997 (mttm) cc_final: 0.7640 (mtmt) REVERT: G 25 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6427 (tt) REVERT: G 30 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7820 (mt0) REVERT: H 9 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.7591 (mtm-85) REVERT: H 12 GLU cc_start: 0.8207 (tt0) cc_final: 0.7763 (tt0) REVERT: H 14 LYS cc_start: 0.7990 (mttm) cc_final: 0.7622 (mtmt) REVERT: H 23 PHE cc_start: 0.7997 (p90) cc_final: 0.7765 (p90) REVERT: H 25 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6461 (tt) REVERT: I 9 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.7356 (mmt-90) REVERT: I 14 LYS cc_start: 0.8147 (mttm) cc_final: 0.7645 (mtmt) REVERT: I 18 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7395 (mp0) REVERT: I 25 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6776 (tt) REVERT: I 32 LYS cc_start: 0.8459 (mptp) cc_final: 0.6284 (pttm) REVERT: J 9 ARG cc_start: 0.8367 (mtm-85) cc_final: 0.7367 (mmt-90) REVERT: J 14 LYS cc_start: 0.8174 (mttm) cc_final: 0.7677 (mtmt) REVERT: J 18 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7354 (mp0) REVERT: J 23 PHE cc_start: 0.7616 (p90) cc_final: 0.3660 (t80) REVERT: J 25 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6798 (tt) REVERT: J 32 LYS cc_start: 0.8435 (mptp) cc_final: 0.6229 (pttm) outliers start: 16 outliers final: 2 residues processed: 60 average time/residue: 0.5151 time to fit residues: 31.4896 Evaluate side-chains 60 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 25 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** 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 = 0.4467 r_free = 0.4467 target = 0.176197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.158694 restraints weight = 3077.451| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 2.21 r_work: 0.4195 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4083 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 2730 Z= 0.269 Angle : 0.665 6.529 3670 Z= 0.371 Chirality : 0.050 0.118 390 Planarity : 0.003 0.015 480 Dihedral : 9.738 54.743 330 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 6.21 % Allowed : 20.00 % Favored : 73.79 % 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: -3.69 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 9 PHE 0.034 0.002 PHE F 23 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.27 ( 2720) covalent geometry : angle 0.66587 / 0.37 ( 3650) SS BOND : bond 0.01011 / 0.68 ( 10) SS BOND : angle 0.40828 / 0.27 ( 20) hydrogen bonds : bond 0.07847 / 5.40 ( 26) hydrogen bonds : angle 10.30989 / 6.78 ( 78) *********************** 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 66 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.8528 (mtm-85) cc_final: 0.8012 (mtm180) REVERT: A 30 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7729 (mt0) REVERT: B 3 SER cc_start: 0.8358 (m) cc_final: 0.8141 (p) REVERT: B 9 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.8007 (mtm180) REVERT: C 14 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8085 (mtpm) REVERT: C 18 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7870 (mt-10) REVERT: E 14 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8085 (mtpp) REVERT: F 14 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8086 (mtpp) REVERT: F 30 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: G 9 ARG cc_start: 0.8325 (mtm-85) cc_final: 0.7697 (mtm-85) REVERT: G 14 LYS cc_start: 0.8038 (mttm) cc_final: 0.7625 (mtmt) REVERT: G 25 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6626 (tt) REVERT: H 9 ARG cc_start: 0.8328 (mtm-85) cc_final: 0.7676 (mtm-85) REVERT: H 12 GLU cc_start: 0.8226 (tt0) cc_final: 0.7863 (tt0) REVERT: H 14 LYS cc_start: 0.8044 (mttm) cc_final: 0.7606 (mtmt) REVERT: H 25 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6625 (tt) REVERT: I 9 ARG cc_start: 0.8452 (mtm-85) cc_final: 0.7487 (mmt-90) REVERT: I 14 LYS cc_start: 0.8203 (mttm) cc_final: 0.7670 (mtmt) REVERT: I 18 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7494 (mp0) REVERT: I 25 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6946 (tt) REVERT: I 32 LYS cc_start: 0.8496 (mptp) cc_final: 0.6238 (pttm) REVERT: J 9 ARG cc_start: 0.8462 (mtm-85) cc_final: 0.7514 (mmt-90) REVERT: J 14 LYS cc_start: 0.8205 (mttm) cc_final: 0.7672 (mtmt) REVERT: J 25 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6959 (tt) REVERT: J 32 LYS cc_start: 0.8514 (mptp) cc_final: 0.6239 (pttm) outliers start: 18 outliers final: 3 residues processed: 61 average time/residue: 0.4814 time to fit residues: 30.0036 Evaluate side-chains 58 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 25 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** 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 = 0.4543 r_free = 0.4543 target = 0.182096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.165164 restraints weight = 3090.572| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 2.22 r_work: 0.4284 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4172 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2730 Z= 0.145 Angle : 0.572 6.479 3670 Z= 0.327 Chirality : 0.045 0.114 390 Planarity : 0.003 0.022 480 Dihedral : 8.457 46.347 330 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.83 % Allowed : 21.38 % Favored : 73.79 % 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: -3.64 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 9 PHE 0.030 0.002 PHE G 23 HIS 0.002 0.001 HIS C 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 2720) covalent geometry : angle 0.57224 / 0.33 ( 3650) SS BOND : bond 0.00634 / 0.44 ( 10) SS BOND : angle 0.58675 / 0.39 ( 20) hydrogen bonds : bond 0.07339 / 5.02 ( 26) hydrogen bonds : angle 9.76036 / 6.44 ( 78) *********************** 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 60 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.063 Fit side-chains REVERT: A 9 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.7860 (ttm-80) REVERT: B 9 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.7862 (ttm-80) REVERT: C 9 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.8033 (mtm-85) REVERT: C 14 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8052 (mtpm) REVERT: D 9 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.8077 (mtm-85) REVERT: D 14 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7844 (mtmm) REVERT: E 9 ARG cc_start: 0.8254 (mtm-85) cc_final: 0.7480 (mtm-85) REVERT: E 14 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8063 (mtpp) REVERT: F 9 ARG cc_start: 0.8206 (mtm-85) cc_final: 0.7471 (mtm-85) REVERT: F 14 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7996 (mtpp) REVERT: G 9 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.7586 (mtm-85) REVERT: G 14 LYS cc_start: 0.8010 (mttm) cc_final: 0.7592 (mtmt) REVERT: G 25 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6569 (tt) REVERT: H 9 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.7588 (mtm-85) REVERT: H 12 GLU cc_start: 0.8227 (tt0) cc_final: 0.7810 (tt0) REVERT: H 14 LYS cc_start: 0.7998 (mttm) cc_final: 0.7543 (mtmt) REVERT: H 23 PHE cc_start: 0.8086 (p90) cc_final: 0.7848 (p90) REVERT: H 25 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6550 (tt) REVERT: I 9 ARG cc_start: 0.8457 (mtm-85) cc_final: 0.7490 (mmt-90) REVERT: I 14 LYS cc_start: 0.8132 (mttm) cc_final: 0.7615 (mtmt) REVERT: I 18 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7351 (mp0) REVERT: I 23 PHE cc_start: 0.7642 (p90) cc_final: 0.3746 (t80) REVERT: I 28 ASN cc_start: 0.8824 (t0) cc_final: 0.8288 (t0) REVERT: I 32 LYS cc_start: 0.8432 (mptp) cc_final: 0.6230 (pttm) REVERT: J 9 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.7521 (mmt-90) REVERT: J 14 LYS cc_start: 0.8149 (mttm) cc_final: 0.7632 (mtmt) REVERT: J 18 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7367 (mp0) REVERT: J 23 PHE cc_start: 0.7622 (p90) cc_final: 0.3678 (t80) REVERT: J 28 ASN cc_start: 0.8829 (t0) cc_final: 0.8101 (t0) REVERT: J 32 LYS cc_start: 0.8434 (mptp) cc_final: 0.6227 (pttm) outliers start: 14 outliers final: 4 residues processed: 55 average time/residue: 0.4332 time to fit residues: 24.2977 Evaluate side-chains 57 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain J residue 22 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.0370 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 0.0170 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN B 4 ASN ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.187265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.170519 restraints weight = 3048.058| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 2.13 r_work: 0.4338 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4228 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2730 Z= 0.104 Angle : 0.524 6.039 3670 Z= 0.305 Chirality : 0.043 0.120 390 Planarity : 0.002 0.017 480 Dihedral : 7.931 47.137 330 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.48 % Allowed : 21.38 % Favored : 74.14 % 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: -3.64 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 9 PHE 0.040 0.002 PHE F 23 HIS 0.001 0.000 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 2720) covalent geometry : angle 0.52409 / 0.30 ( 3650) SS BOND : bond 0.00448 / 0.33 ( 10) SS BOND : angle 0.45795 / 0.31 ( 20) hydrogen bonds : bond 0.06719 / 4.60 ( 26) hydrogen bonds : angle 9.42864 / 6.24 ( 78) *********************** 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 63 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.8524 (mtm-85) cc_final: 0.7948 (ttm-80) REVERT: A 30 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7694 (mt0) REVERT: B 9 ARG cc_start: 0.8510 (mtm-85) cc_final: 0.7938 (ttm-80) REVERT: C 9 ARG cc_start: 0.8424 (mtm-85) cc_final: 0.8073 (mtm-85) REVERT: C 14 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8045 (mtpm) REVERT: D 9 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.8148 (mtm-85) REVERT: D 14 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7861 (mtmm) REVERT: E 9 ARG cc_start: 0.8238 (mtm-85) cc_final: 0.7483 (mtm-85) REVERT: E 14 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8053 (mtpp) REVERT: F 9 ARG cc_start: 0.8217 (mtm-85) cc_final: 0.7547 (mtm-85) REVERT: F 14 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8060 (mtpp) REVERT: G 9 ARG cc_start: 0.8326 (mtm-85) cc_final: 0.7616 (mtm-85) REVERT: G 12 GLU cc_start: 0.8393 (tt0) cc_final: 0.8089 (tt0) REVERT: G 14 LYS cc_start: 0.8016 (mttm) cc_final: 0.7597 (mtmt) REVERT: G 25 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6651 (tt) REVERT: H 9 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.7655 (mtm-85) REVERT: H 12 GLU cc_start: 0.8250 (tt0) cc_final: 0.7766 (tt0) REVERT: H 14 LYS cc_start: 0.8019 (mttm) cc_final: 0.7585 (mtmt) REVERT: H 25 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6694 (tt) REVERT: H 30 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7742 (mt0) REVERT: I 9 ARG cc_start: 0.8465 (mtm-85) cc_final: 0.7507 (mmt-90) REVERT: I 18 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7405 (mp0) REVERT: I 23 PHE cc_start: 0.7481 (p90) cc_final: 0.3616 (t80) REVERT: J 9 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.7539 (mmt-90) REVERT: J 18 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7397 (mp0) REVERT: J 23 PHE cc_start: 0.7402 (p90) cc_final: 0.3427 (t80) outliers start: 13 outliers final: 3 residues processed: 57 average time/residue: 0.4546 time to fit residues: 26.4046 Evaluate side-chains 54 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain J residue 22 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** 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 = 0.4584 r_free = 0.4584 target = 0.187445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.170069 restraints weight = 3085.582| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 2.15 r_work: 0.4322 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4211 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2730 Z= 0.128 Angle : 0.545 6.306 3670 Z= 0.316 Chirality : 0.044 0.115 390 Planarity : 0.002 0.014 480 Dihedral : 7.585 44.892 330 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.48 % Allowed : 22.07 % Favored : 73.45 % 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: -3.66 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 9 PHE 0.033 0.002 PHE G 23 HIS 0.001 0.000 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 2720) covalent geometry : angle 0.54609 / 0.32 ( 3650) SS BOND : bond 0.00578 / 0.41 ( 10) SS BOND : angle 0.37503 / 0.25 ( 20) hydrogen bonds : bond 0.07278 / 4.99 ( 26) hydrogen bonds : angle 9.60132 / 6.34 ( 78) *********************** 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 57 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.7984 (ttm-80) REVERT: A 30 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7685 (mt0) REVERT: B 9 ARG cc_start: 0.8534 (mtm-85) cc_final: 0.7998 (ttm-80) REVERT: B 30 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: C 14 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8092 (mtpm) REVERT: D 14 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7920 (mtmm) REVERT: E 9 ARG cc_start: 0.8217 (mtm-85) cc_final: 0.7524 (mtm-85) REVERT: E 14 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8039 (mtpp) REVERT: F 9 ARG cc_start: 0.8228 (mtm-85) cc_final: 0.7545 (mtm-85) REVERT: F 14 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8033 (mtpp) REVERT: G 9 ARG cc_start: 0.8320 (mtm-85) cc_final: 0.7647 (mtm-85) REVERT: G 12 GLU cc_start: 0.8365 (tt0) cc_final: 0.8075 (tt0) REVERT: G 14 LYS cc_start: 0.8055 (mttm) cc_final: 0.7642 (mtmt) REVERT: G 25 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6565 (tt) REVERT: H 9 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.7656 (mtm-85) REVERT: H 14 LYS cc_start: 0.8006 (mttm) cc_final: 0.7600 (mtmt) REVERT: H 23 PHE cc_start: 0.8037 (p90) cc_final: 0.7782 (p90) REVERT: H 25 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6527 (tt) REVERT: H 30 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7793 (mt0) REVERT: I 9 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.7531 (mmt-90) REVERT: I 18 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7452 (mp0) REVERT: J 9 ARG cc_start: 0.8455 (mtm-85) cc_final: 0.7557 (mmt-90) REVERT: J 18 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7444 (mp0) REVERT: J 23 PHE cc_start: 0.7457 (p90) cc_final: 0.3490 (t80) outliers start: 13 outliers final: 3 residues processed: 53 average time/residue: 0.4821 time to fit residues: 26.0299 Evaluate side-chains 55 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain J residue 22 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** 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 = 0.4538 r_free = 0.4538 target = 0.181007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.163692 restraints weight = 3188.244| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 2.23 r_work: 0.4268 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4155 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2730 Z= 0.178 Angle : 0.576 6.040 3670 Z= 0.329 Chirality : 0.046 0.112 390 Planarity : 0.002 0.018 480 Dihedral : 7.304 38.958 330 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.17 % Allowed : 20.69 % Favored : 74.14 % 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: -3.55 (0.37), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 9 PHE 0.024 0.002 PHE F 23 HIS 0.002 0.001 HIS D 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 2720) covalent geometry : angle 0.57681 / 0.33 ( 3650) SS BOND : bond 0.00793 / 0.55 ( 10) SS BOND : angle 0.34919 / 0.23 ( 20) hydrogen bonds : bond 0.07228 / 4.93 ( 26) hydrogen bonds : angle 9.81200 / 6.48 ( 78) *********************** 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 60 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.7936 (ttm-80) REVERT: A 30 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7657 (mt0) REVERT: B 3 SER cc_start: 0.8335 (m) cc_final: 0.8084 (p) REVERT: B 9 ARG cc_start: 0.8552 (mtm-85) cc_final: 0.7977 (ttm-80) REVERT: B 30 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7721 (mt0) REVERT: C 14 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8050 (mtpm) REVERT: D 14 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7879 (mtmm) REVERT: E 9 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7538 (mtm-85) REVERT: E 14 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8060 (mtpp) REVERT: E 30 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7675 (mt0) REVERT: F 9 ARG cc_start: 0.8211 (mtm-85) cc_final: 0.7546 (mtm-85) REVERT: F 14 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8045 (mtpp) REVERT: G 9 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.7628 (mtm-85) REVERT: G 12 GLU cc_start: 0.8391 (tt0) cc_final: 0.8111 (tt0) REVERT: G 14 LYS cc_start: 0.8014 (mttm) cc_final: 0.7592 (mtmt) REVERT: G 25 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6625 (tt) REVERT: H 9 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.7670 (mtm-85) REVERT: H 14 LYS cc_start: 0.8005 (mttm) cc_final: 0.7590 (mtmt) REVERT: H 25 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6650 (tt) REVERT: H 30 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: I 9 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.7531 (mmt-90) REVERT: I 18 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7470 (mp0) REVERT: I 28 ASN cc_start: 0.8952 (t0) cc_final: 0.8597 (t0) REVERT: J 9 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.7556 (mmt-90) REVERT: J 18 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7484 (mp0) outliers start: 15 outliers final: 2 residues processed: 54 average time/residue: 0.4805 time to fit residues: 26.4278 Evaluate side-chains 57 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain J residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** 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 = 0.4556 r_free = 0.4556 target = 0.182678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.164888 restraints weight = 3123.266| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 2.23 r_work: 0.4280 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4168 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2730 Z= 0.180 Angle : 0.600 6.830 3670 Z= 0.341 Chirality : 0.046 0.113 390 Planarity : 0.003 0.019 480 Dihedral : 7.203 36.611 330 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.79 % Allowed : 22.07 % Favored : 74.14 % 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: -3.58 (0.37), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 9 PHE 0.036 0.002 PHE G 23 HIS 0.002 0.001 HIS D 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 2720) covalent geometry : angle 0.60086 / 0.34 ( 3650) SS BOND : bond 0.00754 / 0.52 ( 10) SS BOND : angle 0.32394 / 0.22 ( 20) hydrogen bonds : bond 0.07873 / 5.40 ( 26) hydrogen bonds : angle 9.99466 / 6.59 ( 78) ********************** 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 57 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8007 (ttm-80) REVERT: A 30 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7672 (mt0) REVERT: B 3 SER cc_start: 0.8329 (m) cc_final: 0.8083 (p) REVERT: B 9 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8010 (ttm-80) REVERT: B 30 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7721 (mt0) REVERT: C 14 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8080 (mtpm) REVERT: D 14 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7905 (mtmm) REVERT: E 9 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7564 (mtm-85) REVERT: E 14 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8069 (mtpp) REVERT: F 9 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7576 (mtm-85) REVERT: F 14 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8071 (mtpp) REVERT: G 9 ARG cc_start: 0.8312 (mtm-85) cc_final: 0.7666 (mtm-85) REVERT: G 12 GLU cc_start: 0.8414 (tt0) cc_final: 0.8143 (tt0) REVERT: G 14 LYS cc_start: 0.8042 (mttm) cc_final: 0.7623 (mtmt) REVERT: G 25 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6629 (tt) REVERT: H 9 ARG cc_start: 0.8315 (mtm-85) cc_final: 0.7681 (mtm-85) REVERT: H 14 LYS cc_start: 0.8019 (mttm) cc_final: 0.7599 (mtmt) REVERT: H 23 PHE cc_start: 0.8193 (p90) cc_final: 0.7981 (p90) REVERT: H 25 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6649 (tt) REVERT: H 30 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7744 (mt0) REVERT: I 9 ARG cc_start: 0.8495 (mtm-85) cc_final: 0.7556 (mmt-90) REVERT: I 18 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7526 (mp0) REVERT: I 23 PHE cc_start: 0.7666 (p90) cc_final: 0.3847 (t80) REVERT: I 28 ASN cc_start: 0.8978 (t0) cc_final: 0.8608 (t0) REVERT: J 9 ARG cc_start: 0.8513 (mtm-85) cc_final: 0.7582 (mmt-90) REVERT: J 18 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7533 (mp0) REVERT: J 23 PHE cc_start: 0.7690 (p90) cc_final: 0.3841 (t80) outliers start: 11 outliers final: 2 residues processed: 53 average time/residue: 0.4383 time to fit residues: 23.7163 Evaluate side-chains 55 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain J residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.0000 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** 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 = 0.4580 r_free = 0.4580 target = 0.185001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.167753 restraints weight = 3108.762| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 2.19 r_work: 0.4314 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4201 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2730 Z= 0.142 Angle : 0.549 6.214 3670 Z= 0.316 Chirality : 0.044 0.115 390 Planarity : 0.002 0.012 480 Dihedral : 7.013 36.750 330 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.17 % Allowed : 19.31 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.37), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.29), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 9 PHE 0.026 0.002 PHE F 23 HIS 0.002 0.001 HIS D 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 2720) covalent geometry : angle 0.54943 / 0.32 ( 3650) SS BOND : bond 0.00625 / 0.44 ( 10) SS BOND : angle 0.34538 / 0.22 ( 20) hydrogen bonds : bond 0.07165 / 4.88 ( 26) hydrogen bonds : angle 9.72124 / 6.43 ( 78) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 981.24 seconds wall clock time: 17 minutes 31.03 seconds (1051.03 seconds total)