Starting phenix.real_space_refine on Wed Sep 17 17:55:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bia_44585/09_2025/9bia_44585.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bia_44585/09_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_44585/09_2025/9bia_44585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bia_44585/09_2025/9bia_44585.map" model { file = "/net/cci-nas-00/data/ceres_data/9bia_44585/09_2025/9bia_44585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bia_44585/09_2025/9bia_44585.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.35, per 1000 atoms: 0.23 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: 1.07 Conformation dependent library (CDL) restraints added in 245.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.24 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: 2.47 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 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: 2.040 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: 0.070 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.420 Find NCS groups from input model: 0.110 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:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.840 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG F 42 TYR 0.021 0.004 TYR E 36 PHE 0.014 0.001 PHE D 74 TRP 0.003 0.001 TRP E 39 HIS 0.011 0.002 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 5265) covalent geometry : angle 0.60415 ( 7161) SS BOND : bond 0.00322 ( 2) SS BOND : angle 1.28743 ( 4) hydrogen bonds : bond 0.09973 ( 403) hydrogen bonds : angle 5.10031 ( 1164) *********************** 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 : 0.302 Fit side-chains 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: 0.8295 (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: 0.7442 (m-80) REVERT: E 102 TYR cc_start: 0.6702 (t80) cc_final: 0.6066 (t80) 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: 1.0241 time to fit residues: 108.9747 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 : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.150648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121459 restraints weight = 15327.882| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.59 r_work: 0.3119 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1667 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= 0.144 Angle : 0.500 5.716 7165 Z= 0.275 Chirality : 0.039 0.158 855 Planarity : 0.004 0.037 905 Dihedral : 4.477 21.754 716 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.79 % Allowed : 7.17 % Favored : 91.04 % 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 aren not related in a simple way. whole: 2.78 (0.31), residues: 660 helix: 2.79 (0.24), residues: 355 sheet: 0.62 (0.56), residues: 94 loop : 0.88 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 34 TYR 0.010 0.001 TYR E 107 PHE 0.008 0.001 PHE D 74 TRP 0.002 0.000 TRP E 39 HIS 0.007 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5265) covalent geometry : angle 0.49974 ( 7161) SS BOND : bond 0.00494 ( 2) SS BOND : angle 0.63550 ( 4) hydrogen bonds : bond 0.04354 ( 403) hydrogen bonds : angle 4.11057 ( 1164) *********************** 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 96 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.7867 (mmp) cc_final: 0.7615 (mmp) REVERT: A 51 MET cc_start: 0.8520 (mmp) cc_final: 0.8275 (mmm) REVERT: D 103 LYS cc_start: 0.8646 (tttt) cc_final: 0.8064 (ttmt) REVERT: D 105 ASP cc_start: 0.8030 (t0) cc_final: 0.7664 (t0) REVERT: D 114 LYS cc_start: 0.6584 (mmtp) cc_final: 0.6179 (mmpt) REVERT: E 20 LEU cc_start: 0.8850 (mt) cc_final: 0.8527 (mm) REVERT: E 28 ASN cc_start: 0.8266 (m-40) cc_final: 0.7634 (t0) REVERT: E 30 TYR cc_start: 0.8637 (m-80) cc_final: 0.8406 (m-80) REVERT: E 83 TYR cc_start: 0.8176 (m-80) cc_final: 0.7709 (m-80) REVERT: E 94 THR cc_start: 0.7985 (t) cc_final: 0.7679 (m) REVERT: F 46 LYS cc_start: 0.7511 (mttt) cc_final: 0.6895 (tmmt) REVERT: F 115 LEU cc_start: 0.8205 (mp) cc_final: 0.7911 (mm) outliers start: 10 outliers final: 4 residues processed: 91 average time/residue: 0.9053 time to fit residues: 87.4641 Evaluate side-chains 85 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 110 SER Chi-restraints excluded: chain F residue 3 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.136337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.101432 restraints weight = 16210.173| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.87 r_work: 0.3291 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5267 Z= 0.186 Angle : 0.483 4.974 7165 Z= 0.266 Chirality : 0.039 0.145 855 Planarity : 0.003 0.039 905 Dihedral : 4.123 21.366 716 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.61 % Allowed : 8.78 % Favored : 89.61 % 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 aren not related in a simple way. whole: 2.83 (0.31), residues: 660 helix: 2.84 (0.23), residues: 357 sheet: 0.55 (0.56), residues: 94 loop : 0.90 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 42 TYR 0.013 0.002 TYR E 107 PHE 0.009 0.001 PHE D 74 TRP 0.003 0.001 TRP F 39 HIS 0.005 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 5265) covalent geometry : angle 0.48281 ( 7161) SS BOND : bond 0.00560 ( 2) SS BOND : angle 0.47960 ( 4) hydrogen bonds : bond 0.04205 ( 403) hydrogen bonds : angle 3.89927 ( 1164) *********************** 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 86 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.8701 (mmp) cc_final: 0.8494 (mmm) REVERT: D 103 LYS cc_start: 0.8815 (tttt) cc_final: 0.8315 (ttmt) REVERT: D 105 ASP cc_start: 0.8341 (t0) cc_final: 0.7966 (t0) REVERT: D 114 LYS cc_start: 0.6981 (mmtp) cc_final: 0.6587 (mmpt) REVERT: E 20 LEU cc_start: 0.9062 (mt) cc_final: 0.8824 (mm) REVERT: E 28 ASN cc_start: 0.8283 (m-40) cc_final: 0.7726 (t0) REVERT: E 93 ASP cc_start: 0.8140 (m-30) cc_final: 0.7918 (m-30) REVERT: F 46 LYS cc_start: 0.7567 (mttt) cc_final: 0.7005 (tmmt) REVERT: F 68 LYS cc_start: 0.7862 (ttpp) cc_final: 0.7661 (tppt) outliers start: 9 outliers final: 4 residues processed: 82 average time/residue: 0.9052 time to fit residues: 78.7681 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 : 0.280 ------------------------------------------------------------------------------- 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 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 5 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.137418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.102619 restraints weight = 15998.500| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.86 r_work: 0.3055 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2376 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= 0.142 Angle : 0.453 4.426 7165 Z= 0.246 Chirality : 0.038 0.141 855 Planarity : 0.003 0.036 905 Dihedral : 3.891 20.028 716 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.79 % Allowed : 9.32 % Favored : 88.89 % 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 aren not related in a simple way. whole: 3.09 (0.31), residues: 660 helix: 3.14 (0.23), residues: 357 sheet: 0.62 (0.56), residues: 94 loop : 0.86 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 42 TYR 0.012 0.001 TYR E 35 PHE 0.014 0.001 PHE F 71 TRP 0.002 0.001 TRP F 39 HIS 0.003 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5265) covalent geometry : angle 0.45266 ( 7161) SS BOND : bond 0.00357 ( 2) SS BOND : angle 0.41389 ( 4) hydrogen bonds : bond 0.03944 ( 403) hydrogen bonds : angle 3.74830 ( 1164) *********************** 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 83 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.7780 (mmp) cc_final: 0.7488 (mmp) REVERT: A 51 MET cc_start: 0.8509 (mmp) cc_final: 0.8156 (mmm) REVERT: A 105 ASP cc_start: 0.7941 (t0) cc_final: 0.7705 (t0) REVERT: D 103 LYS cc_start: 0.8506 (tttt) cc_final: 0.7961 (ttmt) REVERT: D 105 ASP cc_start: 0.8075 (t0) cc_final: 0.7744 (t0) REVERT: D 114 LYS cc_start: 0.6576 (mmtp) cc_final: 0.6112 (mmpt) REVERT: E 20 LEU cc_start: 0.8829 (mt) cc_final: 0.8510 (mm) REVERT: E 93 ASP cc_start: 0.7936 (m-30) cc_final: 0.7553 (m-30) REVERT: F 46 LYS cc_start: 0.7425 (mttt) cc_final: 0.6742 (tmmt) REVERT: F 68 LYS cc_start: 0.7571 (ttpp) cc_final: 0.7354 (tppt) outliers start: 10 outliers final: 4 residues processed: 78 average time/residue: 0.9076 time to fit residues: 75.3150 Evaluate side-chains 76 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 2 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 overall best weight: 0.8340 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.138025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103093 restraints weight = 16096.438| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.88 r_work: 0.3100 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2517 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= 0.135 Angle : 0.441 4.403 7165 Z= 0.240 Chirality : 0.038 0.137 855 Planarity : 0.003 0.034 905 Dihedral : 3.823 19.562 716 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.43 % Allowed : 10.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.19 (0.31), residues: 660 helix: 3.31 (0.23), residues: 358 sheet: 0.38 (0.54), residues: 98 loop : 0.86 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 34 TYR 0.015 0.001 TYR E 35 PHE 0.011 0.001 PHE F 71 TRP 0.002 0.001 TRP F 39 HIS 0.003 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 5265) covalent geometry : angle 0.44144 ( 7161) SS BOND : bond 0.00354 ( 2) SS BOND : angle 0.34388 ( 4) hydrogen bonds : bond 0.03858 ( 403) hydrogen bonds : angle 3.67203 ( 1164) *********************** 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 78 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.7927 (mmp) cc_final: 0.7588 (mmp) REVERT: A 51 MET cc_start: 0.8549 (mmp) cc_final: 0.8211 (mmm) REVERT: A 105 ASP cc_start: 0.7975 (t0) cc_final: 0.7723 (t0) REVERT: D 103 LYS cc_start: 0.8564 (tttt) cc_final: 0.8014 (ttmt) REVERT: D 105 ASP cc_start: 0.8134 (t0) cc_final: 0.7810 (t0) REVERT: D 114 LYS cc_start: 0.6677 (mmtp) cc_final: 0.6200 (mmpt) REVERT: E 20 LEU cc_start: 0.8874 (mt) cc_final: 0.8556 (mm) REVERT: E 93 ASP cc_start: 0.7914 (m-30) cc_final: 0.7516 (m-30) REVERT: F 46 LYS cc_start: 0.7434 (mttt) cc_final: 0.6768 (tmmt) REVERT: F 68 LYS cc_start: 0.7574 (ttpp) cc_final: 0.7349 (tppt) outliers start: 8 outliers final: 3 residues processed: 75 average time/residue: 0.8962 time to fit residues: 71.4099 Evaluate side-chains 72 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 110 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.136113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.100886 restraints weight = 16321.979| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.94 r_work: 0.3061 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5267 Z= 0.180 Angle : 0.462 4.536 7165 Z= 0.252 Chirality : 0.038 0.138 855 Planarity : 0.003 0.038 905 Dihedral : 3.794 19.642 716 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.87 % Allowed : 9.86 % Favored : 87.28 % 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 aren not related in a simple way. whole: 3.05 (0.31), residues: 660 helix: 3.22 (0.23), residues: 358 sheet: 0.35 (0.54), residues: 98 loop : 0.75 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 42 TYR 0.015 0.001 TYR E 35 PHE 0.016 0.001 PHE F 71 TRP 0.002 0.001 TRP F 39 HIS 0.003 0.001 HIS D 112 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 5265) covalent geometry : angle 0.46162 ( 7161) SS BOND : bond 0.00487 ( 2) SS BOND : angle 0.44639 ( 4) hydrogen bonds : bond 0.03930 ( 403) hydrogen bonds : angle 3.70487 ( 1164) *********************** 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 88 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.7967 (mmp) cc_final: 0.7716 (mmp) REVERT: A 51 MET cc_start: 0.8544 (mmp) cc_final: 0.8231 (mmm) REVERT: A 105 ASP cc_start: 0.8003 (t0) cc_final: 0.7736 (t0) REVERT: D 103 LYS cc_start: 0.8548 (tttt) cc_final: 0.7990 (ttmt) REVERT: D 105 ASP cc_start: 0.8166 (t0) cc_final: 0.7886 (t0) REVERT: D 114 LYS cc_start: 0.6635 (mmtp) cc_final: 0.6155 (mmpt) REVERT: E 20 LEU cc_start: 0.8882 (mt) cc_final: 0.8549 (mm) REVERT: E 93 ASP cc_start: 0.7929 (m-30) cc_final: 0.7574 (m-30) REVERT: F 46 LYS cc_start: 0.7402 (mttt) cc_final: 0.6750 (tmmt) outliers start: 16 outliers final: 6 residues processed: 81 average time/residue: 0.9390 time to fit residues: 80.7118 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 : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 56 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 D 33 ASN D 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.137742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.102904 restraints weight = 16093.404| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.85 r_work: 0.3064 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2783 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= 0.123 Angle : 0.433 4.367 7165 Z= 0.235 Chirality : 0.037 0.135 855 Planarity : 0.003 0.035 905 Dihedral : 3.636 19.074 716 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.69 % Allowed : 10.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.27 (0.31), residues: 660 helix: 3.42 (0.22), residues: 359 sheet: 0.43 (0.54), residues: 98 loop : 0.78 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 34 TYR 0.013 0.001 TYR E 35 PHE 0.008 0.001 PHE F 71 TRP 0.002 0.000 TRP F 39 HIS 0.004 0.001 HIS D 112 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 5265) covalent geometry : angle 0.43306 ( 7161) SS BOND : bond 0.00302 ( 2) SS BOND : angle 0.30337 ( 4) hydrogen bonds : bond 0.03775 ( 403) hydrogen bonds : angle 3.58261 ( 1164) *********************** 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: 15 poor density : 69 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.7944 (mmp) cc_final: 0.7655 (mmp) REVERT: A 51 MET cc_start: 0.8488 (mmp) cc_final: 0.8192 (mmm) REVERT: A 105 ASP cc_start: 0.7951 (t0) cc_final: 0.7726 (t0) REVERT: D 103 LYS cc_start: 0.8524 (tttt) cc_final: 0.7959 (ttmt) REVERT: D 105 ASP cc_start: 0.7999 (t0) cc_final: 0.7736 (t0) REVERT: D 114 LYS cc_start: 0.6593 (mmtp) cc_final: 0.6133 (mmpt) REVERT: E 66 SER cc_start: 0.9003 (t) cc_final: 0.8295 (p) REVERT: E 93 ASP cc_start: 0.7893 (m-30) cc_final: 0.7524 (m-30) REVERT: F 46 LYS cc_start: 0.7377 (mttt) cc_final: 0.6738 (tmmt) outliers start: 15 outliers final: 9 residues processed: 78 average time/residue: 0.9592 time to fit residues: 79.2077 Evaluate side-chains 79 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE 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 D residue 33 ASN 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 50 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 D 33 ASN D 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.137251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.101922 restraints weight = 16041.894| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.91 r_work: 0.3221 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2938 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= 0.142 Angle : 0.437 4.414 7165 Z= 0.237 Chirality : 0.038 0.135 855 Planarity : 0.003 0.036 905 Dihedral : 3.586 19.174 716 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.15 % Allowed : 11.29 % Favored : 86.56 % 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 aren not related in a simple way. whole: 3.32 (0.31), residues: 660 helix: 3.45 (0.22), residues: 359 sheet: 0.50 (0.54), residues: 98 loop : 0.80 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 42 TYR 0.010 0.001 TYR F 107 PHE 0.015 0.001 PHE F 71 TRP 0.002 0.001 TRP F 39 HIS 0.002 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5265) covalent geometry : angle 0.43684 ( 7161) SS BOND : bond 0.00332 ( 2) SS BOND : angle 0.32981 ( 4) hydrogen bonds : bond 0.03773 ( 403) hydrogen bonds : angle 3.55211 ( 1164) *********************** 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 83 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.7999 (mmp) cc_final: 0.7757 (mmp) REVERT: A 51 MET cc_start: 0.8525 (mmp) cc_final: 0.8218 (mmm) REVERT: D 103 LYS cc_start: 0.8514 (tttt) cc_final: 0.7937 (ttmt) REVERT: D 105 ASP cc_start: 0.8097 (t0) cc_final: 0.7827 (t0) REVERT: E 93 ASP cc_start: 0.7923 (m-30) cc_final: 0.7599 (m-30) REVERT: F 46 LYS cc_start: 0.7377 (mttt) cc_final: 0.6735 (tmmt) outliers start: 12 outliers final: 6 residues processed: 79 average time/residue: 0.7673 time to fit residues: 64.7730 Evaluate side-chains 76 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain A residue 50 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.136839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.101634 restraints weight = 16070.495| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.90 r_work: 0.3041 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2992 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 : 0.450 5.207 7165 Z= 0.243 Chirality : 0.038 0.135 855 Planarity : 0.003 0.036 905 Dihedral : 3.558 19.102 716 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.25 % Allowed : 12.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.31 (0.31), residues: 660 helix: 3.44 (0.22), residues: 359 sheet: 0.51 (0.54), residues: 98 loop : 0.79 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 42 TYR 0.015 0.001 TYR E 35 PHE 0.015 0.001 PHE F 71 TRP 0.002 0.001 TRP F 39 HIS 0.002 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 5265) covalent geometry : angle 0.44979 ( 7161) SS BOND : bond 0.00353 ( 2) SS BOND : angle 0.37689 ( 4) hydrogen bonds : bond 0.03775 ( 403) hydrogen bonds : angle 3.54948 ( 1164) *********************** 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 77 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.7957 (mmp) cc_final: 0.7706 (mmp) REVERT: A 51 MET cc_start: 0.8482 (mmp) cc_final: 0.8183 (mmm) REVERT: D 103 LYS cc_start: 0.8470 (tttt) cc_final: 0.7894 (ttmt) REVERT: D 105 ASP cc_start: 0.8146 (t0) cc_final: 0.7852 (t0) REVERT: F 46 LYS cc_start: 0.7351 (mttt) cc_final: 0.6694 (tmmt) outliers start: 7 outliers final: 5 residues processed: 74 average time/residue: 0.8670 time to fit residues: 68.0814 Evaluate side-chains 76 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 109 GLU 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 18 optimal weight: 0.9990 chunk 7 optimal weight: 0.0470 chunk 6 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.138934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.103467 restraints weight = 15982.494| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.92 r_work: 0.3327 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5267 Z= 0.115 Angle : 0.432 5.154 7165 Z= 0.232 Chirality : 0.037 0.134 855 Planarity : 0.003 0.034 905 Dihedral : 3.431 18.268 716 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.43 % Allowed : 12.72 % Favored : 85.84 % 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 aren not related in a simple way. whole: 3.54 (0.31), residues: 660 helix: 3.66 (0.22), residues: 359 sheet: 0.57 (0.53), residues: 98 loop : 0.84 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 42 TYR 0.014 0.001 TYR E 35 PHE 0.010 0.001 PHE F 71 TRP 0.001 0.000 TRP F 39 HIS 0.002 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 5265) covalent geometry : angle 0.43198 ( 7161) SS BOND : bond 0.00213 ( 2) SS BOND : angle 0.22726 ( 4) hydrogen bonds : bond 0.03658 ( 403) hydrogen bonds : angle 3.44189 ( 1164) ********************** 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 82 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.8136 (mmp) cc_final: 0.7895 (mmp) REVERT: C 63 GLN cc_start: 0.7759 (tt0) cc_final: 0.7492 (tt0) REVERT: A 51 MET cc_start: 0.8681 (mmp) cc_final: 0.8423 (mmm) REVERT: A 105 ASP cc_start: 0.8015 (t0) cc_final: 0.7774 (t0) REVERT: D 103 LYS cc_start: 0.8749 (tttt) cc_final: 0.8216 (ttmt) REVERT: D 105 ASP cc_start: 0.8192 (t0) cc_final: 0.7972 (t0) REVERT: E 79 LYS cc_start: 0.7772 (mtmm) cc_final: 0.7298 (pttt) REVERT: F 46 LYS cc_start: 0.7483 (mttt) cc_final: 0.6941 (tmmt) outliers start: 8 outliers final: 7 residues processed: 79 average time/residue: 0.7590 time to fit residues: 64.1434 Evaluate side-chains 77 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.0670 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- 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 D 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.135913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.100558 restraints weight = 16162.527| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.91 r_work: 0.3286 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5267 Z= 0.193 Angle : 0.482 5.184 7165 Z= 0.259 Chirality : 0.038 0.136 855 Planarity : 0.003 0.037 905 Dihedral : 3.567 19.462 716 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.06 % Favored : 98.79 % Rotamer: Outliers : 1.43 % Allowed : 12.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.18 (0.31), residues: 660 helix: 3.36 (0.22), residues: 359 sheet: 0.48 (0.53), residues: 98 loop : 0.66 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 42 TYR 0.016 0.002 TYR E 35 PHE 0.014 0.001 PHE F 71 TRP 0.002 0.001 TRP F 39 HIS 0.003 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 5265) covalent geometry : angle 0.48193 ( 7161) SS BOND : bond 0.00539 ( 2) SS BOND : angle 0.60079 ( 4) hydrogen bonds : bond 0.03858 ( 403) hydrogen bonds : angle 3.58533 ( 1164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3727.59 seconds wall clock time: 63 minutes 55.56 seconds (3835.56 seconds total)