Starting phenix.real_space_refine on Thu Mar 13 05:38:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s82_24889/03_2025/7s82_24889.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s82_24889/03_2025/7s82_24889.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/7s82_24889/03_2025/7s82_24889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s82_24889/03_2025/7s82_24889.map" model { file = "/net/cci-nas-00/data/ceres_data/7s82_24889/03_2025/7s82_24889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s82_24889/03_2025/7s82_24889.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 Anisotropic ADP refinement not supported. Converting 4806 atoms to isotropic. 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 44 5.16 5 C 3104 2.51 5 N 836 2.21 5 O 920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4904 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2368 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 292} 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: "B" Number of atoms: 2368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2368 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Time building chain proxies: 3.47, per 1000 atoms: 0.71 Number of scatterers: 4904 At special positions: 0 Unit cell: (73.789, 88.808, 73.789, 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 44 16.00 O 920 8.00 N 836 7.00 C 3104 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: 1.18 Conformation dependent library (CDL) restraints added in 627.4 milliseconds 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 9 sheets defined 28.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 removed outlier: 4.306A pdb=" N GLY A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 53 through 61 removed outlier: 3.725A pdb=" N ILE A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 226 through 236 removed outlier: 4.239A pdb=" N LYS A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) 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 301 Processing helix chain 'B' and resid 10 through 15 removed outlier: 4.113A pdb=" N GLY B 15 " --> pdb=" O GLY B 11 " (cutoff:3.500A) 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 45 through 49 removed outlier: 3.698A pdb=" N MET B 49 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 removed outlier: 3.780A pdb=" N ILE B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 214 Processing helix chain 'B' and resid 226 through 236 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 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: 4.165A pdb=" N VAL A 68 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 25 " --> pdb=" O CYS A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 removed outlier: 4.192A pdb=" N GLY A 79 " --> pdb=" O LYS A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.616A pdb=" N TYR A 126 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 166 removed outlier: 7.006A pdb=" N ALA A 173 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 75 removed outlier: 4.256A pdb=" N VAL B 68 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ASN B 28 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS B 38 " --> pdb=" O LEU B 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 73 through 75 removed outlier: 4.256A pdb=" N VAL B 68 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 118 removed outlier: 5.681A pdb=" N TYR B 118 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 166 removed outlier: 6.853A pdb=" N ALA B 173 " --> pdb=" O HIS B 164 " (cutoff:3.500A) 170 hydrogen bonds defined for protein. 462 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: 1.15 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: 1.22 - 1.34: 1603 1.34 - 1.45: 759 1.45 - 1.57: 2582 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 5010 Sorted by residual: bond pdb=" CA MET B 82 " pdb=" C MET B 82 " ideal model delta sigma weight residual 1.533 1.513 0.020 9.60e-03 1.09e+04 4.17e+00 bond pdb=" CB THR A 175 " pdb=" CG2 THR A 175 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.18e+00 bond pdb=" CG MET B 264 " pdb=" SD MET B 264 " ideal model delta sigma weight residual 1.803 1.768 0.035 2.50e-02 1.60e+03 1.94e+00 bond pdb=" C PRO A 122 " pdb=" N SER A 123 " ideal model delta sigma weight residual 1.331 1.307 0.024 1.73e-02 3.34e+03 1.90e+00 bond pdb=" CG LEU B 87 " pdb=" CD1 LEU B 87 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.85e+00 ... (remaining 5005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 6465 1.47 - 2.94: 261 2.94 - 4.41: 60 4.41 - 5.87: 10 5.87 - 7.34: 4 Bond angle restraints: 6800 Sorted by residual: angle pdb=" CA MET B 6 " pdb=" CB MET B 6 " pdb=" CG MET B 6 " ideal model delta sigma weight residual 114.10 121.44 -7.34 2.00e+00 2.50e-01 1.35e+01 angle pdb=" CG MET B 264 " pdb=" SD MET B 264 " pdb=" CE MET B 264 " ideal model delta sigma weight residual 100.90 94.43 6.47 2.20e+00 2.07e-01 8.65e+00 angle pdb=" N ILE A 78 " pdb=" CA ILE A 78 " pdb=" C ILE A 78 " ideal model delta sigma weight residual 111.88 108.85 3.03 1.06e+00 8.90e-01 8.20e+00 angle pdb=" CA GLN B 83 " pdb=" CB GLN B 83 " pdb=" CG GLN B 83 " ideal model delta sigma weight residual 114.10 119.76 -5.66 2.00e+00 2.50e-01 8.00e+00 angle pdb=" N GLN B 83 " pdb=" CA GLN B 83 " pdb=" C GLN B 83 " ideal model delta sigma weight residual 110.36 106.14 4.22 1.55e+00 4.16e-01 7.40e+00 ... (remaining 6795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 2694 17.98 - 35.95: 223 35.95 - 53.93: 30 53.93 - 71.90: 4 71.90 - 89.88: 3 Dihedral angle restraints: 2954 sinusoidal: 1142 harmonic: 1812 Sorted by residual: dihedral pdb=" CA GLN B 83 " pdb=" C GLN B 83 " pdb=" N ASN B 84 " pdb=" CA ASN B 84 " ideal model delta harmonic sigma weight residual -180.00 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA THR A 175 " pdb=" C THR A 175 " pdb=" N ASP A 176 " pdb=" CA ASP A 176 " ideal model delta harmonic sigma weight residual 180.00 158.13 21.87 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA PRO A 9 " pdb=" C PRO A 9 " pdb=" N SER A 10 " pdb=" CA SER A 10 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 2951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 380 0.027 - 0.053: 233 0.053 - 0.080: 92 0.080 - 0.106: 50 0.106 - 0.133: 11 Chirality restraints: 766 Sorted by residual: chirality pdb=" CA ILE A 281 " pdb=" N ILE A 281 " pdb=" C ILE A 281 " pdb=" CB ILE A 281 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ASP B 155 " pdb=" N ASP B 155 " pdb=" C ASP B 155 " pdb=" CB ASP B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.40e-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 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 763 not shown) Planarity restraints: 884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 209 " -0.015 2.00e-02 2.50e+03 1.81e-02 6.53e+00 pdb=" CG TYR B 209 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 209 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 209 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 209 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 209 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR B 209 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 209 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 251 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO B 252 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 252 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 252 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 51 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO B 52 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 52 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 52 " 0.022 5.00e-02 4.00e+02 ... (remaining 881 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 121 2.66 - 3.22: 4905 3.22 - 3.78: 7818 3.78 - 4.34: 10519 4.34 - 4.90: 17589 Nonbonded interactions: 40952 Sorted by model distance: nonbonded pdb=" NE2 GLN B 83 " pdb=" O GLU B 178 " model vdw 2.097 3.120 nonbonded pdb=" OG1 THR B 292 " pdb=" OD2 ASP B 295 " model vdw 2.179 3.040 nonbonded pdb=" OG SER A 145 " pdb=" O GLN C 0 " model vdw 2.187 3.040 nonbonded pdb=" NE2 GLN A 19 " pdb=" OD1 ASN A 119 " model vdw 2.205 3.120 nonbonded pdb=" OG1 THR A 224 " pdb=" OD1 ASP A 263 " model vdw 2.227 3.040 ... (remaining 40947 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=0.69 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.330 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.005 0.049 5010 Z= 0.329 Angle : 0.720 7.342 6800 Z= 0.389 Chirality : 0.042 0.133 766 Planarity : 0.005 0.045 884 Dihedral : 13.223 89.878 1794 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -1.35 (0.34), residues: 626 helix: 0.93 (0.43), residues: 154 sheet: -3.05 (0.48), residues: 108 loop : -0.97 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 31 HIS 0.005 0.001 HIS A 41 PHE 0.026 0.002 PHE B 185 TYR 0.040 0.003 TYR B 209 ARG 0.007 0.001 ARG C 4 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.529 Fit side-chains REVERT: A 119 ASN cc_start: 0.8211 (t0) cc_final: 0.7954 (t0) REVERT: A 240 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7329 (tm-30) REVERT: C 4 ARG cc_start: 0.7966 (ttt-90) cc_final: 0.7755 (ttt-90) REVERT: B 16 CYS cc_start: 0.7927 (p) cc_final: 0.7536 (p) REVERT: B 130 MET cc_start: 0.8387 (tpp) cc_final: 0.8178 (ttt) REVERT: B 175 THR cc_start: 0.8938 (p) cc_final: 0.8668 (t) REVERT: B 240 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7554 (tm-30) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1390 time to fit residues: 24.8830 Evaluate side-chains 108 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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: 0.8980 chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 74 GLN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN A 299 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.127206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107045 restraints weight = 8531.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.111259 restraints weight = 4401.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.114162 restraints weight = 2807.009| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5010 Z= 0.320 Angle : 0.691 7.994 6800 Z= 0.354 Chirality : 0.043 0.150 766 Planarity : 0.005 0.051 884 Dihedral : 5.274 31.270 678 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.29 % Allowed : 11.58 % Favored : 87.13 % 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: -1.38 (0.33), residues: 626 helix: 0.87 (0.41), residues: 152 sheet: -3.97 (0.48), residues: 64 loop : -1.11 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 31 HIS 0.005 0.001 HIS B 41 PHE 0.017 0.001 PHE A 181 TYR 0.019 0.002 TYR B 209 ARG 0.006 0.001 ARG C 4 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8354 (t0) cc_final: 0.7967 (t0) REVERT: A 289 ASP cc_start: 0.8410 (p0) cc_final: 0.8117 (p0) REVERT: B 16 CYS cc_start: 0.8093 (p) cc_final: 0.7582 (p) REVERT: B 82 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.8057 (ttt) REVERT: B 130 MET cc_start: 0.8462 (tpp) cc_final: 0.8229 (ttt) REVERT: B 175 THR cc_start: 0.9057 (p) cc_final: 0.8716 (t) REVERT: B 240 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7535 (tm-30) REVERT: D 0 GLN cc_start: 0.8311 (mm110) cc_final: 0.8089 (mm-40) outliers start: 7 outliers final: 4 residues processed: 116 average time/residue: 0.1233 time to fit residues: 19.6159 Evaluate side-chains 115 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 177 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 0 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 = 0.3778 r_free = 0.3778 target = 0.130178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.110157 restraints weight = 8475.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.114549 restraints weight = 4224.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117581 restraints weight = 2633.041| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5010 Z= 0.211 Angle : 0.620 6.504 6800 Z= 0.316 Chirality : 0.042 0.175 766 Planarity : 0.004 0.045 884 Dihedral : 4.962 26.033 678 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.02 % Allowed : 12.13 % Favored : 85.85 % 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: -1.25 (0.33), residues: 626 helix: 1.04 (0.42), residues: 152 sheet: -2.87 (0.52), residues: 88 loop : -1.10 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 31 HIS 0.015 0.002 HIS B 41 PHE 0.012 0.001 PHE A 181 TYR 0.031 0.002 TYR A 161 ARG 0.004 0.000 ARG C 4 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8253 (t0) cc_final: 0.7877 (t0) REVERT: A 289 ASP cc_start: 0.8284 (p0) cc_final: 0.8042 (p0) REVERT: B 16 CYS cc_start: 0.7983 (p) cc_final: 0.7539 (p) REVERT: B 119 ASN cc_start: 0.8214 (t0) cc_final: 0.7949 (t0) REVERT: B 175 THR cc_start: 0.8992 (p) cc_final: 0.8615 (t) outliers start: 11 outliers final: 2 residues processed: 134 average time/residue: 0.1345 time to fit residues: 24.1447 Evaluate side-chains 117 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain C residue 1 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 6 optimal weight: 0.0970 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 HIS ** 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 = 0.3719 r_free = 0.3719 target = 0.125973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.105978 restraints weight = 8637.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.110062 restraints weight = 4424.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.112879 restraints weight = 2809.655| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5010 Z= 0.208 Angle : 0.644 7.983 6800 Z= 0.322 Chirality : 0.041 0.140 766 Planarity : 0.004 0.047 884 Dihedral : 4.822 23.463 678 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.92 % Allowed : 16.91 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.33), residues: 626 helix: 1.13 (0.42), residues: 152 sheet: -3.70 (0.52), residues: 64 loop : -1.10 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 31 HIS 0.006 0.001 HIS B 41 PHE 0.010 0.001 PHE B 140 TYR 0.027 0.002 TYR B 161 ARG 0.007 0.001 ARG C 4 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8311 (t0) cc_final: 0.7878 (t0) REVERT: A 270 GLU cc_start: 0.7822 (tp30) cc_final: 0.7424 (tp30) REVERT: A 289 ASP cc_start: 0.8402 (p0) cc_final: 0.8090 (p0) REVERT: B 6 MET cc_start: 0.7827 (tpt) cc_final: 0.7507 (tpt) REVERT: B 16 CYS cc_start: 0.8123 (p) cc_final: 0.7714 (p) REVERT: B 83 GLN cc_start: 0.8170 (tt0) cc_final: 0.7839 (tt0) REVERT: B 119 ASN cc_start: 0.8307 (t0) cc_final: 0.8042 (t0) REVERT: B 130 MET cc_start: 0.8457 (tpp) cc_final: 0.8115 (ttt) REVERT: B 175 THR cc_start: 0.9010 (p) cc_final: 0.8566 (t) outliers start: 5 outliers final: 4 residues processed: 122 average time/residue: 0.1272 time to fit residues: 21.3845 Evaluate side-chains 118 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain C residue 1 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.124439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104170 restraints weight = 8794.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.108248 restraints weight = 4464.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.111030 restraints weight = 2845.030| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5010 Z= 0.289 Angle : 0.657 7.715 6800 Z= 0.324 Chirality : 0.042 0.160 766 Planarity : 0.004 0.047 884 Dihedral : 4.878 23.486 678 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.02 % Allowed : 17.83 % Favored : 80.15 % 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: -1.17 (0.33), residues: 626 helix: 1.28 (0.43), residues: 152 sheet: -3.62 (0.52), residues: 64 loop : -1.13 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 31 HIS 0.004 0.001 HIS A 164 PHE 0.011 0.001 PHE B 140 TYR 0.027 0.002 TYR B 161 ARG 0.009 0.001 ARG C 4 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8511 (p0) cc_final: 0.8276 (p0) REVERT: A 119 ASN cc_start: 0.8356 (t0) cc_final: 0.7931 (t0) REVERT: A 270 GLU cc_start: 0.7887 (tp30) cc_final: 0.7475 (tp30) REVERT: B 16 CYS cc_start: 0.8252 (p) cc_final: 0.7822 (p) REVERT: B 119 ASN cc_start: 0.8311 (t0) cc_final: 0.8045 (t0) REVERT: B 175 THR cc_start: 0.9026 (p) cc_final: 0.8533 (t) outliers start: 11 outliers final: 7 residues processed: 126 average time/residue: 0.1345 time to fit residues: 23.2198 Evaluate side-chains 121 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.126398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.106627 restraints weight = 8722.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.110641 restraints weight = 4477.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.113463 restraints weight = 2850.640| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5010 Z= 0.203 Angle : 0.647 8.806 6800 Z= 0.317 Chirality : 0.042 0.209 766 Planarity : 0.004 0.048 884 Dihedral : 4.787 25.219 678 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.21 % Allowed : 19.85 % Favored : 77.94 % 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: -1.11 (0.33), residues: 626 helix: 1.28 (0.42), residues: 154 sheet: -3.35 (0.55), residues: 64 loop : -1.13 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 31 HIS 0.004 0.001 HIS A 164 PHE 0.015 0.001 PHE B 150 TYR 0.026 0.002 TYR B 161 ARG 0.008 0.001 ARG C 4 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8502 (p0) cc_final: 0.8291 (p0) REVERT: A 119 ASN cc_start: 0.8318 (t0) cc_final: 0.7893 (t0) REVERT: A 270 GLU cc_start: 0.7858 (tp30) cc_final: 0.7492 (tp30) REVERT: A 276 MET cc_start: 0.8768 (tpp) cc_final: 0.8095 (mmm) REVERT: A 289 ASP cc_start: 0.8379 (p0) cc_final: 0.8101 (p0) REVERT: C 0 GLN cc_start: 0.8237 (mp10) cc_final: 0.7514 (mp10) REVERT: B 6 MET cc_start: 0.7522 (tpt) cc_final: 0.6952 (tpt) REVERT: B 16 CYS cc_start: 0.8236 (p) cc_final: 0.7855 (p) REVERT: B 119 ASN cc_start: 0.8286 (t0) cc_final: 0.8005 (t0) REVERT: B 130 MET cc_start: 0.8380 (tpp) cc_final: 0.7979 (ttt) REVERT: B 175 THR cc_start: 0.8995 (p) cc_final: 0.8514 (t) outliers start: 12 outliers final: 8 residues processed: 133 average time/residue: 0.1480 time to fit residues: 26.3322 Evaluate side-chains 119 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 HIS ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.127856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.107880 restraints weight = 8685.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.111980 restraints weight = 4424.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114820 restraints weight = 2802.042| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5010 Z= 0.199 Angle : 0.634 8.242 6800 Z= 0.313 Chirality : 0.042 0.151 766 Planarity : 0.004 0.048 884 Dihedral : 4.704 21.981 678 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.39 % Allowed : 21.14 % Favored : 76.47 % 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: -1.11 (0.33), residues: 626 helix: 1.29 (0.43), residues: 154 sheet: -3.20 (0.56), residues: 64 loop : -1.16 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 31 HIS 0.006 0.001 HIS A 164 PHE 0.011 0.001 PHE B 140 TYR 0.025 0.002 TYR B 161 ARG 0.008 0.001 ARG C 4 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8520 (p0) cc_final: 0.8289 (p0) REVERT: A 119 ASN cc_start: 0.8327 (t0) cc_final: 0.7871 (t0) REVERT: A 270 GLU cc_start: 0.7910 (tp30) cc_final: 0.7565 (tp30) REVERT: A 289 ASP cc_start: 0.8401 (p0) cc_final: 0.8112 (p0) REVERT: C 0 GLN cc_start: 0.8108 (mp10) cc_final: 0.7381 (mp10) REVERT: B 16 CYS cc_start: 0.8352 (p) cc_final: 0.7948 (p) REVERT: B 119 ASN cc_start: 0.8313 (t0) cc_final: 0.8035 (t0) REVERT: B 130 MET cc_start: 0.8402 (tpp) cc_final: 0.7941 (ttt) REVERT: B 175 THR cc_start: 0.8994 (p) cc_final: 0.8472 (t) outliers start: 13 outliers final: 9 residues processed: 125 average time/residue: 0.1720 time to fit residues: 29.2136 Evaluate side-chains 120 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.131835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.111860 restraints weight = 8663.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.116151 restraints weight = 4359.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.118987 restraints weight = 2739.536| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5010 Z= 0.200 Angle : 0.660 10.316 6800 Z= 0.325 Chirality : 0.043 0.165 766 Planarity : 0.004 0.048 884 Dihedral : 4.703 20.870 678 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.57 % Allowed : 22.24 % Favored : 75.18 % 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: -1.15 (0.33), residues: 626 helix: 1.34 (0.43), residues: 154 sheet: -3.42 (0.53), residues: 74 loop : -1.11 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 31 HIS 0.005 0.001 HIS A 164 PHE 0.011 0.001 PHE B 150 TYR 0.022 0.002 TYR B 161 ARG 0.010 0.001 ARG C 4 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8351 (t0) cc_final: 0.7891 (t0) REVERT: A 175 THR cc_start: 0.8991 (p) cc_final: 0.8721 (p) REVERT: A 270 GLU cc_start: 0.7799 (tp30) cc_final: 0.7499 (tp30) REVERT: A 276 MET cc_start: 0.8760 (tpp) cc_final: 0.8385 (mmm) REVERT: A 289 ASP cc_start: 0.8363 (p0) cc_final: 0.8071 (p0) REVERT: C 0 GLN cc_start: 0.8030 (mp10) cc_final: 0.7325 (mp10) REVERT: B 16 CYS cc_start: 0.8286 (p) cc_final: 0.7903 (p) REVERT: B 119 ASN cc_start: 0.8272 (t0) cc_final: 0.8010 (t0) REVERT: B 130 MET cc_start: 0.8362 (tpp) cc_final: 0.7857 (ttt) REVERT: B 175 THR cc_start: 0.8968 (p) cc_final: 0.8478 (t) REVERT: B 235 MET cc_start: 0.7967 (tpp) cc_final: 0.7689 (tpp) REVERT: B 279 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7872 (ptt180) outliers start: 14 outliers final: 10 residues processed: 123 average time/residue: 0.1701 time to fit residues: 28.3280 Evaluate side-chains 122 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 279 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 0.3980 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 4 optimal weight: 0.0000 chunk 48 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.134227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114150 restraints weight = 8436.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.118365 restraints weight = 4304.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.121166 restraints weight = 2718.429| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5010 Z= 0.173 Angle : 0.634 9.953 6800 Z= 0.312 Chirality : 0.042 0.168 766 Planarity : 0.004 0.048 884 Dihedral : 4.538 20.614 678 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.47 % Allowed : 22.98 % Favored : 75.55 % 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: -1.09 (0.33), residues: 626 helix: 1.36 (0.42), residues: 154 sheet: -3.33 (0.53), residues: 74 loop : -1.06 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 31 HIS 0.005 0.001 HIS B 41 PHE 0.012 0.001 PHE B 140 TYR 0.022 0.002 TYR A 209 ARG 0.009 0.001 ARG C 4 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8277 (t0) cc_final: 0.7777 (t0) REVERT: A 166 GLU cc_start: 0.8265 (tt0) cc_final: 0.8029 (mt-10) REVERT: A 270 GLU cc_start: 0.7794 (tp30) cc_final: 0.7509 (tp30) REVERT: A 276 MET cc_start: 0.8736 (tpp) cc_final: 0.8391 (mmm) REVERT: A 289 ASP cc_start: 0.8307 (p0) cc_final: 0.8012 (p0) REVERT: A 294 PHE cc_start: 0.8292 (t80) cc_final: 0.8051 (t80) REVERT: C 0 GLN cc_start: 0.7709 (mp10) cc_final: 0.7237 (mp10) REVERT: B 6 MET cc_start: 0.6782 (tpt) cc_final: 0.6315 (tpt) REVERT: B 16 CYS cc_start: 0.8396 (p) cc_final: 0.8023 (p) REVERT: B 119 ASN cc_start: 0.8270 (t0) cc_final: 0.7991 (t0) REVERT: B 130 MET cc_start: 0.8382 (tpp) cc_final: 0.8034 (ttt) REVERT: B 166 GLU cc_start: 0.8057 (mp0) cc_final: 0.7441 (mp0) REVERT: B 175 THR cc_start: 0.8962 (p) cc_final: 0.8511 (t) REVERT: B 238 ASN cc_start: 0.8722 (t0) cc_final: 0.8372 (t0) outliers start: 8 outliers final: 7 residues processed: 131 average time/residue: 0.1867 time to fit residues: 32.6796 Evaluate side-chains 118 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 15 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN B 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.132004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.111820 restraints weight = 8593.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115996 restraints weight = 4389.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.118845 restraints weight = 2785.781| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5010 Z= 0.228 Angle : 0.667 9.816 6800 Z= 0.331 Chirality : 0.044 0.291 766 Planarity : 0.004 0.048 884 Dihedral : 4.633 20.380 678 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.65 % Allowed : 25.00 % Favored : 73.35 % 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: -1.08 (0.33), residues: 626 helix: 1.31 (0.42), residues: 154 sheet: -3.26 (0.55), residues: 74 loop : -1.05 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 207 HIS 0.012 0.001 HIS A 164 PHE 0.015 0.001 PHE B 150 TYR 0.020 0.002 TYR A 209 ARG 0.008 0.001 ARG C 4 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8277 (t0) cc_final: 0.7983 (t0) REVERT: A 240 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7553 (tm-30) REVERT: A 270 GLU cc_start: 0.7836 (tp30) cc_final: 0.7529 (tp30) REVERT: A 276 MET cc_start: 0.8790 (tpp) cc_final: 0.8385 (mmm) REVERT: A 289 ASP cc_start: 0.8318 (p0) cc_final: 0.8015 (p0) REVERT: A 294 PHE cc_start: 0.8300 (t80) cc_final: 0.8079 (t80) REVERT: C 0 GLN cc_start: 0.7820 (mp10) cc_final: 0.7276 (mp10) REVERT: B 6 MET cc_start: 0.6814 (tpt) cc_final: 0.6394 (tpt) REVERT: B 16 CYS cc_start: 0.8490 (p) cc_final: 0.8189 (p) REVERT: B 26 THR cc_start: 0.8083 (m) cc_final: 0.7763 (m) REVERT: B 119 ASN cc_start: 0.8307 (t0) cc_final: 0.8045 (t0) REVERT: B 175 THR cc_start: 0.8972 (p) cc_final: 0.8541 (t) outliers start: 9 outliers final: 7 residues processed: 120 average time/residue: 0.1493 time to fit residues: 24.3014 Evaluate side-chains 117 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 154 TYR Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 chunk 50 optimal weight: 9.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** 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 = 0.3792 r_free = 0.3792 target = 0.131346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.111021 restraints weight = 8573.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115250 restraints weight = 4374.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.118131 restraints weight = 2771.838| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5010 Z= 0.230 Angle : 0.666 9.707 6800 Z= 0.329 Chirality : 0.044 0.214 766 Planarity : 0.004 0.049 884 Dihedral : 4.614 20.228 678 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.84 % Allowed : 24.82 % Favored : 73.35 % 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: -1.10 (0.33), residues: 626 helix: 1.30 (0.42), residues: 154 sheet: -3.25 (0.54), residues: 74 loop : -1.06 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 207 HIS 0.003 0.001 HIS B 41 PHE 0.011 0.001 PHE B 140 TYR 0.021 0.002 TYR A 209 ARG 0.008 0.001 ARG D 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1994.95 seconds wall clock time: 36 minutes 1.41 seconds (2161.41 seconds total)