Starting phenix.real_space_refine on Thu Mar 6 03:59:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ey2_28666/03_2025/8ey2_28666.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ey2_28666/03_2025/8ey2_28666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ey2_28666/03_2025/8ey2_28666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ey2_28666/03_2025/8ey2_28666.map" model { file = "/net/cci-nas-00/data/ceres_data/8ey2_28666/03_2025/8ey2_28666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ey2_28666/03_2025/8ey2_28666.cif" } resolution = 3.5 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= 1.000 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 46 5.16 5 C 3108 2.51 5 N 836 2.21 5 O 918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4908 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2370 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} bond proxies already assigned to first conformer: 2416 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "B" Number of atoms: 2370 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} bond proxies already assigned to first conformer: 2416 Time building chain proxies: 5.70, per 1000 atoms: 1.16 Number of scatterers: 4908 At special positions: 0 Unit cell: (72.483, 86.849, 74.442, 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 46 16.00 O 918 8.00 N 836 7.00 C 3108 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: 1.19 Conformation dependent library (CDL) restraints added in 1.2 seconds 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 7 sheets defined 27.8% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 200 through 215 Processing helix chain 'A' and resid 226 through 237 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 292 through 300 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 200 through 215 Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.549A pdb=" N MET B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.960A pdb=" N VAL A 68 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN A 28 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.960A pdb=" N VAL A 68 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.072A pdb=" N LYS A 102 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR A 161 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY A 149 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 148 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE A 152 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 11.604A pdb=" N THR A 111 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR A 118 " --> pdb=" O PRO A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.072A pdb=" N LYS A 102 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR A 161 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA A 173 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.949A pdb=" N VAL B 68 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASN B 28 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 103 removed outlier: 6.120A pdb=" N LYS B 102 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE B 152 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 11.637A pdb=" N THR B 111 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR B 118 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 162 through 166 removed outlier: 6.904A pdb=" N ALA B 173 " --> pdb=" O HIS B 164 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 576 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: 1.30 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1612 1.34 - 1.46: 1160 1.46 - 1.58: 2176 1.58 - 1.70: 0 1.70 - 1.81: 68 Bond restraints: 5016 Sorted by residual: bond pdb=" CG LEU B 32 " pdb=" CD1 LEU B 32 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CB MET A 264 " pdb=" CG MET A 264 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.04e-01 bond pdb=" CG LEU B 272 " pdb=" CD1 LEU B 272 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.03e-01 bond pdb=" CG LEU C -1 " pdb=" CD2 LEU C -1 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 6.95e-01 bond pdb=" CB THR B 175 " pdb=" CG2 THR B 175 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.59e-01 ... (remaining 5011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 6682 1.94 - 3.88: 119 3.88 - 5.82: 6 5.82 - 7.75: 1 7.75 - 9.69: 2 Bond angle restraints: 6810 Sorted by residual: angle pdb=" N VAL B 13 " pdb=" CA VAL B 13 " pdb=" C VAL B 13 " ideal model delta sigma weight residual 112.96 109.13 3.83 1.00e+00 1.00e+00 1.46e+01 angle pdb=" N VAL A 13 " pdb=" CA VAL A 13 " pdb=" C VAL A 13 " ideal model delta sigma weight residual 112.96 109.20 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" CA LEU C -1 " pdb=" CB LEU C -1 " pdb=" CG LEU C -1 " ideal model delta sigma weight residual 116.30 125.99 -9.69 3.50e+00 8.16e-02 7.67e+00 angle pdb=" CA LEU D -1 " pdb=" CB LEU D -1 " pdb=" CG LEU D -1 " ideal model delta sigma weight residual 116.30 125.27 -8.97 3.50e+00 8.16e-02 6.57e+00 angle pdb=" C VAL C -2 " pdb=" N LEU C -1 " pdb=" CA LEU C -1 " ideal model delta sigma weight residual 121.26 124.71 -3.45 1.59e+00 3.96e-01 4.70e+00 ... (remaining 6805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.12: 2616 14.12 - 28.24: 240 28.24 - 42.35: 88 42.35 - 56.47: 12 56.47 - 70.59: 6 Dihedral angle restraints: 2962 sinusoidal: 1142 harmonic: 1820 Sorted by residual: dihedral pdb=" CA GLN C 0 " pdb=" C GLN C 0 " pdb=" N SER C 1 " pdb=" CA SER C 1 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA LEU C -1 " pdb=" C LEU C -1 " pdb=" N GLN C 0 " pdb=" CA GLN C 0 " ideal model delta harmonic sigma weight residual -180.00 -158.79 -21.21 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA THR B 175 " pdb=" C THR B 175 " pdb=" N ASP B 176 " pdb=" CA ASP B 176 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 2959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 447 0.031 - 0.062: 218 0.062 - 0.093: 74 0.093 - 0.123: 27 0.123 - 0.154: 2 Chirality restraints: 768 Sorted by residual: chirality pdb=" CG LEU D -1 " pdb=" CB LEU D -1 " pdb=" CD1 LEU D -1 " pdb=" CD2 LEU D -1 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA VAL C -2 " pdb=" N VAL C -2 " pdb=" C VAL C -2 " pdb=" CB VAL C -2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE B 281 " pdb=" N ILE B 281 " pdb=" C ILE B 281 " pdb=" CB ILE B 281 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.24e-01 ... (remaining 765 not shown) Planarity restraints: 884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 51 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO A 52 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 51 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO B 52 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 52 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 52 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 3 " 0.011 2.00e-02 2.50e+03 1.11e-02 2.15e+00 pdb=" CG PHE D 3 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE D 3 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 3 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 3 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 3 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 3 " 0.002 2.00e-02 2.50e+03 ... (remaining 881 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 134 2.70 - 3.25: 4949 3.25 - 3.80: 8026 3.80 - 4.35: 10191 4.35 - 4.90: 17041 Nonbonded interactions: 40341 Sorted by model distance: nonbonded pdb=" OG1 THR A 292 " pdb=" OD2 ASP A 295 " model vdw 2.149 3.040 nonbonded pdb=" OG1 THR B 292 " pdb=" OD2 ASP B 295 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR A 209 " pdb=" OG SER A 254 " model vdw 2.177 3.040 nonbonded pdb=" O THR A 26 " pdb=" OG SER C 1 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR B 45 " pdb=" OD1 ASP B 48 " model vdw 2.217 3.040 ... (remaining 40336 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 116 or resid 118 through 306)) selection = (chain 'B' and (resid 1 through 116 or resid 118 through 306)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.17 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.080 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 0.034 5016 Z= 0.189 Angle : 0.600 9.693 6810 Z= 0.315 Chirality : 0.042 0.154 768 Planarity : 0.005 0.055 884 Dihedral : 13.039 70.588 1798 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.29 (0.35), residues: 628 helix: 1.88 (0.44), residues: 150 sheet: -1.02 (0.54), residues: 102 loop : -0.82 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 218 HIS 0.007 0.001 HIS A 41 PHE 0.026 0.001 PHE D 3 TYR 0.024 0.002 TYR A 239 ARG 0.002 0.000 ARG D 4 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8298 (p0) cc_final: 0.7777 (p0) REVERT: A 49 MET cc_start: 0.5976 (mmt) cc_final: 0.5328 (tpp) REVERT: A 100 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8622 (mtpp) REVERT: A 121 SER cc_start: 0.8685 (m) cc_final: 0.8476 (p) REVERT: A 214 ASN cc_start: 0.8538 (t0) cc_final: 0.8086 (t0) REVERT: A 232 LEU cc_start: 0.7767 (mt) cc_final: 0.7127 (mp) REVERT: A 286 LEU cc_start: 0.8563 (mt) cc_final: 0.8051 (pt) REVERT: C 4 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7848 (ttp80) REVERT: B 34 ASP cc_start: 0.8166 (p0) cc_final: 0.7786 (p0) REVERT: B 121 SER cc_start: 0.8664 (m) cc_final: 0.8438 (p) REVERT: B 214 ASN cc_start: 0.8604 (t0) cc_final: 0.8103 (t0) REVERT: B 232 LEU cc_start: 0.7754 (mt) cc_final: 0.7142 (mp) REVERT: B 286 LEU cc_start: 0.8542 (mt) cc_final: 0.8058 (pt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1743 time to fit residues: 38.0379 Evaluate side-chains 136 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.0070 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.138276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.117995 restraints weight = 13395.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.123380 restraints weight = 5361.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.126829 restraints weight = 2939.472| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5016 Z= 0.200 Angle : 0.662 9.415 6810 Z= 0.337 Chirality : 0.043 0.200 768 Planarity : 0.005 0.045 884 Dihedral : 5.121 20.673 680 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.65 % Allowed : 11.90 % Favored : 86.45 % 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: -0.75 (0.33), residues: 628 helix: 0.71 (0.38), residues: 168 sheet: -0.98 (0.53), residues: 102 loop : -0.92 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 218 HIS 0.009 0.001 HIS B 41 PHE 0.015 0.001 PHE D 3 TYR 0.010 0.002 TYR A 239 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8325 (p0) cc_final: 0.7766 (p0) REVERT: A 49 MET cc_start: 0.5929 (mmt) cc_final: 0.4366 (mmm) REVERT: A 214 ASN cc_start: 0.8601 (t0) cc_final: 0.8214 (t0) REVERT: A 286 LEU cc_start: 0.8538 (mt) cc_final: 0.8062 (pt) REVERT: C 4 ARG cc_start: 0.8339 (ttt90) cc_final: 0.7898 (ttp80) REVERT: B 34 ASP cc_start: 0.8203 (p0) cc_final: 0.7765 (p0) REVERT: B 214 ASN cc_start: 0.8754 (t0) cc_final: 0.8459 (t0) REVERT: B 286 LEU cc_start: 0.8529 (mt) cc_final: 0.8045 (pt) outliers start: 9 outliers final: 6 residues processed: 134 average time/residue: 0.1564 time to fit residues: 27.2776 Evaluate side-chains 128 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 12 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.132128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.111042 restraints weight = 13244.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.116343 restraints weight = 5400.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.119789 restraints weight = 3054.184| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5016 Z= 0.309 Angle : 0.670 7.536 6810 Z= 0.345 Chirality : 0.044 0.197 768 Planarity : 0.005 0.042 884 Dihedral : 5.322 23.217 680 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.30 % Allowed : 14.47 % Favored : 82.23 % 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: -0.83 (0.32), residues: 628 helix: 0.59 (0.38), residues: 168 sheet: -1.44 (0.59), residues: 80 loop : -0.86 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 218 HIS 0.007 0.001 HIS B 41 PHE 0.015 0.002 PHE B 181 TYR 0.022 0.002 TYR B 161 ARG 0.002 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8306 (p0) cc_final: 0.7863 (p0) REVERT: A 214 ASN cc_start: 0.8660 (t0) cc_final: 0.8225 (t0) REVERT: A 286 LEU cc_start: 0.8542 (mt) cc_final: 0.8094 (pt) REVERT: C 4 ARG cc_start: 0.8534 (ttt90) cc_final: 0.8034 (ttp80) REVERT: B 34 ASP cc_start: 0.8232 (p0) cc_final: 0.7776 (p0) REVERT: B 95 ASN cc_start: 0.8720 (t0) cc_final: 0.8389 (t0) REVERT: B 286 LEU cc_start: 0.8466 (mt) cc_final: 0.8043 (pt) outliers start: 18 outliers final: 14 residues processed: 121 average time/residue: 0.1401 time to fit residues: 22.6232 Evaluate side-chains 125 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain C residue -1 LEU Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 6 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 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 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.137136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115267 restraints weight = 17516.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.121151 restraints weight = 6257.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.124999 restraints weight = 3263.453| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5016 Z= 0.188 Angle : 0.619 7.915 6810 Z= 0.316 Chirality : 0.042 0.147 768 Planarity : 0.004 0.037 884 Dihedral : 5.154 25.403 680 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.38 % Allowed : 15.57 % Favored : 82.05 % 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: -0.77 (0.33), residues: 628 helix: 0.80 (0.38), residues: 172 sheet: -2.32 (0.64), residues: 56 loop : -0.83 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 218 HIS 0.010 0.001 HIS B 41 PHE 0.010 0.001 PHE A 181 TYR 0.027 0.002 TYR B 161 ARG 0.001 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8261 (p0) cc_final: 0.7832 (p0) REVERT: A 100 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8624 (mtpp) REVERT: A 214 ASN cc_start: 0.8627 (t0) cc_final: 0.8225 (t0) REVERT: A 286 LEU cc_start: 0.8514 (mt) cc_final: 0.8047 (pt) REVERT: C 4 ARG cc_start: 0.8570 (ttt90) cc_final: 0.8065 (ttp80) REVERT: B 34 ASP cc_start: 0.8237 (p0) cc_final: 0.7817 (p0) REVERT: B 95 ASN cc_start: 0.8728 (t0) cc_final: 0.8362 (t0) REVERT: B 286 LEU cc_start: 0.8489 (mt) cc_final: 0.8022 (pt) outliers start: 13 outliers final: 10 residues processed: 122 average time/residue: 0.1639 time to fit residues: 26.4306 Evaluate side-chains 116 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.0870 chunk 40 optimal weight: 7.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.133040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.111751 restraints weight = 14913.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.117244 restraints weight = 5667.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.120807 restraints weight = 3084.276| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5016 Z= 0.267 Angle : 0.686 9.054 6810 Z= 0.349 Chirality : 0.043 0.141 768 Planarity : 0.004 0.036 884 Dihedral : 5.263 24.676 680 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.75 % Allowed : 17.40 % Favored : 79.85 % 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: -0.88 (0.33), residues: 628 helix: 0.57 (0.38), residues: 172 sheet: -2.36 (0.63), residues: 56 loop : -0.83 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 218 HIS 0.008 0.001 HIS B 41 PHE 0.011 0.001 PHE B 181 TYR 0.031 0.002 TYR B 161 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.577 Fit side-chains REVERT: A 34 ASP cc_start: 0.8293 (p0) cc_final: 0.7834 (p0) REVERT: A 49 MET cc_start: 0.6714 (mmt) cc_final: 0.5880 (mmm) REVERT: A 119 ASN cc_start: 0.7982 (t0) cc_final: 0.7751 (t0) REVERT: A 214 ASN cc_start: 0.8688 (t0) cc_final: 0.8266 (t0) REVERT: A 286 LEU cc_start: 0.8506 (mt) cc_final: 0.8061 (pt) REVERT: C 4 ARG cc_start: 0.8635 (ttt90) cc_final: 0.8066 (ttp80) REVERT: B 95 ASN cc_start: 0.8670 (t0) cc_final: 0.8353 (t0) REVERT: B 119 ASN cc_start: 0.8064 (t0) cc_final: 0.7819 (t0) REVERT: B 286 LEU cc_start: 0.8518 (mt) cc_final: 0.8059 (pt) outliers start: 15 outliers final: 12 residues processed: 117 average time/residue: 0.1304 time to fit residues: 20.8393 Evaluate side-chains 117 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.137440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116226 restraints weight = 14776.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.121817 restraints weight = 5666.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.125405 restraints weight = 3080.432| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5016 Z= 0.177 Angle : 0.619 9.514 6810 Z= 0.315 Chirality : 0.041 0.140 768 Planarity : 0.004 0.037 884 Dihedral : 5.078 22.895 680 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.20 % Allowed : 18.32 % Favored : 79.49 % 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: -0.74 (0.33), residues: 628 helix: 0.85 (0.39), residues: 172 sheet: -1.63 (0.56), residues: 78 loop : -0.86 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 218 HIS 0.006 0.001 HIS B 41 PHE 0.009 0.001 PHE A 181 TYR 0.031 0.002 TYR B 161 ARG 0.001 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.581 Fit side-chains REVERT: A 34 ASP cc_start: 0.8290 (p0) cc_final: 0.7871 (p0) REVERT: A 49 MET cc_start: 0.6840 (mmt) cc_final: 0.6087 (mmm) REVERT: A 119 ASN cc_start: 0.7931 (t0) cc_final: 0.7657 (t0) REVERT: A 165 MET cc_start: 0.7367 (mtt) cc_final: 0.7076 (mtt) REVERT: A 214 ASN cc_start: 0.8660 (t0) cc_final: 0.8272 (t0) REVERT: A 286 LEU cc_start: 0.8472 (mt) cc_final: 0.8034 (pt) REVERT: C 0 GLN cc_start: 0.6987 (mp10) cc_final: 0.6677 (mm-40) REVERT: C 4 ARG cc_start: 0.8655 (ttt90) cc_final: 0.8134 (ttp80) REVERT: B 34 ASP cc_start: 0.8260 (p0) cc_final: 0.7887 (p0) REVERT: B 119 ASN cc_start: 0.7971 (t0) cc_final: 0.7685 (t0) REVERT: B 286 LEU cc_start: 0.8510 (mt) cc_final: 0.8012 (pt) outliers start: 12 outliers final: 11 residues processed: 113 average time/residue: 0.1357 time to fit residues: 20.7146 Evaluate side-chains 115 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 0.0070 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.138943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.117430 restraints weight = 17811.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.123265 restraints weight = 6258.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.127015 restraints weight = 3236.834| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5016 Z= 0.160 Angle : 0.621 8.617 6810 Z= 0.318 Chirality : 0.042 0.134 768 Planarity : 0.004 0.037 884 Dihedral : 4.933 21.736 680 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.01 % Allowed : 19.05 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.85 (0.33), residues: 628 helix: 0.66 (0.39), residues: 172 sheet: -1.63 (0.55), residues: 78 loop : -0.89 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 218 HIS 0.007 0.001 HIS A 41 PHE 0.010 0.001 PHE A 223 TYR 0.030 0.002 TYR A 161 ARG 0.001 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.579 Fit side-chains REVERT: A 34 ASP cc_start: 0.8303 (p0) cc_final: 0.7718 (p0) REVERT: A 49 MET cc_start: 0.6791 (mmt) cc_final: 0.6105 (mmm) REVERT: A 119 ASN cc_start: 0.7924 (t0) cc_final: 0.7632 (t0) REVERT: A 214 ASN cc_start: 0.8686 (t0) cc_final: 0.8293 (t0) REVERT: A 286 LEU cc_start: 0.8474 (mt) cc_final: 0.8027 (pt) REVERT: C 0 GLN cc_start: 0.6674 (mp10) cc_final: 0.6121 (mp10) REVERT: C 4 ARG cc_start: 0.8687 (ttt90) cc_final: 0.8103 (ttp80) REVERT: B 34 ASP cc_start: 0.8290 (p0) cc_final: 0.7903 (p0) REVERT: B 119 ASN cc_start: 0.7912 (t0) cc_final: 0.7580 (t0) REVERT: B 286 LEU cc_start: 0.8519 (mt) cc_final: 0.7982 (pt) outliers start: 11 outliers final: 10 residues processed: 113 average time/residue: 0.1330 time to fit residues: 20.4806 Evaluate side-chains 110 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 65 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.132920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.112577 restraints weight = 11739.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.117645 restraints weight = 5005.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.120916 restraints weight = 2890.344| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5016 Z= 0.288 Angle : 0.665 9.736 6810 Z= 0.340 Chirality : 0.044 0.166 768 Planarity : 0.004 0.037 884 Dihedral : 5.212 25.519 680 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.01 % Allowed : 19.78 % Favored : 78.21 % 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: -0.82 (0.33), residues: 628 helix: 0.83 (0.38), residues: 172 sheet: -1.74 (0.55), residues: 78 loop : -0.92 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 218 HIS 0.006 0.001 HIS A 41 PHE 0.011 0.001 PHE B 181 TYR 0.030 0.002 TYR B 161 ARG 0.003 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.549 Fit side-chains REVERT: A 34 ASP cc_start: 0.8309 (p0) cc_final: 0.7845 (p0) REVERT: A 214 ASN cc_start: 0.8720 (t0) cc_final: 0.8329 (t0) REVERT: A 286 LEU cc_start: 0.8518 (mt) cc_final: 0.8087 (pt) REVERT: C 4 ARG cc_start: 0.8711 (ttt90) cc_final: 0.8202 (ttp80) REVERT: B 34 ASP cc_start: 0.8301 (p0) cc_final: 0.7877 (p0) REVERT: B 286 LEU cc_start: 0.8560 (mt) cc_final: 0.8105 (pt) outliers start: 11 outliers final: 9 residues processed: 126 average time/residue: 0.1291 time to fit residues: 22.1575 Evaluate side-chains 114 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.135988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113909 restraints weight = 16810.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119726 restraints weight = 6108.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.123493 restraints weight = 3253.647| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5016 Z= 0.211 Angle : 0.648 7.316 6810 Z= 0.337 Chirality : 0.043 0.148 768 Planarity : 0.004 0.038 884 Dihedral : 5.192 24.634 680 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.38 % Allowed : 19.23 % Favored : 78.39 % 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: -0.94 (0.33), residues: 628 helix: 0.72 (0.38), residues: 172 sheet: -1.69 (0.55), residues: 78 loop : -1.03 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 207 HIS 0.006 0.001 HIS B 41 PHE 0.009 0.001 PHE B 181 TYR 0.030 0.002 TYR A 161 ARG 0.003 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.592 Fit side-chains REVERT: A 34 ASP cc_start: 0.8288 (p0) cc_final: 0.7839 (p0) REVERT: A 214 ASN cc_start: 0.8698 (t0) cc_final: 0.8304 (t0) REVERT: A 286 LEU cc_start: 0.8497 (mt) cc_final: 0.8067 (pt) REVERT: C 4 ARG cc_start: 0.8709 (ttt90) cc_final: 0.8041 (ttp80) REVERT: B 34 ASP cc_start: 0.8299 (p0) cc_final: 0.7887 (p0) REVERT: B 270 GLU cc_start: 0.7496 (pm20) cc_final: 0.7279 (pm20) REVERT: B 286 LEU cc_start: 0.8554 (mt) cc_final: 0.8133 (pt) outliers start: 13 outliers final: 10 residues processed: 120 average time/residue: 0.1325 time to fit residues: 21.8457 Evaluate side-chains 113 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 28 optimal weight: 0.0970 chunk 60 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 0.0010 chunk 36 optimal weight: 0.0050 chunk 41 optimal weight: 0.4980 chunk 11 optimal weight: 0.0030 chunk 7 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 overall best weight: 0.1208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.141609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.121476 restraints weight = 12648.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.126715 restraints weight = 5189.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.130071 restraints weight = 2896.438| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5016 Z= 0.161 Angle : 0.629 7.152 6810 Z= 0.330 Chirality : 0.042 0.122 768 Planarity : 0.005 0.039 884 Dihedral : 5.020 22.056 680 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.73 % Allowed : 20.88 % Favored : 78.39 % 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: -1.06 (0.32), residues: 628 helix: 0.84 (0.39), residues: 172 sheet: -1.69 (0.52), residues: 82 loop : -1.24 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 207 HIS 0.004 0.001 HIS B 164 PHE 0.009 0.001 PHE B 294 TYR 0.030 0.002 TYR A 161 ARG 0.001 0.000 ARG D 4 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.538 Fit side-chains REVERT: A 34 ASP cc_start: 0.8269 (p0) cc_final: 0.7869 (p0) REVERT: A 49 MET cc_start: 0.5902 (mmm) cc_final: 0.4724 (mmm) REVERT: A 214 ASN cc_start: 0.8594 (t0) cc_final: 0.8221 (t0) REVERT: C 4 ARG cc_start: 0.8678 (ttt90) cc_final: 0.8041 (ttp80) REVERT: B 6 MET cc_start: 0.7981 (ttt) cc_final: 0.7629 (ttp) REVERT: B 34 ASP cc_start: 0.8286 (p0) cc_final: 0.7912 (p0) REVERT: B 270 GLU cc_start: 0.7389 (pm20) cc_final: 0.7149 (pm20) REVERT: B 286 LEU cc_start: 0.8520 (mt) cc_final: 0.8108 (pt) outliers start: 4 outliers final: 3 residues processed: 116 average time/residue: 0.1426 time to fit residues: 22.2511 Evaluate side-chains 104 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 28 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 8 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 21 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.139957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.120378 restraints weight = 10890.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125316 restraints weight = 4762.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.128519 restraints weight = 2745.691| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5016 Z= 0.172 Angle : 0.664 9.892 6810 Z= 0.340 Chirality : 0.043 0.156 768 Planarity : 0.004 0.038 884 Dihedral : 4.951 21.243 680 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.10 % Allowed : 21.98 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.12 (0.32), residues: 628 helix: 0.67 (0.39), residues: 172 sheet: -1.73 (0.51), residues: 82 loop : -1.21 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 207 HIS 0.004 0.001 HIS B 41 PHE 0.008 0.001 PHE A 181 TYR 0.029 0.002 TYR A 161 ARG 0.002 0.000 ARG A 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2033.01 seconds wall clock time: 35 minutes 59.55 seconds (2159.55 seconds total)