Starting phenix.real_space_refine on Thu May 1 04:19:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bia_44585/05_2025/9bia_44585.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bia_44585/05_2025/9bia_44585.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bia_44585/05_2025/9bia_44585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bia_44585/05_2025/9bia_44585.map" model { file = "/net/cci-nas-00/data/ceres_data/9bia_44585/05_2025/9bia_44585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bia_44585/05_2025/9bia_44585.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 3371 2.51 5 N 841 2.21 5 O 941 1.98 5 H 5263 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10430 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1735 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "C" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1688 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "A" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1735 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "D" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1718 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1777 Classifications: {'peptide': 118} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "F" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1777 Classifications: {'peptide': 118} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Time building chain proxies: 5.50, per 1000 atoms: 0.53 Number of scatterers: 10430 At special positions: 0 Unit cell: (67.252, 67.983, 108.188, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 941 8.00 N 841 7.00 C 3371 6.00 H 5263 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 99 " distance=2.03 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: 2.75 Conformation dependent library (CDL) restraints added in 691.3 milliseconds 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1248 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 5 sheets defined 60.1% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'B' and resid 37 through 71 removed outlier: 3.756A pdb=" N GLN B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 76 through 104 Processing helix chain 'B' and resid 111 through 141 Processing helix chain 'C' and resid 37 through 71 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 76 through 104 Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 111 through 139 Processing helix chain 'A' and resid 37 through 69 Processing helix chain 'A' and resid 70 through 74 removed outlier: 4.372A pdb=" N ASP A 73 " --> pdb=" O GLN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 102 Processing helix chain 'A' and resid 111 through 141 Processing helix chain 'D' and resid 37 through 71 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 76 through 104 Processing helix chain 'D' and resid 111 through 141 removed outlier: 3.524A pdb=" N PHE D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'F' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.432A pdb=" N GLY E 10 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG E 41 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU E 50 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.432A pdb=" N GLY E 10 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'F' and resid 61 through 63 removed outlier: 5.042A pdb=" N GLY F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA F 43 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARG F 53 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL F 37 " --> pdb=" O ARG F 53 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1164 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: 3.72 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5263 1.03 - 1.22: 0 1.22 - 1.42: 2210 1.42 - 1.61: 3031 1.61 - 1.80: 24 Bond restraints: 10528 Sorted by residual: bond pdb=" CB GLN A 91 " pdb=" CG GLN A 91 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.64e-01 bond pdb=" CB MET B 58 " pdb=" CG MET B 58 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 6.85e-01 bond pdb=" C LYS B 114 " pdb=" N LEU B 115 " ideal model delta sigma weight residual 1.335 1.325 0.010 1.31e-02 5.83e+03 6.23e-01 bond pdb=" CB PRO B 109 " pdb=" CG PRO B 109 " ideal model delta sigma weight residual 1.492 1.453 0.039 5.00e-02 4.00e+02 6.13e-01 bond pdb=" CA ARG C 34 " pdb=" C ARG C 34 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.10e-02 2.27e+03 6.11e-01 ... (remaining 10523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 17863 1.22 - 2.43: 1119 2.43 - 3.65: 37 3.65 - 4.87: 12 4.87 - 6.09: 1 Bond angle restraints: 19032 Sorted by residual: angle pdb=" N VAL F 116 " pdb=" CA VAL F 116 " pdb=" C VAL F 116 " ideal model delta sigma weight residual 109.34 115.43 -6.09 2.08e+00 2.31e-01 8.56e+00 angle pdb=" N GLN A 91 " pdb=" CA GLN A 91 " pdb=" CB GLN A 91 " ideal model delta sigma weight residual 110.20 106.83 3.37 1.49e+00 4.50e-01 5.11e+00 angle pdb=" N PRO A 109 " pdb=" CA PRO A 109 " pdb=" C PRO A 109 " ideal model delta sigma weight residual 112.47 116.83 -4.36 2.06e+00 2.36e-01 4.49e+00 angle pdb=" C VAL B 141 " pdb=" CA VAL B 141 " pdb=" CB VAL B 141 " ideal model delta sigma weight residual 111.29 108.03 3.26 1.64e+00 3.72e-01 3.95e+00 angle pdb=" CA GLN A 91 " pdb=" CB GLN A 91 " pdb=" CG GLN A 91 " ideal model delta sigma weight residual 114.10 117.86 -3.76 2.00e+00 2.50e-01 3.54e+00 ... (remaining 19027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4482 17.52 - 35.04: 296 35.04 - 52.55: 107 52.55 - 70.07: 53 70.07 - 87.59: 18 Dihedral angle restraints: 4956 sinusoidal: 2636 harmonic: 2320 Sorted by residual: dihedral pdb=" CA ASP E 76 " pdb=" C ASP E 76 " pdb=" N THR E 77 " pdb=" CA THR E 77 " ideal model delta harmonic sigma weight residual -180.00 -154.00 -26.00 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ILE C 36 " pdb=" C ILE C 36 " pdb=" N ASN C 37 " pdb=" CA ASN C 37 " ideal model delta harmonic sigma weight residual 180.00 155.79 24.21 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA GLN F 106 " pdb=" C GLN F 106 " pdb=" N TYR F 107 " pdb=" CA TYR F 107 " ideal model delta harmonic sigma weight residual 180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 4953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 542 0.031 - 0.062: 234 0.062 - 0.093: 47 0.093 - 0.124: 26 0.124 - 0.155: 6 Chirality restraints: 855 Sorted by residual: chirality pdb=" CA PRO A 109 " pdb=" N PRO A 109 " pdb=" C PRO A 109 " pdb=" CB PRO A 109 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA PRO B 109 " pdb=" N PRO B 109 " pdb=" C PRO B 109 " pdb=" CB PRO B 109 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA VAL E 40 " pdb=" N VAL E 40 " pdb=" C VAL E 40 " pdb=" CB VAL E 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 852 not shown) Planarity restraints: 1553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 113 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.35e+00 pdb=" C ALA B 113 " -0.053 2.00e-02 2.50e+03 pdb=" O ALA B 113 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS B 114 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 58 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C MET B 58 " 0.050 2.00e-02 2.50e+03 pdb=" O MET B 58 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA B 59 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 123 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C THR C 123 " -0.036 2.00e-02 2.50e+03 pdb=" O THR C 123 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY C 124 " 0.012 2.00e-02 2.50e+03 ... (remaining 1550 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 290 2.16 - 2.77: 20231 2.77 - 3.38: 30650 3.38 - 3.99: 38827 3.99 - 4.60: 61943 Nonbonded interactions: 151941 Sorted by model distance: nonbonded pdb=" HZ2 LYS B 44 " pdb=" OD1 ASN D 120 " model vdw 1.546 2.450 nonbonded pdb=" HZ2 LYS C 44 " pdb=" OD1 ASN A 120 " model vdw 1.568 2.450 nonbonded pdb=" OE1 GLU E 6 " pdb=" H GLU E 6 " model vdw 1.697 2.450 nonbonded pdb=" H ARG E 90 " pdb=" OD2 ASP E 93 " model vdw 1.707 2.450 nonbonded pdb=" OD1 ASP F 76 " pdb=" HG SER F 78 " model vdw 1.724 2.450 ... (remaining 151936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 34 through 140) selection = (chain 'B' and resid 34 through 140) selection = chain 'C' selection = (chain 'D' and resid 34 through 140) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.550 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 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 : 0.003 0.039 5267 Z= 0.170 Angle : 0.605 6.087 7165 Z= 0.380 Chirality : 0.039 0.155 855 Planarity : 0.005 0.031 905 Dihedral : 13.715 87.588 1837 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.30), residues: 660 helix: 1.07 (0.23), residues: 355 sheet: 0.15 (0.50), residues: 116 loop : 0.48 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 39 HIS 0.011 0.002 HIS B 112 PHE 0.014 0.001 PHE D 74 TYR 0.021 0.004 TYR E 36 ARG 0.002 0.000 ARG F 42 Details of bonding type rmsd hydrogen bonds : bond 0.09973 ( 403) hydrogen bonds : angle 5.10031 ( 1164) SS BOND : bond 0.00322 ( 2) SS BOND : angle 1.28743 ( 4) covalent geometry : bond 0.00349 ( 5265) covalent geometry : angle 0.60415 ( 7161) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: C 57 LEU cc_start: 0.7684 (tt) cc_final: 0.7477 (tt) REVERT: A 51 MET cc_start: 0.7949 (mmp) cc_final: 0.7705 (mmm) REVERT: D 103 LYS cc_start: 0.8154 (tttt) cc_final: 0.7551 (ttmt) REVERT: D 114 LYS cc_start: 0.5866 (mmtp) cc_final: 0.5469 (mmpt) REVERT: E 20 LEU cc_start: 0.8503 (mt) cc_final: 0.8248 (mm) REVERT: E 28 ASN cc_start: 0.8345 (m-40) cc_final: 0.7673 (t0) REVERT: E 83 TYR cc_start: 0.7646 (m-80) cc_final: 0.7443 (m-80) REVERT: E 102 TYR cc_start: 0.6702 (t80) cc_final: 0.6066 (t80) REVERT: F 18 LEU cc_start: 0.6622 (mt) cc_final: 0.6421 (mt) REVERT: F 46 LYS cc_start: 0.7403 (mttt) cc_final: 0.6670 (tmmt) REVERT: F 88 SER cc_start: 0.7053 (m) cc_final: 0.6755 (t) REVERT: F 115 LEU cc_start: 0.8175 (mp) cc_final: 0.7881 (mm) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 1.9320 time to fit residues: 206.6824 Evaluate side-chains 77 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.147637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118443 restraints weight = 15383.321| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.59 r_work: 0.3327 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5267 Z= 0.213 Angle : 0.532 5.771 7165 Z= 0.295 Chirality : 0.040 0.157 855 Planarity : 0.004 0.039 905 Dihedral : 4.559 22.206 716 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.33 % Allowed : 6.81 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.31), residues: 660 helix: 2.51 (0.24), residues: 355 sheet: 0.55 (0.57), residues: 94 loop : 0.74 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 39 HIS 0.008 0.001 HIS B 112 PHE 0.009 0.001 PHE D 74 TYR 0.013 0.002 TYR E 107 ARG 0.004 0.001 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 403) hydrogen bonds : angle 4.18373 ( 1164) SS BOND : bond 0.00667 ( 2) SS BOND : angle 0.73524 ( 4) covalent geometry : bond 0.00492 ( 5265) covalent geometry : angle 0.53203 ( 7161) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.805 Fit side-chains REVERT: B 51 MET cc_start: 0.8022 (mmp) cc_final: 0.7772 (mmp) REVERT: A 70 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: D 103 LYS cc_start: 0.8839 (tttt) cc_final: 0.8298 (ttmt) REVERT: D 105 ASP cc_start: 0.8293 (t0) cc_final: 0.7979 (t0) REVERT: D 114 LYS cc_start: 0.6899 (mmtp) cc_final: 0.6543 (mmpt) REVERT: E 28 ASN cc_start: 0.8239 (m-40) cc_final: 0.7723 (t0) REVERT: E 94 THR cc_start: 0.8165 (t) cc_final: 0.7880 (m) REVERT: F 46 LYS cc_start: 0.7595 (mttt) cc_final: 0.7049 (tmmt) REVERT: F 68 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7457 (ttpp) REVERT: F 79 LYS cc_start: 0.8198 (ptmm) cc_final: 0.7963 (ptpp) REVERT: F 115 LEU cc_start: 0.8317 (mp) cc_final: 0.8045 (mm) outliers start: 13 outliers final: 4 residues processed: 83 average time/residue: 1.5365 time to fit residues: 136.6008 Evaluate side-chains 84 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 68 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.101175 restraints weight = 16456.259| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.90 r_work: 0.3314 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5267 Z= 0.170 Angle : 0.479 4.995 7165 Z= 0.263 Chirality : 0.039 0.143 855 Planarity : 0.003 0.039 905 Dihedral : 4.156 21.252 716 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.97 % Allowed : 8.96 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.31), residues: 660 helix: 2.83 (0.24), residues: 357 sheet: 0.55 (0.56), residues: 94 loop : 0.81 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 39 HIS 0.005 0.001 HIS B 112 PHE 0.008 0.001 PHE D 74 TYR 0.012 0.001 TYR E 107 ARG 0.002 0.000 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 403) hydrogen bonds : angle 3.89164 ( 1164) SS BOND : bond 0.00467 ( 2) SS BOND : angle 0.48999 ( 4) covalent geometry : bond 0.00388 ( 5265) covalent geometry : angle 0.47894 ( 7161) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 103 LYS cc_start: 0.8841 (tttt) cc_final: 0.8319 (ttmt) REVERT: D 105 ASP cc_start: 0.8327 (t0) cc_final: 0.7971 (t0) REVERT: D 114 LYS cc_start: 0.6980 (mmtp) cc_final: 0.6597 (mmpt) REVERT: E 18 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6880 (mp) REVERT: E 28 ASN cc_start: 0.8261 (m-40) cc_final: 0.7737 (t0) REVERT: E 93 ASP cc_start: 0.8125 (m-30) cc_final: 0.7778 (m-30) REVERT: F 46 LYS cc_start: 0.7541 (mttt) cc_final: 0.6969 (tmmt) REVERT: F 115 LEU cc_start: 0.8260 (mp) cc_final: 0.8003 (mm) outliers start: 11 outliers final: 4 residues processed: 86 average time/residue: 1.9152 time to fit residues: 176.2260 Evaluate side-chains 82 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 3 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN A 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.136138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.102081 restraints weight = 16162.734| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.89 r_work: 0.3054 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5267 Z= 0.143 Angle : 0.460 4.461 7165 Z= 0.250 Chirality : 0.038 0.141 855 Planarity : 0.003 0.037 905 Dihedral : 3.964 20.314 716 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.51 % Allowed : 9.50 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.31), residues: 660 helix: 3.05 (0.23), residues: 357 sheet: 0.50 (0.56), residues: 94 loop : 0.83 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 39 HIS 0.003 0.001 HIS B 112 PHE 0.007 0.001 PHE D 127 TYR 0.013 0.001 TYR E 35 ARG 0.002 0.000 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 403) hydrogen bonds : angle 3.75594 ( 1164) SS BOND : bond 0.00355 ( 2) SS BOND : angle 0.39461 ( 4) covalent geometry : bond 0.00321 ( 5265) covalent geometry : angle 0.45963 ( 7161) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7973 (t0) cc_final: 0.7688 (t0) REVERT: D 103 LYS cc_start: 0.8503 (tttt) cc_final: 0.7959 (ttmt) REVERT: D 105 ASP cc_start: 0.8049 (t0) cc_final: 0.7700 (t0) REVERT: D 114 LYS cc_start: 0.6566 (mmtp) cc_final: 0.6114 (mmpt) REVERT: E 28 ASN cc_start: 0.8321 (m-40) cc_final: 0.7660 (t0) REVERT: E 93 ASP cc_start: 0.7928 (m-30) cc_final: 0.7540 (m-30) REVERT: F 46 LYS cc_start: 0.7373 (mttt) cc_final: 0.6715 (tmmt) outliers start: 14 outliers final: 4 residues processed: 85 average time/residue: 1.8807 time to fit residues: 170.7872 Evaluate side-chains 80 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain E residue 110 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.136475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.101796 restraints weight = 16189.716| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.00 r_work: 0.3065 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5267 Z= 0.147 Angle : 0.458 4.440 7165 Z= 0.248 Chirality : 0.038 0.137 855 Planarity : 0.003 0.036 905 Dihedral : 3.895 19.837 716 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.79 % Allowed : 10.04 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.31), residues: 660 helix: 3.19 (0.23), residues: 357 sheet: 0.28 (0.54), residues: 98 loop : 0.80 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 39 HIS 0.003 0.001 HIS B 112 PHE 0.010 0.001 PHE F 71 TYR 0.014 0.001 TYR E 35 ARG 0.003 0.000 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 403) hydrogen bonds : angle 3.68062 ( 1164) SS BOND : bond 0.00360 ( 2) SS BOND : angle 0.35885 ( 4) covalent geometry : bond 0.00333 ( 5265) covalent geometry : angle 0.45854 ( 7161) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8037 (t0) cc_final: 0.7765 (t0) REVERT: D 103 LYS cc_start: 0.8578 (tttt) cc_final: 0.8043 (ttmt) REVERT: D 105 ASP cc_start: 0.8138 (t0) cc_final: 0.7843 (t0) REVERT: D 114 LYS cc_start: 0.6718 (mmtp) cc_final: 0.6248 (mmpt) REVERT: E 93 ASP cc_start: 0.8008 (m-30) cc_final: 0.7650 (m-30) REVERT: F 46 LYS cc_start: 0.7392 (mttt) cc_final: 0.6745 (tmmt) outliers start: 10 outliers final: 4 residues processed: 76 average time/residue: 1.7176 time to fit residues: 139.6011 Evaluate side-chains 74 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain E residue 110 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 58 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN D 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.137683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.102407 restraints weight = 16127.598| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.96 r_work: 0.3250 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5267 Z= 0.134 Angle : 0.443 4.395 7165 Z= 0.240 Chirality : 0.038 0.136 855 Planarity : 0.003 0.035 905 Dihedral : 3.718 18.958 716 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.33 % Allowed : 10.04 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.31), residues: 660 helix: 3.38 (0.23), residues: 358 sheet: 0.29 (0.54), residues: 98 loop : 0.80 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 39 HIS 0.003 0.001 HIS B 112 PHE 0.009 0.001 PHE F 71 TYR 0.017 0.001 TYR E 35 ARG 0.002 0.000 ARG F 42 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 403) hydrogen bonds : angle 3.58941 ( 1164) SS BOND : bond 0.00302 ( 2) SS BOND : angle 0.33082 ( 4) covalent geometry : bond 0.00299 ( 5265) covalent geometry : angle 0.44308 ( 7161) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.824 Fit side-chains REVERT: A 105 ASP cc_start: 0.8025 (t0) cc_final: 0.7748 (t0) REVERT: D 103 LYS cc_start: 0.8559 (tttt) cc_final: 0.8002 (ttmt) REVERT: D 105 ASP cc_start: 0.8153 (t0) cc_final: 0.7898 (t0) REVERT: E 93 ASP cc_start: 0.7987 (m-30) cc_final: 0.7650 (m-30) REVERT: F 19 ARG cc_start: 0.8617 (ttm170) cc_final: 0.8404 (ttt90) REVERT: F 46 LYS cc_start: 0.7396 (mttt) cc_final: 0.6779 (tmmt) outliers start: 13 outliers final: 6 residues processed: 78 average time/residue: 2.4159 time to fit residues: 200.4101 Evaluate side-chains 77 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 3 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 62 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 21 optimal weight: 0.0670 chunk 27 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN D 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103198 restraints weight = 16179.053| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.95 r_work: 0.3317 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5267 Z= 0.125 Angle : 0.440 4.642 7165 Z= 0.237 Chirality : 0.037 0.134 855 Planarity : 0.003 0.034 905 Dihedral : 3.586 18.963 716 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.79 % Allowed : 11.47 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.31), residues: 660 helix: 3.52 (0.22), residues: 359 sheet: 0.35 (0.54), residues: 98 loop : 0.80 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 39 HIS 0.003 0.001 HIS D 112 PHE 0.010 0.001 PHE F 71 TYR 0.016 0.001 TYR E 35 ARG 0.002 0.000 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 403) hydrogen bonds : angle 3.53202 ( 1164) SS BOND : bond 0.00243 ( 2) SS BOND : angle 0.27976 ( 4) covalent geometry : bond 0.00280 ( 5265) covalent geometry : angle 0.44039 ( 7161) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: D 103 LYS cc_start: 0.8732 (tttt) cc_final: 0.8197 (ttmt) REVERT: D 105 ASP cc_start: 0.8141 (t0) cc_final: 0.7898 (t0) REVERT: E 66 SER cc_start: 0.9036 (t) cc_final: 0.8362 (p) REVERT: E 93 ASP cc_start: 0.8108 (m-30) cc_final: 0.7812 (m-30) REVERT: F 19 ARG cc_start: 0.8803 (ttm170) cc_final: 0.8601 (ttt90) REVERT: F 46 LYS cc_start: 0.7483 (mttt) cc_final: 0.6936 (tmmt) outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 1.6525 time to fit residues: 141.1844 Evaluate side-chains 81 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 3 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN D 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.103611 restraints weight = 16079.469| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.86 r_work: 0.3335 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5267 Z= 0.124 Angle : 0.441 4.604 7165 Z= 0.237 Chirality : 0.037 0.135 855 Planarity : 0.003 0.034 905 Dihedral : 3.513 18.424 716 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.97 % Allowed : 12.01 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.31), residues: 660 helix: 3.59 (0.22), residues: 359 sheet: 0.47 (0.53), residues: 98 loop : 0.83 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 39 HIS 0.002 0.000 HIS B 112 PHE 0.012 0.001 PHE F 71 TYR 0.011 0.001 TYR E 107 ARG 0.001 0.000 ARG F 42 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 403) hydrogen bonds : angle 3.48132 ( 1164) SS BOND : bond 0.00258 ( 2) SS BOND : angle 0.23085 ( 4) covalent geometry : bond 0.00276 ( 5265) covalent geometry : angle 0.44105 ( 7161) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.8013 (mmp) cc_final: 0.7707 (mtp) REVERT: D 103 LYS cc_start: 0.8789 (tttt) cc_final: 0.8263 (ttmt) REVERT: E 66 SER cc_start: 0.9011 (t) cc_final: 0.8379 (p) REVERT: F 46 LYS cc_start: 0.7520 (mttt) cc_final: 0.6996 (tmmt) outliers start: 11 outliers final: 6 residues processed: 82 average time/residue: 1.5966 time to fit residues: 140.1809 Evaluate side-chains 78 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 3 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.0570 chunk 32 optimal weight: 0.0170 chunk 41 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN E 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.139737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104140 restraints weight = 16042.609| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.94 r_work: 0.3334 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5267 Z= 0.111 Angle : 0.439 4.808 7165 Z= 0.234 Chirality : 0.037 0.133 855 Planarity : 0.003 0.033 905 Dihedral : 3.441 17.981 716 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.79 % Allowed : 12.72 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.31), residues: 660 helix: 3.72 (0.22), residues: 359 sheet: 0.58 (0.53), residues: 98 loop : 0.87 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 39 HIS 0.002 0.000 HIS B 112 PHE 0.010 0.001 PHE F 71 TYR 0.014 0.001 TYR E 35 ARG 0.001 0.000 ARG F 42 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 403) hydrogen bonds : angle 3.43816 ( 1164) SS BOND : bond 0.00144 ( 2) SS BOND : angle 0.14826 ( 4) covalent geometry : bond 0.00243 ( 5265) covalent geometry : angle 0.43862 ( 7161) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.8038 (mmp) cc_final: 0.7740 (mtp) REVERT: D 103 LYS cc_start: 0.8725 (tttt) cc_final: 0.8202 (ttmt) REVERT: E 66 SER cc_start: 0.9021 (t) cc_final: 0.8360 (p) REVERT: F 19 ARG cc_start: 0.8762 (ttm170) cc_final: 0.8559 (ttt90) REVERT: F 46 LYS cc_start: 0.7506 (mttt) cc_final: 0.6965 (tmmt) outliers start: 10 outliers final: 6 residues processed: 79 average time/residue: 1.6178 time to fit residues: 136.9056 Evaluate side-chains 77 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 3 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103074 restraints weight = 15941.657| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.93 r_work: 0.3062 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5267 Z= 0.138 Angle : 0.454 4.594 7165 Z= 0.242 Chirality : 0.038 0.133 855 Planarity : 0.003 0.034 905 Dihedral : 3.523 20.110 716 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.06 % Favored : 98.79 % Rotamer: Outliers : 1.25 % Allowed : 13.08 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.31), residues: 660 helix: 3.66 (0.22), residues: 359 sheet: 0.57 (0.52), residues: 98 loop : 0.85 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 39 HIS 0.002 0.001 HIS B 112 PHE 0.017 0.001 PHE F 71 TYR 0.014 0.001 TYR E 35 ARG 0.006 0.000 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 403) hydrogen bonds : angle 3.45986 ( 1164) SS BOND : bond 0.00276 ( 2) SS BOND : angle 0.32574 ( 4) covalent geometry : bond 0.00314 ( 5265) covalent geometry : angle 0.45356 ( 7161) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.7809 (mmp) cc_final: 0.7463 (mtp) REVERT: D 103 LYS cc_start: 0.8435 (tttt) cc_final: 0.7873 (ttmt) REVERT: E 66 SER cc_start: 0.9016 (t) cc_final: 0.8291 (p) REVERT: F 46 LYS cc_start: 0.7331 (mttt) cc_final: 0.6681 (tmmt) outliers start: 7 outliers final: 6 residues processed: 78 average time/residue: 1.6739 time to fit residues: 139.4828 Evaluate side-chains 79 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 3 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN D 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.137212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102669 restraints weight = 16148.206| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.96 r_work: 0.3059 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5267 Z= 0.135 Angle : 0.450 4.969 7165 Z= 0.241 Chirality : 0.037 0.133 855 Planarity : 0.003 0.034 905 Dihedral : 3.461 18.189 716 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 0.91 % Favored : 98.94 % Rotamer: Outliers : 1.08 % Allowed : 13.26 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.31), residues: 660 helix: 3.67 (0.22), residues: 359 sheet: 0.55 (0.52), residues: 98 loop : 0.80 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 39 HIS 0.002 0.001 HIS B 112 PHE 0.014 0.001 PHE F 71 TYR 0.014 0.001 TYR E 35 ARG 0.002 0.000 ARG F 42 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 403) hydrogen bonds : angle 3.44734 ( 1164) SS BOND : bond 0.00269 ( 2) SS BOND : angle 0.26626 ( 4) covalent geometry : bond 0.00304 ( 5265) covalent geometry : angle 0.44985 ( 7161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7385.18 seconds wall clock time: 128 minutes 21.49 seconds (7701.49 seconds total)