Starting phenix.real_space_refine on Tue Feb 11 11:57:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7saz_24959/02_2025/7saz_24959.cif Found real_map, /net/cci-nas-00/data/ceres_data/7saz_24959/02_2025/7saz_24959.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/7saz_24959/02_2025/7saz_24959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7saz_24959/02_2025/7saz_24959.map" model { file = "/net/cci-nas-00/data/ceres_data/7saz_24959/02_2025/7saz_24959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7saz_24959/02_2025/7saz_24959.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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 3743 2.51 5 N 896 2.21 5 O 1044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5708 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1740 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 4, 'TRANS': 212} Chain: "B" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1723 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain: "C" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 472 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "D" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 456 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain: "F" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 442 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "G" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 442 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Time building chain proxies: 3.81, per 1000 atoms: 0.67 Number of scatterers: 5708 At special positions: 0 Unit cell: (68.224, 75.712, 114.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1044 8.00 N 896 7.00 C 3743 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 676.6 milliseconds 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1294 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 4 sheets defined 77.6% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 6 through 22 Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 28 through 67 removed outlier: 3.706A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 101 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.547A pdb=" N VAL A 112 " --> pdb=" O ASP A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 130 through 150 Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 183 through 190 Processing helix chain 'A' and resid 193 through 221 removed outlier: 3.712A pdb=" N LYS A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 29 removed outlier: 3.853A pdb=" N MET B 11 " --> pdb=" O PRO B 7 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU B 17 " --> pdb=" O ASN B 13 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 67 removed outlier: 3.673A pdb=" N GLY B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 101 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 132 through 152 removed outlier: 3.536A pdb=" N VAL B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.727A pdb=" N GLU B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 218 Processing helix chain 'C' and resid 8 through 33 removed outlier: 3.719A pdb=" N PHE C 12 " --> pdb=" O THR C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 65 removed outlier: 3.551A pdb=" N ALA C 64 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE C 65 " --> pdb=" O PHE C 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 33 Processing helix chain 'D' and resid 43 through 63 removed outlier: 4.080A pdb=" N PHE D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 48 " --> pdb=" O GLY D 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 33 Processing helix chain 'E' and resid 43 through 65 removed outlier: 4.010A pdb=" N PHE E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR E 55 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE E 65 " --> pdb=" O PHE E 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 33 removed outlier: 4.684A pdb=" N TYR F 16 " --> pdb=" O PHE F 12 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY F 17 " --> pdb=" O GLN F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 63 removed outlier: 3.959A pdb=" N PHE F 47 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU F 48 " --> pdb=" O GLY F 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 33 Processing helix chain 'G' and resid 43 through 64 removed outlier: 4.079A pdb=" N PHE G 47 " --> pdb=" O LEU G 43 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA3, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA4, first strand: chain 'B' and resid 174 through 175 434 hydrogen bonds defined for protein. 1281 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: 1.76 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1786 1.34 - 1.46: 897 1.46 - 1.57: 3090 1.57 - 1.69: 0 1.69 - 1.80: 50 Bond restraints: 5823 Sorted by residual: bond pdb=" CG LEU B 42 " pdb=" CD2 LEU B 42 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.75e+00 bond pdb=" CG1 ILE D 59 " pdb=" CD1 ILE D 59 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.43e+00 bond pdb=" CG MET B 11 " pdb=" SD MET B 11 " ideal model delta sigma weight residual 1.803 1.769 0.034 2.50e-02 1.60e+03 1.84e+00 bond pdb=" CA GLY F 40 " pdb=" C GLY F 40 " ideal model delta sigma weight residual 1.514 1.531 -0.016 1.41e-02 5.03e+03 1.37e+00 bond pdb=" CG1 ILE F 59 " pdb=" CD1 ILE F 59 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.35e+00 ... (remaining 5818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 7673 1.98 - 3.96: 126 3.96 - 5.94: 14 5.94 - 7.92: 2 7.92 - 9.90: 1 Bond angle restraints: 7816 Sorted by residual: angle pdb=" N GLU B 47 " pdb=" CA GLU B 47 " pdb=" CB GLU B 47 " ideal model delta sigma weight residual 110.12 114.89 -4.77 1.47e+00 4.63e-01 1.05e+01 angle pdb=" CA MET B 11 " pdb=" CB MET B 11 " pdb=" CG MET B 11 " ideal model delta sigma weight residual 114.10 107.86 6.24 2.00e+00 2.50e-01 9.74e+00 angle pdb=" C MET A 113 " pdb=" N ASP A 114 " pdb=" CA ASP A 114 " ideal model delta sigma weight residual 121.54 127.11 -5.57 1.91e+00 2.74e-01 8.50e+00 angle pdb=" C THR A 157 " pdb=" N TYR A 158 " pdb=" CA TYR A 158 " ideal model delta sigma weight residual 121.54 127.01 -5.47 1.91e+00 2.74e-01 8.20e+00 angle pdb=" C ILE A 12 " pdb=" N ASN A 13 " pdb=" CA ASN A 13 " ideal model delta sigma weight residual 121.14 116.17 4.97 1.75e+00 3.27e-01 8.06e+00 ... (remaining 7811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 2962 15.25 - 30.50: 323 30.50 - 45.74: 90 45.74 - 60.99: 10 60.99 - 76.24: 6 Dihedral angle restraints: 3391 sinusoidal: 1355 harmonic: 2036 Sorted by residual: dihedral pdb=" CA MET A 113 " pdb=" C MET A 113 " pdb=" N ASP A 114 " pdb=" CA ASP A 114 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA TYR A 158 " pdb=" C TYR A 158 " pdb=" N GLY A 159 " pdb=" CA GLY A 159 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA PRO B 131 " pdb=" C PRO B 131 " pdb=" N GLU B 132 " pdb=" CA GLU B 132 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 3388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 665 0.050 - 0.101: 161 0.101 - 0.151: 12 0.151 - 0.202: 1 0.202 - 0.252: 1 Chirality restraints: 840 Sorted by residual: chirality pdb=" CG LEU B 42 " pdb=" CB LEU B 42 " pdb=" CD1 LEU B 42 " pdb=" CD2 LEU B 42 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ASP A 114 " pdb=" N ASP A 114 " pdb=" C ASP A 114 " pdb=" CB ASP A 114 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA PRO A 131 " pdb=" N PRO A 131 " pdb=" C PRO A 131 " pdb=" CB PRO A 131 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 837 not shown) Planarity restraints: 997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 130 " -0.052 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO B 131 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 131 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 131 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 130 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 131 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 66 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO C 67 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 67 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 67 " 0.017 5.00e-02 4.00e+02 ... (remaining 994 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 348 2.73 - 3.27: 6021 3.27 - 3.82: 9696 3.82 - 4.36: 11341 4.36 - 4.90: 19652 Nonbonded interactions: 47058 Sorted by model distance: nonbonded pdb=" OH TYR A 187 " pdb=" OE1 GLU B 30 " model vdw 2.188 3.040 nonbonded pdb=" NH2 ARG B 8 " pdb=" OE2 GLU C 56 " model vdw 2.237 3.120 nonbonded pdb=" ND2 ASN B 186 " pdb=" OE1 GLU B 190 " model vdw 2.285 3.120 nonbonded pdb=" O ILE F 59 " pdb=" OG SER F 63 " model vdw 2.287 3.040 nonbonded pdb=" OE1 GLU B 98 " pdb=" NZ LYS B 122 " model vdw 2.291 3.120 ... (remaining 47053 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 6 through 220) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 10 through 65) selection = (chain 'D' and resid 10 through 65) selection = chain 'E' selection = (chain 'F' and resid 10 through 65) selection = (chain 'G' and resid 10 through 65) } 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: 1.090 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.940 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 5823 Z= 0.271 Angle : 0.628 9.899 7816 Z= 0.354 Chirality : 0.041 0.252 840 Planarity : 0.004 0.077 997 Dihedral : 13.698 76.236 2097 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.67 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: 0.22 (0.31), residues: 708 helix: 1.14 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -3.14 (0.40), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 34 HIS 0.010 0.002 HIS G 33 PHE 0.013 0.001 PHE A 123 TYR 0.020 0.002 TYR B 216 ARG 0.015 0.001 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.591 Fit side-chains REVERT: A 173 ASP cc_start: 0.8789 (m-30) cc_final: 0.8425 (m-30) REVERT: B 100 MET cc_start: 0.8448 (mmp) cc_final: 0.8242 (mmt) REVERT: B 203 MET cc_start: 0.7223 (tpp) cc_final: 0.6960 (tpt) REVERT: B 207 ASP cc_start: 0.7846 (m-30) cc_final: 0.7641 (m-30) REVERT: C 10 LYS cc_start: 0.8166 (pptt) cc_final: 0.7060 (mptt) REVERT: D 14 MET cc_start: 0.8412 (ttm) cc_final: 0.8189 (ttp) REVERT: F 14 MET cc_start: 0.7609 (ttm) cc_final: 0.7184 (ttt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 1.2691 time to fit residues: 177.3002 Evaluate side-chains 94 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.8980 chunk 51 optimal weight: 0.0270 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN A 121 GLN B 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.149208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.112045 restraints weight = 6817.785| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.30 r_work: 0.3089 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5823 Z= 0.172 Angle : 0.501 6.282 7816 Z= 0.277 Chirality : 0.038 0.178 840 Planarity : 0.003 0.047 997 Dihedral : 4.440 26.114 752 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.55 % Allowed : 12.05 % Favored : 85.40 % 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: 1.16 (0.31), residues: 708 helix: 1.88 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -3.08 (0.41), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 34 HIS 0.004 0.001 HIS D 33 PHE 0.011 0.001 PHE C 47 TYR 0.015 0.001 TYR E 16 ARG 0.003 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7457 (p0) cc_final: 0.6666 (m-40) REVERT: A 105 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7733 (tm-30) REVERT: B 73 GLU cc_start: 0.7917 (pp20) cc_final: 0.7604 (tm-30) REVERT: B 100 MET cc_start: 0.8575 (mmp) cc_final: 0.8308 (mmt) REVERT: D 14 MET cc_start: 0.8558 (ttm) cc_final: 0.8335 (ttp) REVERT: F 14 MET cc_start: 0.7445 (ttm) cc_final: 0.7224 (ttt) outliers start: 15 outliers final: 3 residues processed: 103 average time/residue: 1.2940 time to fit residues: 139.0265 Evaluate side-chains 84 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 65 optimal weight: 0.0060 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 0.0050 chunk 25 optimal weight: 3.9990 overall best weight: 0.3810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN B 102 GLN B 172 ASN B 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114561 restraints weight = 6827.623| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.30 r_work: 0.3119 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5823 Z= 0.130 Angle : 0.454 5.864 7816 Z= 0.253 Chirality : 0.037 0.172 840 Planarity : 0.003 0.048 997 Dihedral : 4.117 25.577 752 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.53 % Allowed : 16.13 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.64 (0.31), residues: 708 helix: 2.27 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -3.09 (0.40), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 34 HIS 0.003 0.001 HIS D 33 PHE 0.008 0.001 PHE D 60 TYR 0.013 0.001 TYR E 16 ARG 0.005 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7317 (p0) cc_final: 0.6689 (m-40) REVERT: A 58 GLN cc_start: 0.7512 (mt0) cc_final: 0.7309 (mt0) REVERT: A 61 GLU cc_start: 0.7629 (tp30) cc_final: 0.6948 (tm-30) REVERT: A 219 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.6958 (mtp) REVERT: B 73 GLU cc_start: 0.7937 (pp20) cc_final: 0.7607 (tm-30) REVERT: C 36 ILE cc_start: 0.7780 (tt) cc_final: 0.7490 (tp) outliers start: 9 outliers final: 3 residues processed: 105 average time/residue: 1.2012 time to fit residues: 131.9304 Evaluate side-chains 92 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 0.0670 chunk 16 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 102 GLN B 172 ASN B 213 GLN D 13 GLN G 33 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.148476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.111259 restraints weight = 6905.739| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.21 r_work: 0.3080 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5823 Z= 0.246 Angle : 0.507 6.527 7816 Z= 0.273 Chirality : 0.040 0.300 840 Planarity : 0.003 0.046 997 Dihedral : 4.169 24.065 752 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.72 % Allowed : 17.66 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.31), residues: 708 helix: 2.25 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -3.07 (0.41), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 184 HIS 0.004 0.001 HIS G 33 PHE 0.011 0.001 PHE D 60 TYR 0.017 0.001 TYR E 16 ARG 0.005 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7434 (p0) cc_final: 0.6677 (m-40) REVERT: A 61 GLU cc_start: 0.7636 (tp30) cc_final: 0.7329 (tt0) REVERT: A 111 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8184 (pt0) REVERT: A 219 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7116 (mtp) REVERT: B 79 LYS cc_start: 0.8371 (mtpt) cc_final: 0.8142 (mtpp) REVERT: B 102 GLN cc_start: 0.8239 (pt0) cc_final: 0.7960 (pp30) REVERT: C 48 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8397 (mt) outliers start: 16 outliers final: 7 residues processed: 99 average time/residue: 1.2860 time to fit residues: 132.8570 Evaluate side-chains 98 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN B 172 ASN B 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.113987 restraints weight = 6788.418| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.23 r_work: 0.3168 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5823 Z= 0.147 Angle : 0.474 11.471 7816 Z= 0.256 Chirality : 0.038 0.296 840 Planarity : 0.003 0.049 997 Dihedral : 4.008 25.229 752 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.89 % Allowed : 18.34 % Favored : 78.78 % 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: 1.83 (0.31), residues: 708 helix: 2.41 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -3.04 (0.40), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 34 HIS 0.004 0.001 HIS G 33 PHE 0.009 0.001 PHE D 60 TYR 0.017 0.001 TYR E 16 ARG 0.005 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7421 (p0) cc_final: 0.6769 (m-40) REVERT: A 61 GLU cc_start: 0.7706 (tp30) cc_final: 0.7414 (tt0) REVERT: A 105 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: A 219 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7352 (mtp) REVERT: B 73 GLU cc_start: 0.7889 (pp20) cc_final: 0.7537 (tm-30) REVERT: B 79 LYS cc_start: 0.8419 (mtpt) cc_final: 0.8179 (mtpp) REVERT: B 102 GLN cc_start: 0.8211 (pt0) cc_final: 0.7899 (pp30) REVERT: C 48 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8567 (mt) outliers start: 17 outliers final: 6 residues processed: 105 average time/residue: 1.2256 time to fit residues: 134.6551 Evaluate side-chains 99 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN B 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.113738 restraints weight = 6822.068| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.21 r_work: 0.3098 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5823 Z= 0.190 Angle : 0.480 8.939 7816 Z= 0.260 Chirality : 0.039 0.290 840 Planarity : 0.003 0.048 997 Dihedral : 4.001 24.554 752 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.89 % Allowed : 19.52 % Favored : 77.59 % 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: 1.83 (0.31), residues: 708 helix: 2.39 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -2.97 (0.41), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 184 HIS 0.003 0.001 HIS G 33 PHE 0.010 0.001 PHE A 75 TYR 0.017 0.001 TYR E 16 ARG 0.006 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7306 (p0) cc_final: 0.6541 (m-40) REVERT: A 61 GLU cc_start: 0.7681 (tp30) cc_final: 0.7373 (tt0) REVERT: A 219 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7258 (mtp) REVERT: B 73 GLU cc_start: 0.7901 (pp20) cc_final: 0.7522 (tm-30) REVERT: B 79 LYS cc_start: 0.8372 (mtpt) cc_final: 0.8100 (mtpp) REVERT: B 102 GLN cc_start: 0.8248 (pt0) cc_final: 0.7907 (pp30) outliers start: 17 outliers final: 9 residues processed: 103 average time/residue: 1.2707 time to fit residues: 136.5449 Evaluate side-chains 102 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 0.0370 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.152039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.114812 restraints weight = 6880.154| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.24 r_work: 0.3124 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5823 Z= 0.152 Angle : 0.467 7.030 7816 Z= 0.255 Chirality : 0.038 0.217 840 Planarity : 0.003 0.051 997 Dihedral : 3.936 24.811 752 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.06 % Allowed : 19.69 % Favored : 77.25 % 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: 1.97 (0.31), residues: 708 helix: 2.46 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -2.81 (0.41), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 34 HIS 0.004 0.001 HIS G 33 PHE 0.009 0.001 PHE D 60 TYR 0.014 0.001 TYR E 16 ARG 0.006 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7661 (tp30) cc_final: 0.7389 (tt0) REVERT: A 105 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: B 73 GLU cc_start: 0.7884 (pp20) cc_final: 0.7518 (tm-30) REVERT: B 79 LYS cc_start: 0.8379 (mtpt) cc_final: 0.8095 (mtpp) REVERT: B 102 GLN cc_start: 0.8268 (pt0) cc_final: 0.7916 (pp30) REVERT: C 48 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8410 (mt) outliers start: 18 outliers final: 7 residues processed: 109 average time/residue: 1.2121 time to fit residues: 138.4053 Evaluate side-chains 97 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 0.0040 chunk 39 optimal weight: 0.8980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.151861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.115101 restraints weight = 6736.705| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.20 r_work: 0.3115 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5823 Z= 0.155 Angle : 0.474 9.564 7816 Z= 0.257 Chirality : 0.039 0.354 840 Planarity : 0.003 0.052 997 Dihedral : 3.874 24.414 752 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.04 % Allowed : 21.56 % Favored : 76.40 % 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: 2.01 (0.32), residues: 708 helix: 2.47 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -2.73 (0.42), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 184 HIS 0.003 0.001 HIS G 33 PHE 0.008 0.001 PHE D 60 TYR 0.017 0.001 TYR E 16 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7651 (tp30) cc_final: 0.7390 (tt0) REVERT: A 105 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: A 219 MET cc_start: 0.8011 (mtp) cc_final: 0.7805 (mtp) REVERT: B 73 GLU cc_start: 0.7895 (pp20) cc_final: 0.7523 (tm-30) REVERT: B 79 LYS cc_start: 0.8365 (mtpt) cc_final: 0.8080 (mtpp) REVERT: B 102 GLN cc_start: 0.8254 (pt0) cc_final: 0.7916 (pp30) REVERT: C 48 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8423 (mt) outliers start: 12 outliers final: 8 residues processed: 101 average time/residue: 1.2268 time to fit residues: 129.6802 Evaluate side-chains 98 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN B 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.148947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.111472 restraints weight = 6850.548| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.26 r_work: 0.3096 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5823 Z= 0.215 Angle : 0.531 15.091 7816 Z= 0.280 Chirality : 0.042 0.514 840 Planarity : 0.003 0.051 997 Dihedral : 3.959 23.377 752 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.72 % Allowed : 21.90 % Favored : 75.38 % 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: 1.83 (0.31), residues: 708 helix: 2.30 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -2.66 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 184 HIS 0.003 0.001 HIS G 33 PHE 0.008 0.001 PHE D 60 TYR 0.020 0.001 TYR E 16 ARG 0.007 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7648 (tp30) cc_final: 0.7378 (tt0) REVERT: A 105 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: B 73 GLU cc_start: 0.7926 (pp20) cc_final: 0.7522 (tm-30) REVERT: B 79 LYS cc_start: 0.8392 (mtpt) cc_final: 0.8095 (mtpp) REVERT: B 102 GLN cc_start: 0.8300 (pt0) cc_final: 0.8030 (pp30) REVERT: C 48 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8427 (mt) outliers start: 16 outliers final: 8 residues processed: 103 average time/residue: 1.2612 time to fit residues: 135.8487 Evaluate side-chains 105 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.149890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.112501 restraints weight = 6939.327| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.26 r_work: 0.3093 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5823 Z= 0.195 Angle : 0.526 15.178 7816 Z= 0.278 Chirality : 0.041 0.492 840 Planarity : 0.003 0.053 997 Dihedral : 3.952 24.033 752 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.04 % Allowed : 22.75 % Favored : 75.21 % 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: 1.87 (0.31), residues: 708 helix: 2.33 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -2.63 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 184 HIS 0.003 0.001 HIS G 33 PHE 0.009 0.001 PHE D 60 TYR 0.020 0.001 TYR E 16 ARG 0.007 0.001 ARG B 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.6885 (mptt) cc_final: 0.6638 (mmtm) REVERT: A 61 GLU cc_start: 0.7608 (tp30) cc_final: 0.7321 (tt0) REVERT: A 105 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: B 73 GLU cc_start: 0.7924 (pp20) cc_final: 0.7517 (tm-30) REVERT: B 79 LYS cc_start: 0.8369 (mtpt) cc_final: 0.8071 (mtpp) REVERT: B 102 GLN cc_start: 0.8269 (pt0) cc_final: 0.7964 (pp30) outliers start: 12 outliers final: 8 residues processed: 108 average time/residue: 1.2512 time to fit residues: 141.1695 Evaluate side-chains 104 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 66 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.148403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.111375 restraints weight = 6912.709| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.21 r_work: 0.3066 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5823 Z= 0.283 Angle : 0.567 15.203 7816 Z= 0.299 Chirality : 0.043 0.520 840 Planarity : 0.003 0.055 997 Dihedral : 4.091 23.190 752 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.70 % Allowed : 22.92 % Favored : 75.38 % 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: 1.63 (0.31), residues: 708 helix: 2.16 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -2.69 (0.42), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 184 HIS 0.003 0.001 HIS D 33 PHE 0.010 0.001 PHE D 60 TYR 0.021 0.001 TYR E 16 ARG 0.008 0.001 ARG B 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4605.95 seconds wall clock time: 81 minutes 54.21 seconds (4914.21 seconds total)