Starting phenix.real_space_refine on Fri Jan 17 01:51:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bia_44585/01_2025/9bia_44585.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bia_44585/01_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_44585/01_2025/9bia_44585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bia_44585/01_2025/9bia_44585.map" model { file = "/net/cci-nas-00/data/ceres_data/9bia_44585/01_2025/9bia_44585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bia_44585/01_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-5571/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: 5.70, per 1000 atoms: 0.55 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: 2.48 Conformation dependent library (CDL) restraints added in 666.7 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: 1.00 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: 3.88 Time building geometry restraints manager: 3.01 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.150 Find NCS groups from input model: 0.270 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:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.090 ------------------------------------------------------------------------------- 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 5265 Z= 0.228 Angle : 0.604 6.087 7161 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 *********************** 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 : 0.745 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: 1.9457 time to fit residues: 208.2713 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 : 0.788 ------------------------------------------------------------------------------- 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 = 0.147642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118450 restraints weight = 15383.145| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.59 r_work: 0.3332 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 5265 Z= 0.323 Angle : 0.532 5.771 7161 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 *********************** 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 : 0.735 Fit side-chains REVERT: B 51 MET cc_start: 0.8024 (mmp) cc_final: 0.7774 (mmp) REVERT: A 70 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: D 103 LYS cc_start: 0.8840 (tttt) cc_final: 0.8300 (ttmt) REVERT: D 105 ASP cc_start: 0.8295 (t0) cc_final: 0.7982 (t0) REVERT: D 114 LYS cc_start: 0.6904 (mmtp) cc_final: 0.6549 (mmpt) REVERT: E 28 ASN cc_start: 0.8238 (m-40) cc_final: 0.7723 (t0) REVERT: E 94 THR cc_start: 0.8166 (t) cc_final: 0.7880 (m) REVERT: F 46 LYS cc_start: 0.7597 (mttt) cc_final: 0.7050 (tmmt) REVERT: F 68 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7460 (ttpp) REVERT: F 79 LYS cc_start: 0.8200 (ptmm) cc_final: 0.7966 (ptpp) REVERT: F 115 LEU cc_start: 0.8317 (mp) cc_final: 0.8044 (mm) outliers start: 13 outliers final: 4 residues processed: 83 average time/residue: 1.6398 time to fit residues: 145.4899 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 : 0.735 ------------------------------------------------------------------------------- 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: 0.8980 chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 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: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.135310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101487 restraints weight = 16448.563| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.89 r_work: 0.3321 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5265 Z= 0.251 Angle : 0.476 4.974 7161 Z= 0.261 Chirality : 0.039 0.141 855 Planarity : 0.003 0.038 905 Dihedral : 4.127 21.122 716 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.15 % Allowed : 8.78 % 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: 2.82 (0.31), residues: 660 helix: 2.87 (0.24), residues: 357 sheet: 0.56 (0.56), residues: 94 loop : 0.82 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 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 E 42 *********************** 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 91 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 103 LYS cc_start: 0.8852 (tttt) cc_final: 0.8333 (ttmt) REVERT: D 105 ASP cc_start: 0.8287 (t0) cc_final: 0.7899 (t0) REVERT: D 114 LYS cc_start: 0.6996 (mmtp) cc_final: 0.6616 (mmpt) REVERT: E 18 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6881 (mp) REVERT: E 28 ASN cc_start: 0.8271 (m-40) cc_final: 0.7736 (t0) REVERT: E 93 ASP cc_start: 0.8127 (m-30) cc_final: 0.7743 (m-30) REVERT: F 46 LYS cc_start: 0.7543 (mttt) cc_final: 0.6976 (tmmt) REVERT: F 115 LEU cc_start: 0.8259 (mp) cc_final: 0.8002 (mm) outliers start: 12 outliers final: 4 residues processed: 86 average time/residue: 1.7559 time to fit residues: 160.4618 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 : 0.756 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.9980 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.135517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.101038 restraints weight = 16214.224| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.96 r_work: 0.3072 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5265 Z= 0.234 Angle : 0.464 4.479 7161 Z= 0.253 Chirality : 0.038 0.140 855 Planarity : 0.003 0.038 905 Dihedral : 3.938 20.261 716 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.33 % Allowed : 9.68 % 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: 2.97 (0.31), residues: 660 helix: 3.06 (0.23), residues: 357 sheet: 0.51 (0.56), residues: 94 loop : 0.82 (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 C 135 TYR 0.013 0.001 TYR E 35 ARG 0.002 0.000 ARG F 42 *********************** 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 87 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.663 Fit side-chains REVERT: B 51 MET cc_start: 0.7890 (mmp) cc_final: 0.7686 (mmp) REVERT: A 105 ASP cc_start: 0.8054 (t0) cc_final: 0.7764 (t0) REVERT: D 103 LYS cc_start: 0.8613 (tttt) cc_final: 0.8083 (ttmt) REVERT: D 105 ASP cc_start: 0.8196 (t0) cc_final: 0.7897 (t0) REVERT: D 114 LYS cc_start: 0.6719 (mmtp) cc_final: 0.6264 (mmpt) REVERT: E 28 ASN cc_start: 0.8333 (m-40) cc_final: 0.7696 (t0) REVERT: E 93 ASP cc_start: 0.7998 (m-30) cc_final: 0.7628 (m-30) REVERT: F 46 LYS cc_start: 0.7404 (mttt) cc_final: 0.6756 (tmmt) outliers start: 13 outliers final: 4 residues processed: 82 average time/residue: 1.6019 time to fit residues: 140.3917 Evaluate side-chains 78 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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: 1.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.135324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.100788 restraints weight = 16242.356| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.99 r_work: 0.3041 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5265 Z= 0.244 Angle : 0.467 4.561 7161 Z= 0.252 Chirality : 0.038 0.136 855 Planarity : 0.003 0.036 905 Dihedral : 3.907 19.937 716 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.74 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 (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: 2.99 (0.31), residues: 660 helix: 3.15 (0.23), residues: 357 sheet: 0.25 (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 0.015 0.001 TYR E 35 ARG 0.003 0.000 ARG D 34 *********************** 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 79 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.746 Fit side-chains REVERT: A 105 ASP cc_start: 0.8039 (t0) cc_final: 0.7767 (t0) REVERT: D 103 LYS cc_start: 0.8583 (tttt) cc_final: 0.8046 (ttmt) REVERT: D 105 ASP cc_start: 0.8139 (t0) cc_final: 0.7894 (t0) REVERT: D 114 LYS cc_start: 0.6728 (mmtp) cc_final: 0.6258 (mmpt) REVERT: E 93 ASP cc_start: 0.7999 (m-30) cc_final: 0.7656 (m-30) REVERT: F 46 LYS cc_start: 0.7395 (mttt) cc_final: 0.6770 (tmmt) outliers start: 8 outliers final: 5 residues processed: 76 average time/residue: 1.6610 time to fit residues: 134.9506 Evaluate side-chains 75 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 58 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3568 r_free = 0.3568 target = 0.136662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.102098 restraints weight = 16369.406| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.99 r_work: 0.3078 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5265 Z= 0.191 Angle : 0.443 4.442 7161 Z= 0.239 Chirality : 0.038 0.136 855 Planarity : 0.003 0.035 905 Dihedral : 3.677 18.842 716 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.97 % Allowed : 10.93 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.22 (0.31), residues: 660 helix: 3.39 (0.23), residues: 358 sheet: 0.31 (0.54), residues: 98 loop : 0.82 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 39 HIS 0.004 0.001 HIS D 112 PHE 0.008 0.001 PHE F 71 TYR 0.016 0.001 TYR E 35 ARG 0.002 0.000 ARG F 42 *********************** 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 83 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7985 (t0) cc_final: 0.7732 (t0) REVERT: D 103 LYS cc_start: 0.8598 (tttt) cc_final: 0.8055 (ttmt) REVERT: D 105 ASP cc_start: 0.8065 (t0) cc_final: 0.7790 (t0) REVERT: D 114 LYS cc_start: 0.6716 (mmtp) cc_final: 0.6245 (mmpt) REVERT: E 93 ASP cc_start: 0.7999 (m-30) cc_final: 0.7673 (m-30) REVERT: F 46 LYS cc_start: 0.7391 (mttt) cc_final: 0.6767 (tmmt) outliers start: 11 outliers final: 5 residues processed: 77 average time/residue: 1.9078 time to fit residues: 156.6848 Evaluate side-chains 75 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 0.0370 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.9664 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.137039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.102347 restraints weight = 16268.390| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.87 r_work: 0.3061 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5265 Z= 0.220 Angle : 0.452 4.519 7161 Z= 0.244 Chirality : 0.038 0.136 855 Planarity : 0.003 0.035 905 Dihedral : 3.633 19.237 716 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.97 % Allowed : 11.29 % 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: 3.24 (0.31), residues: 660 helix: 3.42 (0.23), residues: 359 sheet: 0.33 (0.53), residues: 98 loop : 0.78 (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 A 112 PHE 0.010 0.001 PHE F 71 TYR 0.018 0.001 TYR E 35 ARG 0.002 0.000 ARG E 42 *********************** 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 81 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.7844 (mmp) cc_final: 0.7433 (mtp) REVERT: D 69 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7105 (mm-30) REVERT: D 103 LYS cc_start: 0.8500 (tttt) cc_final: 0.7927 (ttmt) REVERT: D 105 ASP cc_start: 0.8075 (t0) cc_final: 0.7788 (t0) REVERT: F 46 LYS cc_start: 0.7356 (mttt) cc_final: 0.6715 (tmmt) outliers start: 11 outliers final: 8 residues processed: 77 average time/residue: 1.7572 time to fit residues: 144.0354 Evaluate side-chains 77 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.138259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103047 restraints weight = 16076.604| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.94 r_work: 0.3061 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5265 Z= 0.174 Angle : 0.442 4.580 7161 Z= 0.237 Chirality : 0.037 0.134 855 Planarity : 0.003 0.034 905 Dihedral : 3.644 23.574 716 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.97 % Allowed : 12.37 % 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: 3.41 (0.31), residues: 660 helix: 3.58 (0.22), residues: 359 sheet: 0.38 (0.53), residues: 98 loop : 0.81 (0.45), 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 0.010 0.001 PHE F 71 TYR 0.012 0.001 TYR E 35 ARG 0.004 0.000 ARG D 34 *********************** 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 85 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.7948 (mmp) cc_final: 0.7535 (mtp) REVERT: A 105 ASP cc_start: 0.7961 (t0) cc_final: 0.7687 (t0) REVERT: D 103 LYS cc_start: 0.8571 (tttt) cc_final: 0.8013 (ttmt) REVERT: D 105 ASP cc_start: 0.8105 (t0) cc_final: 0.7827 (t0) REVERT: E 66 SER cc_start: 0.9007 (t) cc_final: 0.8319 (p) REVERT: F 46 LYS cc_start: 0.7390 (mttt) cc_final: 0.6756 (tmmt) outliers start: 11 outliers final: 7 residues processed: 80 average time/residue: 1.7136 time to fit residues: 146.7796 Evaluate side-chains 79 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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 36 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 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 = 0.3584 r_free = 0.3584 target = 0.138655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103018 restraints weight = 16134.725| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.94 r_work: 0.3321 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5265 Z= 0.185 Angle : 0.448 5.024 7161 Z= 0.239 Chirality : 0.038 0.134 855 Planarity : 0.003 0.034 905 Dihedral : 3.577 20.713 716 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.61 % Allowed : 12.72 % 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: 3.49 (0.31), residues: 660 helix: 3.65 (0.22), residues: 359 sheet: 0.44 (0.53), residues: 98 loop : 0.82 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 39 HIS 0.001 0.000 HIS B 112 PHE 0.012 0.001 PHE F 71 TYR 0.014 0.001 TYR E 35 ARG 0.002 0.000 ARG D 34 *********************** 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 82 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: D 103 LYS cc_start: 0.8754 (tttt) cc_final: 0.8220 (ttmt) REVERT: D 105 ASP cc_start: 0.8200 (t0) cc_final: 0.7986 (t0) REVERT: E 66 SER cc_start: 0.9029 (t) cc_final: 0.8386 (p) REVERT: F 46 LYS cc_start: 0.7496 (mttt) cc_final: 0.6938 (tmmt) outliers start: 9 outliers final: 5 residues processed: 78 average time/residue: 1.7023 time to fit residues: 141.4964 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 : 0.746 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 E 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.101652 restraints weight = 16014.460| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.93 r_work: 0.3302 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5265 Z= 0.246 Angle : 0.467 4.558 7161 Z= 0.251 Chirality : 0.038 0.135 855 Planarity : 0.003 0.035 905 Dihedral : 3.590 18.830 716 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.06 % Favored : 98.79 % Rotamer: Outliers : 1.08 % Allowed : 13.44 % 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: 3.30 (0.31), residues: 660 helix: 3.46 (0.22), residues: 359 sheet: 0.45 (0.52), residues: 98 loop : 0.77 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 39 HIS 0.002 0.001 HIS A 112 PHE 0.008 0.001 PHE C 135 TYR 0.015 0.001 TYR E 35 ARG 0.002 0.000 ARG F 42 ********************** 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 76 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.8018 (mmp) cc_final: 0.7685 (mtp) REVERT: D 103 LYS cc_start: 0.8769 (tttt) cc_final: 0.8241 (ttmt) REVERT: D 105 ASP cc_start: 0.8249 (t0) cc_final: 0.8031 (t0) REVERT: E 66 SER cc_start: 0.9042 (t) cc_final: 0.8384 (p) REVERT: F 46 LYS cc_start: 0.7480 (mttt) cc_final: 0.6941 (tmmt) outliers start: 6 outliers final: 5 residues processed: 74 average time/residue: 1.7558 time to fit residues: 138.6689 Evaluate side-chains 74 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 59 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.138383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.103456 restraints weight = 15911.145| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.85 r_work: 0.3071 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5265 Z= 0.190 Angle : 0.450 5.480 7161 Z= 0.240 Chirality : 0.037 0.134 855 Planarity : 0.003 0.034 905 Dihedral : 3.501 18.242 716 Min Nonbonded Distance : 2.411 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: 3.43 (0.31), residues: 660 helix: 3.61 (0.22), residues: 359 sheet: 0.46 (0.52), residues: 98 loop : 0.75 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 39 HIS 0.002 0.001 HIS B 112 PHE 0.015 0.001 PHE F 71 TYR 0.015 0.001 TYR E 35 ARG 0.002 0.000 ARG F 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6739.83 seconds wall clock time: 119 minutes 24.05 seconds (7164.05 seconds total)