Starting phenix.real_space_refine on Tue Mar 3 12:59:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ytq_73489/03_2026/9ytq_73489.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ytq_73489/03_2026/9ytq_73489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ytq_73489/03_2026/9ytq_73489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ytq_73489/03_2026/9ytq_73489.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ytq_73489/03_2026/9ytq_73489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ytq_73489/03_2026/9ytq_73489.map" } resolution = 4.34 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= 0.001 sd= 0.031 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 8 5.16 5 C 3016 2.51 5 N 740 2.21 5 O 832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4596 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1149 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 136} Chain: "B" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1149 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 136} Chain: "C" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1149 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 136} Chain: "D" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1149 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 136} Time building chain proxies: 1.16, per 1000 atoms: 0.25 Number of scatterers: 4596 At special positions: 0 Unit cell: (63.64, 106.64, 101.48, 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 8 16.00 O 832 8.00 N 740 7.00 C 3016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 290.4 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1072 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 95.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 2 through 25 removed outlier: 3.741A pdb=" N ALA A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 48 removed outlier: 3.562A pdb=" N GLU A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 93 through 110 Processing helix chain 'A' and resid 111 through 138 Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 28 through 48 removed outlier: 3.510A pdb=" N GLU B 48 " --> pdb=" O ASN B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 65 Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 76 through 91 Processing helix chain 'B' and resid 93 through 110 Processing helix chain 'B' and resid 111 through 138 Processing helix chain 'C' and resid 2 through 25 removed outlier: 4.016A pdb=" N ALA C 25 " --> pdb=" O LEU C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 50 removed outlier: 3.692A pdb=" N GLU C 48 " --> pdb=" O ASN C 44 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.508A pdb=" N TYR C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 91 Processing helix chain 'C' and resid 93 through 110 Processing helix chain 'C' and resid 111 through 138 Processing helix chain 'D' and resid 2 through 25 Processing helix chain 'D' and resid 28 through 50 removed outlier: 3.587A pdb=" N GLU D 48 " --> pdb=" O ASN D 44 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 76 through 91 Processing helix chain 'D' and resid 92 through 110 removed outlier: 3.734A pdb=" N ALA D 96 " --> pdb=" O ASP D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 138 403 hydrogen bonds defined for protein. 1209 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: 0.87 Time building geometry restraints manager: 0.52 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: 1406 1.34 - 1.46: 746 1.46 - 1.57: 2536 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 4704 Sorted by residual: bond pdb=" CG MET B 84 " pdb=" SD MET B 84 " ideal model delta sigma weight residual 1.803 1.760 0.043 2.50e-02 1.60e+03 2.99e+00 bond pdb=" CG GLU D 8 " pdb=" CD GLU D 8 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.60e+00 bond pdb=" CB TRP B 80 " pdb=" CG TRP B 80 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.04e+00 bond pdb=" CD GLU A 8 " pdb=" OE1 GLU A 8 " ideal model delta sigma weight residual 1.249 1.222 0.027 1.90e-02 2.77e+03 1.97e+00 bond pdb=" CG MET D 84 " pdb=" SD MET D 84 " ideal model delta sigma weight residual 1.803 1.769 0.034 2.50e-02 1.60e+03 1.88e+00 ... (remaining 4699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 6189 2.80 - 5.59: 102 5.59 - 8.39: 14 8.39 - 11.19: 0 11.19 - 13.98: 3 Bond angle restraints: 6308 Sorted by residual: angle pdb=" N GLU A 8 " pdb=" CA GLU A 8 " pdb=" CB GLU A 8 " ideal model delta sigma weight residual 110.28 117.29 -7.01 1.55e+00 4.16e-01 2.05e+01 angle pdb=" N GLU D 8 " pdb=" CA GLU D 8 " pdb=" CB GLU D 8 " ideal model delta sigma weight residual 110.28 116.72 -6.44 1.55e+00 4.16e-01 1.72e+01 angle pdb=" CA LEU B 16 " pdb=" CB LEU B 16 " pdb=" CG LEU B 16 " ideal model delta sigma weight residual 116.30 130.28 -13.98 3.50e+00 8.16e-02 1.60e+01 angle pdb=" N MET B 84 " pdb=" CA MET B 84 " pdb=" CB MET B 84 " ideal model delta sigma weight residual 110.12 115.79 -5.67 1.47e+00 4.63e-01 1.49e+01 angle pdb=" N GLU D 98 " pdb=" CA GLU D 98 " pdb=" CB GLU D 98 " ideal model delta sigma weight residual 110.28 115.75 -5.47 1.55e+00 4.16e-01 1.24e+01 ... (remaining 6303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.54: 2390 14.54 - 29.09: 329 29.09 - 43.63: 91 43.63 - 58.17: 6 58.17 - 72.71: 4 Dihedral angle restraints: 2820 sinusoidal: 1168 harmonic: 1652 Sorted by residual: dihedral pdb=" CA ASP C 92 " pdb=" C ASP C 92 " pdb=" N LYS C 93 " pdb=" CA LYS C 93 " ideal model delta harmonic sigma weight residual 180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ASP D 92 " pdb=" C ASP D 92 " pdb=" N LYS D 93 " pdb=" CA LYS D 93 " ideal model delta harmonic sigma weight residual -180.00 -159.77 -20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LYS D 75 " pdb=" C LYS D 75 " pdb=" N ASP D 76 " pdb=" CA ASP D 76 " ideal model delta harmonic sigma weight residual 180.00 161.42 18.58 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 2817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 548 0.059 - 0.117: 96 0.117 - 0.176: 18 0.176 - 0.235: 1 0.235 - 0.293: 1 Chirality restraints: 664 Sorted by residual: chirality pdb=" CG LEU B 16 " pdb=" CB LEU B 16 " pdb=" CD1 LEU B 16 " pdb=" CD2 LEU B 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA HIS C 104 " pdb=" N HIS C 104 " pdb=" C HIS C 104 " pdb=" CB HIS C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CA HIS B 104 " pdb=" N HIS B 104 " pdb=" C HIS B 104 " pdb=" CB HIS B 104 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 661 not shown) Planarity restraints: 784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 80 " -0.019 2.00e-02 2.50e+03 2.71e-02 1.84e+01 pdb=" CG TRP B 80 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP B 80 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP B 80 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 80 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 80 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 80 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 80 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 80 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 80 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 39 " 0.013 2.00e-02 2.50e+03 1.82e-02 8.28e+00 pdb=" CG TRP B 39 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 39 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 39 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 39 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 39 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 39 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 39 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 39 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 39 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 80 " -0.016 2.00e-02 2.50e+03 1.54e-02 5.90e+00 pdb=" CG TRP C 80 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 80 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 80 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 80 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 80 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 80 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 80 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 80 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 80 " 0.000 2.00e-02 2.50e+03 ... (remaining 781 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1383 2.83 - 3.35: 5037 3.35 - 3.86: 8022 3.86 - 4.38: 8697 4.38 - 4.90: 14176 Nonbonded interactions: 37315 Sorted by model distance: nonbonded pdb=" O ASP A 4 " pdb=" OE1 GLU A 8 " model vdw 2.312 3.040 nonbonded pdb=" O ASP D 4 " pdb=" OE1 GLU D 8 " model vdw 2.349 3.040 nonbonded pdb=" O LYS D 82 " pdb=" OE1 GLU D 86 " model vdw 2.353 3.040 nonbonded pdb=" O ASP B 94 " pdb=" OE1 GLU B 98 " model vdw 2.376 3.040 nonbonded pdb=" O LYS B 120 " pdb=" OE1 GLU B 124 " model vdw 2.394 3.040 ... (remaining 37310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.150 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.620 Find NCS groups from input model: 0.070 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 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 : 0.004 0.044 4704 Z= 0.199 Angle : 0.879 13.983 6308 Z= 0.490 Chirality : 0.047 0.293 664 Planarity : 0.004 0.027 784 Dihedral : 14.117 72.712 1748 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 0.30 (0.36), residues: 544 helix: 0.56 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -3.82 (1.21), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 108 TYR 0.019 0.002 TYR A 69 PHE 0.030 0.002 PHE D 58 TRP 0.070 0.008 TRP B 80 HIS 0.019 0.003 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 4704) covalent geometry : angle 0.87922 ( 6308) hydrogen bonds : bond 0.08211 ( 403) hydrogen bonds : angle 5.29292 ( 1209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8925 (m-70) cc_final: 0.8612 (t70) REVERT: A 55 LYS cc_start: 0.8814 (pttt) cc_final: 0.8438 (mmtt) REVERT: A 104 HIS cc_start: 0.8756 (m-70) cc_final: 0.8094 (m90) REVERT: B 12 LEU cc_start: 0.9228 (tp) cc_final: 0.9027 (tp) REVERT: B 14 LEU cc_start: 0.8941 (mt) cc_final: 0.8550 (mt) REVERT: B 41 LYS cc_start: 0.9358 (tttt) cc_final: 0.8987 (mttt) REVERT: B 84 MET cc_start: 0.8999 (mpp) cc_final: 0.8474 (mpp) REVERT: C 11 LYS cc_start: 0.8055 (tptt) cc_final: 0.7693 (mttp) REVERT: C 37 LYS cc_start: 0.9125 (mmtm) cc_final: 0.8724 (mmtt) REVERT: C 58 PHE cc_start: 0.9015 (t80) cc_final: 0.8753 (t80) REVERT: C 59 TYR cc_start: 0.8914 (t80) cc_final: 0.8679 (t80) REVERT: C 88 PHE cc_start: 0.6027 (t80) cc_final: 0.5694 (t80) REVERT: D 40 HIS cc_start: 0.9163 (t-90) cc_final: 0.8747 (t70) REVERT: D 43 LEU cc_start: 0.9624 (tp) cc_final: 0.9281 (pp) REVERT: D 47 TYR cc_start: 0.8780 (t80) cc_final: 0.8467 (t80) REVERT: D 69 TYR cc_start: 0.9063 (m-80) cc_final: 0.8465 (m-80) REVERT: D 84 MET cc_start: 0.7248 (mpp) cc_final: 0.6629 (mpp) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.0892 time to fit residues: 18.6055 Evaluate side-chains 113 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 HIS B 104 HIS ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 HIS ** 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 = 0.4681 r_free = 0.4681 target = 0.150050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.121222 restraints weight = 20217.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.123733 restraints weight = 15777.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.125690 restraints weight = 13004.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.127036 restraints weight = 11129.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.128271 restraints weight = 9895.319| |-----------------------------------------------------------------------------| r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4704 Z= 0.164 Angle : 0.719 9.473 6308 Z= 0.383 Chirality : 0.040 0.147 664 Planarity : 0.003 0.020 784 Dihedral : 4.771 19.795 592 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.27 % Allowed : 6.99 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.36), residues: 544 helix: 0.89 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -3.97 (1.20), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 108 TYR 0.021 0.001 TYR A 57 PHE 0.028 0.002 PHE D 58 TRP 0.053 0.006 TRP A 39 HIS 0.017 0.003 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4704) covalent geometry : angle 0.71897 ( 6308) hydrogen bonds : bond 0.04405 ( 403) hydrogen bonds : angle 4.34959 ( 1209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.9120 (m-70) cc_final: 0.8806 (t70) REVERT: A 55 LYS cc_start: 0.8821 (pttt) cc_final: 0.8188 (mmmt) REVERT: A 93 LYS cc_start: 0.7662 (mttp) cc_final: 0.7436 (mmtm) REVERT: A 104 HIS cc_start: 0.8787 (m-70) cc_final: 0.8094 (m90) REVERT: B 14 LEU cc_start: 0.8474 (mt) cc_final: 0.7781 (mt) REVERT: B 15 ILE cc_start: 0.8321 (mm) cc_final: 0.8087 (mm) REVERT: B 86 GLU cc_start: 0.9497 (OUTLIER) cc_final: 0.9013 (pm20) REVERT: B 104 HIS cc_start: 0.7216 (m90) cc_final: 0.6932 (m90) REVERT: C 11 LYS cc_start: 0.8100 (tptt) cc_final: 0.7705 (mttp) REVERT: C 37 LYS cc_start: 0.9331 (mmtm) cc_final: 0.8998 (mmtt) REVERT: D 80 TRP cc_start: 0.8301 (t-100) cc_final: 0.7896 (t-100) outliers start: 6 outliers final: 0 residues processed: 140 average time/residue: 0.0803 time to fit residues: 14.1339 Evaluate side-chains 99 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 45 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 HIS ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.146737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.118961 restraints weight = 20733.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.121718 restraints weight = 15683.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.123715 restraints weight = 12599.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.125291 restraints weight = 10593.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.126465 restraints weight = 9220.264| |-----------------------------------------------------------------------------| r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 4704 Z= 0.171 Angle : 0.719 8.989 6308 Z= 0.388 Chirality : 0.040 0.158 664 Planarity : 0.004 0.055 784 Dihedral : 4.816 19.569 592 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.06 % Allowed : 6.99 % Favored : 91.95 % 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: 0.98 (0.36), residues: 544 helix: 1.02 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -3.88 (1.22), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 123 TYR 0.045 0.002 TYR B 69 PHE 0.051 0.003 PHE B 115 TRP 0.032 0.003 TRP A 39 HIS 0.015 0.002 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4704) covalent geometry : angle 0.71939 ( 6308) hydrogen bonds : bond 0.04253 ( 403) hydrogen bonds : angle 4.27136 ( 1209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TRP cc_start: 0.7626 (m-10) cc_final: 0.7207 (m-90) REVERT: A 40 HIS cc_start: 0.9090 (m-70) cc_final: 0.8799 (t-90) REVERT: A 55 LYS cc_start: 0.8812 (pttt) cc_final: 0.8149 (mmmt) REVERT: A 62 HIS cc_start: 0.8768 (m170) cc_final: 0.8496 (m170) REVERT: A 104 HIS cc_start: 0.8698 (m-70) cc_final: 0.7944 (m90) REVERT: B 14 LEU cc_start: 0.7995 (mt) cc_final: 0.7560 (mt) REVERT: B 41 LYS cc_start: 0.9130 (mtmm) cc_final: 0.8836 (ptpt) REVERT: B 81 HIS cc_start: 0.8411 (m-70) cc_final: 0.7771 (m-70) REVERT: C 11 LYS cc_start: 0.7988 (tptt) cc_final: 0.7500 (mmtt) REVERT: C 37 LYS cc_start: 0.9320 (mmtm) cc_final: 0.8582 (mmmt) REVERT: C 47 TYR cc_start: 0.8790 (t80) cc_final: 0.8289 (t80) REVERT: D 48 GLU cc_start: 0.8789 (mp0) cc_final: 0.8504 (mp0) outliers start: 5 outliers final: 2 residues processed: 132 average time/residue: 0.0737 time to fit residues: 12.4474 Evaluate side-chains 99 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.144073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.113695 restraints weight = 20153.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.116436 restraints weight = 15122.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.118570 restraints weight = 12137.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.120185 restraints weight = 10134.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.121245 restraints weight = 8808.393| |-----------------------------------------------------------------------------| r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4704 Z= 0.191 Angle : 0.720 8.134 6308 Z= 0.394 Chirality : 0.040 0.176 664 Planarity : 0.003 0.023 784 Dihedral : 4.842 19.569 592 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.21 % Allowed : 4.87 % Favored : 94.92 % 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: 0.94 (0.36), residues: 544 helix: 1.00 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -3.97 (1.16), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 123 TYR 0.025 0.002 TYR B 69 PHE 0.024 0.002 PHE D 58 TRP 0.025 0.004 TRP D 80 HIS 0.014 0.002 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 4704) covalent geometry : angle 0.71957 ( 6308) hydrogen bonds : bond 0.04174 ( 403) hydrogen bonds : angle 4.39641 ( 1209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8577 (m-80) cc_final: 0.8199 (m-80) REVERT: A 62 HIS cc_start: 0.8816 (m170) cc_final: 0.8519 (m170) REVERT: A 104 HIS cc_start: 0.8737 (m-70) cc_final: 0.7973 (m90) REVERT: B 14 LEU cc_start: 0.8190 (mt) cc_final: 0.7780 (mt) REVERT: B 41 LYS cc_start: 0.9178 (mtmm) cc_final: 0.8921 (mttt) REVERT: C 37 LYS cc_start: 0.9207 (mmtm) cc_final: 0.8687 (mmmt) REVERT: C 41 LYS cc_start: 0.9261 (mppt) cc_final: 0.9031 (mmtt) REVERT: D 12 LEU cc_start: 0.9226 (tp) cc_final: 0.8880 (pp) REVERT: D 69 TYR cc_start: 0.8850 (m-80) cc_final: 0.8185 (m-80) REVERT: D 80 TRP cc_start: 0.8408 (t-100) cc_final: 0.7950 (t-100) REVERT: D 127 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8256 (mt-10) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.0692 time to fit residues: 12.0791 Evaluate side-chains 101 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 40 HIS A 44 ASN ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 HIS ** 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 = 0.4632 r_free = 0.4632 target = 0.143183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.114331 restraints weight = 20118.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.116985 restraints weight = 15169.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.118981 restraints weight = 12207.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.120558 restraints weight = 10301.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.121851 restraints weight = 8963.961| |-----------------------------------------------------------------------------| r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4704 Z= 0.164 Angle : 0.712 9.152 6308 Z= 0.382 Chirality : 0.041 0.249 664 Planarity : 0.003 0.019 784 Dihedral : 4.893 18.607 592 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.21 % Allowed : 4.87 % Favored : 94.92 % 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: 1.05 (0.36), residues: 544 helix: 1.07 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -4.04 (1.12), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 108 TYR 0.043 0.002 TYR C 69 PHE 0.024 0.002 PHE D 58 TRP 0.021 0.003 TRP B 80 HIS 0.012 0.002 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 4704) covalent geometry : angle 0.71244 ( 6308) hydrogen bonds : bond 0.04121 ( 403) hydrogen bonds : angle 4.35168 ( 1209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8646 (m-80) cc_final: 0.7922 (m-80) REVERT: A 36 HIS cc_start: 0.8912 (t-90) cc_final: 0.8573 (t-170) REVERT: A 55 LYS cc_start: 0.8874 (pttt) cc_final: 0.8565 (pptt) REVERT: A 62 HIS cc_start: 0.8758 (m170) cc_final: 0.8479 (m170) REVERT: A 93 LYS cc_start: 0.7148 (mmtm) cc_final: 0.6778 (tmtt) REVERT: A 104 HIS cc_start: 0.8733 (m-70) cc_final: 0.8093 (m-70) REVERT: B 41 LYS cc_start: 0.9207 (mtmm) cc_final: 0.8905 (mttt) REVERT: B 104 HIS cc_start: 0.7863 (m90) cc_final: 0.7636 (m90) REVERT: C 37 LYS cc_start: 0.9223 (mmtm) cc_final: 0.8933 (mmtt) REVERT: C 47 TYR cc_start: 0.8840 (t80) cc_final: 0.8261 (t80) REVERT: C 62 HIS cc_start: 0.8998 (m-70) cc_final: 0.8460 (p-80) REVERT: C 75 LYS cc_start: 0.8304 (mtmt) cc_final: 0.8024 (tptp) REVERT: C 88 PHE cc_start: 0.5455 (t80) cc_final: 0.5188 (t80) REVERT: D 12 LEU cc_start: 0.9267 (tp) cc_final: 0.8785 (pp) REVERT: D 48 GLU cc_start: 0.8901 (mp0) cc_final: 0.8699 (mp0) REVERT: D 69 TYR cc_start: 0.8956 (m-80) cc_final: 0.8344 (m-80) REVERT: D 80 TRP cc_start: 0.8599 (t-100) cc_final: 0.8372 (t-100) REVERT: D 127 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8227 (mt-10) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.0622 time to fit residues: 10.5542 Evaluate side-chains 104 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN C 26 ASN C 101 ASN ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.141603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.115298 restraints weight = 20078.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.117982 restraints weight = 14930.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.120008 restraints weight = 11921.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.121255 restraints weight = 10071.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.122416 restraints weight = 8991.955| |-----------------------------------------------------------------------------| r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4704 Z= 0.159 Angle : 0.726 8.480 6308 Z= 0.385 Chirality : 0.039 0.134 664 Planarity : 0.003 0.019 784 Dihedral : 4.881 20.024 592 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.42 % Allowed : 2.97 % Favored : 96.61 % 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: 0.95 (0.36), residues: 544 helix: 1.00 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -4.05 (1.08), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 108 TYR 0.025 0.002 TYR C 69 PHE 0.031 0.002 PHE D 18 TRP 0.022 0.003 TRP C 39 HIS 0.009 0.002 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 4704) covalent geometry : angle 0.72582 ( 6308) hydrogen bonds : bond 0.03965 ( 403) hydrogen bonds : angle 4.44514 ( 1209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8543 (mt) cc_final: 0.8177 (mm) REVERT: A 18 PHE cc_start: 0.8777 (m-80) cc_final: 0.8378 (m-80) REVERT: A 55 LYS cc_start: 0.8982 (pttt) cc_final: 0.8310 (mmtt) REVERT: A 62 HIS cc_start: 0.8584 (m170) cc_final: 0.8314 (m170) REVERT: A 104 HIS cc_start: 0.8516 (m-70) cc_final: 0.7869 (m-70) REVERT: B 14 LEU cc_start: 0.8495 (mt) cc_final: 0.8293 (mt) REVERT: B 41 LYS cc_start: 0.9272 (mtmm) cc_final: 0.8932 (mttt) REVERT: B 61 MET cc_start: 0.7538 (mmp) cc_final: 0.7011 (mmm) REVERT: B 69 TYR cc_start: 0.8702 (m-10) cc_final: 0.8306 (m-80) REVERT: C 37 LYS cc_start: 0.9144 (mmtm) cc_final: 0.8852 (mmtt) REVERT: C 47 TYR cc_start: 0.8683 (t80) cc_final: 0.8074 (t80) REVERT: C 75 LYS cc_start: 0.8462 (mtmt) cc_final: 0.8209 (tptp) REVERT: D 69 TYR cc_start: 0.8936 (m-80) cc_final: 0.8399 (m-80) REVERT: D 127 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8240 (mt-10) outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.0625 time to fit residues: 10.6450 Evaluate side-chains 105 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS C 17 ASN C 100 HIS C 101 ASN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.140740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.112805 restraints weight = 21271.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.115314 restraints weight = 16064.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.116894 restraints weight = 12984.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.118413 restraints weight = 11199.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.119568 restraints weight = 9762.412| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4704 Z= 0.166 Angle : 0.747 10.061 6308 Z= 0.398 Chirality : 0.041 0.176 664 Planarity : 0.003 0.027 784 Dihedral : 4.846 19.679 592 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % 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: 0.90 (0.36), residues: 544 helix: 0.98 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -4.18 (1.05), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 123 TYR 0.021 0.002 TYR D 60 PHE 0.026 0.002 PHE D 18 TRP 0.031 0.004 TRP D 80 HIS 0.009 0.002 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4704) covalent geometry : angle 0.74666 ( 6308) hydrogen bonds : bond 0.04209 ( 403) hydrogen bonds : angle 4.46266 ( 1209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 HIS cc_start: 0.8723 (m170) cc_final: 0.8486 (m170) REVERT: A 104 HIS cc_start: 0.8542 (m-70) cc_final: 0.7848 (m-70) REVERT: B 41 LYS cc_start: 0.9104 (mtmm) cc_final: 0.8713 (mttt) REVERT: B 61 MET cc_start: 0.7745 (mmp) cc_final: 0.7100 (mmt) REVERT: C 47 TYR cc_start: 0.8404 (t80) cc_final: 0.7748 (t80) REVERT: C 119 LEU cc_start: 0.8842 (mt) cc_final: 0.8627 (mt) REVERT: D 69 TYR cc_start: 0.8725 (m-80) cc_final: 0.8320 (m-80) REVERT: D 127 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8244 (mt-10) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0634 time to fit residues: 10.8491 Evaluate side-chains 97 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 43 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 HIS C 17 ASN ** D 101 ASN ** 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 = 0.4596 r_free = 0.4596 target = 0.139952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.112705 restraints weight = 22065.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.115254 restraints weight = 16548.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.117039 restraints weight = 13298.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.118484 restraints weight = 11333.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.119666 restraints weight = 9871.824| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4704 Z= 0.164 Angle : 0.751 9.486 6308 Z= 0.405 Chirality : 0.042 0.156 664 Planarity : 0.004 0.061 784 Dihedral : 4.968 20.732 592 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: 0.86 (0.36), residues: 544 helix: 0.94 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -3.39 (1.02), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 108 TYR 0.035 0.002 TYR A 47 PHE 0.040 0.002 PHE D 18 TRP 0.033 0.004 TRP D 80 HIS 0.009 0.002 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 4704) covalent geometry : angle 0.75089 ( 6308) hydrogen bonds : bond 0.04102 ( 403) hydrogen bonds : angle 4.46673 ( 1209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.9189 (m-70) cc_final: 0.8591 (t-90) REVERT: A 44 ASN cc_start: 0.9081 (m-40) cc_final: 0.8718 (m-40) REVERT: A 55 LYS cc_start: 0.8836 (pttt) cc_final: 0.8592 (pptt) REVERT: A 104 HIS cc_start: 0.8558 (m-70) cc_final: 0.7974 (m-70) REVERT: B 41 LYS cc_start: 0.9215 (mtmm) cc_final: 0.8839 (mttt) REVERT: B 62 HIS cc_start: 0.8845 (m170) cc_final: 0.8134 (m90) REVERT: B 81 HIS cc_start: 0.8528 (m90) cc_final: 0.8153 (m90) REVERT: B 102 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8393 (mm-30) REVERT: C 47 TYR cc_start: 0.8748 (t80) cc_final: 0.8108 (t80) REVERT: D 69 TYR cc_start: 0.8891 (m-80) cc_final: 0.8463 (m-80) REVERT: D 84 MET cc_start: 0.7515 (mmt) cc_final: 0.6985 (mmm) REVERT: D 127 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8197 (mt-10) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0634 time to fit residues: 10.5477 Evaluate side-chains 100 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.139723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.111613 restraints weight = 21295.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.114052 restraints weight = 16192.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.115818 restraints weight = 13114.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.117264 restraints weight = 11112.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.118276 restraints weight = 9768.687| |-----------------------------------------------------------------------------| r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4704 Z= 0.161 Angle : 0.775 10.918 6308 Z= 0.416 Chirality : 0.042 0.214 664 Planarity : 0.003 0.039 784 Dihedral : 4.926 20.984 592 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: 0.81 (0.36), residues: 544 helix: 0.89 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -3.21 (1.05), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 108 TYR 0.037 0.002 TYR A 47 PHE 0.030 0.002 PHE D 18 TRP 0.019 0.003 TRP D 39 HIS 0.019 0.002 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4704) covalent geometry : angle 0.77468 ( 6308) hydrogen bonds : bond 0.04161 ( 403) hydrogen bonds : angle 4.58775 ( 1209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8833 (m-80) cc_final: 0.8175 (m-80) REVERT: A 39 TRP cc_start: 0.8053 (m-10) cc_final: 0.7508 (m-10) REVERT: A 40 HIS cc_start: 0.9124 (m-70) cc_final: 0.8613 (t70) REVERT: A 44 ASN cc_start: 0.9088 (m-40) cc_final: 0.8737 (m-40) REVERT: A 55 LYS cc_start: 0.8804 (pttt) cc_final: 0.8578 (pttp) REVERT: A 58 PHE cc_start: 0.8745 (t80) cc_final: 0.8080 (t80) REVERT: A 62 HIS cc_start: 0.9048 (m170) cc_final: 0.8805 (m170) REVERT: A 104 HIS cc_start: 0.8597 (m-70) cc_final: 0.8002 (m-70) REVERT: B 41 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8843 (mttt) REVERT: B 81 HIS cc_start: 0.8484 (m90) cc_final: 0.8214 (m90) REVERT: B 102 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8491 (mm-30) REVERT: C 41 LYS cc_start: 0.9363 (mppt) cc_final: 0.9148 (mmtt) REVERT: C 47 TYR cc_start: 0.8733 (t80) cc_final: 0.8234 (t80) REVERT: C 59 TYR cc_start: 0.9019 (t80) cc_final: 0.8753 (t80) REVERT: D 5 LYS cc_start: 0.9431 (ptpp) cc_final: 0.9230 (pttt) REVERT: D 15 ILE cc_start: 0.7783 (mm) cc_final: 0.7545 (mm) REVERT: D 69 TYR cc_start: 0.8907 (m-80) cc_final: 0.8330 (m-80) REVERT: D 84 MET cc_start: 0.8035 (mmt) cc_final: 0.7540 (mmm) REVERT: D 127 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8154 (mt-10) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0621 time to fit residues: 10.0937 Evaluate side-chains 98 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.139965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.112542 restraints weight = 21692.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.115110 restraints weight = 16345.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.116944 restraints weight = 13180.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.118436 restraints weight = 11165.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.119649 restraints weight = 9769.992| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.6595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4704 Z= 0.162 Angle : 0.787 10.578 6308 Z= 0.425 Chirality : 0.043 0.193 664 Planarity : 0.003 0.036 784 Dihedral : 4.935 22.032 592 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: 0.59 (0.35), residues: 544 helix: 0.76 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -3.31 (1.03), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 108 TYR 0.039 0.002 TYR A 47 PHE 0.051 0.002 PHE D 18 TRP 0.031 0.003 TRP D 80 HIS 0.017 0.002 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4704) covalent geometry : angle 0.78734 ( 6308) hydrogen bonds : bond 0.04140 ( 403) hydrogen bonds : angle 4.62723 ( 1209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8872 (m-80) cc_final: 0.8291 (m-80) REVERT: A 44 ASN cc_start: 0.8923 (m-40) cc_final: 0.8562 (m-40) REVERT: A 48 GLU cc_start: 0.9112 (tp30) cc_final: 0.8903 (tm-30) REVERT: A 55 LYS cc_start: 0.8821 (pttt) cc_final: 0.8562 (pttp) REVERT: A 58 PHE cc_start: 0.8475 (t80) cc_final: 0.8170 (t80) REVERT: A 62 HIS cc_start: 0.8977 (m170) cc_final: 0.8677 (m170) REVERT: A 104 HIS cc_start: 0.8594 (m-70) cc_final: 0.7937 (m-70) REVERT: B 41 LYS cc_start: 0.9227 (mtmm) cc_final: 0.8835 (mttt) REVERT: B 81 HIS cc_start: 0.8474 (m90) cc_final: 0.8235 (m90) REVERT: B 102 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8582 (mm-30) REVERT: B 104 HIS cc_start: 0.8881 (m-70) cc_final: 0.8449 (m170) REVERT: C 11 LYS cc_start: 0.8107 (tptt) cc_final: 0.7427 (mmtp) REVERT: C 44 ASN cc_start: 0.9520 (m-40) cc_final: 0.9217 (m110) REVERT: C 47 TYR cc_start: 0.8768 (t80) cc_final: 0.8301 (t80) REVERT: C 62 HIS cc_start: 0.8896 (m170) cc_final: 0.8571 (m170) REVERT: D 18 PHE cc_start: 0.7511 (m-80) cc_final: 0.7058 (m-80) REVERT: D 80 TRP cc_start: 0.8042 (t-100) cc_final: 0.7228 (t60) REVERT: D 84 MET cc_start: 0.7880 (mmt) cc_final: 0.7388 (mmm) REVERT: D 127 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8181 (mt-10) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0636 time to fit residues: 10.4446 Evaluate side-chains 99 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.135982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.110241 restraints weight = 20190.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.112557 restraints weight = 15328.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.114206 restraints weight = 12452.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.115434 restraints weight = 10643.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.116234 restraints weight = 9496.155| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.6892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4704 Z= 0.173 Angle : 0.856 19.846 6308 Z= 0.448 Chirality : 0.044 0.200 664 Planarity : 0.003 0.034 784 Dihedral : 4.970 21.363 592 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: 0.49 (0.35), residues: 544 helix: 0.69 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -3.48 (0.99), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 108 TYR 0.036 0.002 TYR A 47 PHE 0.035 0.002 PHE D 18 TRP 0.028 0.003 TRP D 80 HIS 0.018 0.002 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4704) covalent geometry : angle 0.85577 ( 6308) hydrogen bonds : bond 0.04258 ( 403) hydrogen bonds : angle 4.74811 ( 1209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1015.62 seconds wall clock time: 18 minutes 14.69 seconds (1094.69 seconds total)