Starting phenix.real_space_refine on Tue Sep 24 18:43:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s82_24889/09_2024/7s82_24889.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s82_24889/09_2024/7s82_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s82_24889/09_2024/7s82_24889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s82_24889/09_2024/7s82_24889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s82_24889/09_2024/7s82_24889.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s82_24889/09_2024/7s82_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-5461/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: 3.58, per 1000 atoms: 0.73 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: 1.16 Conformation dependent library (CDL) restraints added in 589.8 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: 0.56 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: 1.19 Time building geometry restraints manager: 1.38 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: 0.00 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: 0.560 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.270 Find NCS groups from input model: 0.130 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.030 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.546 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: 0.1350 time to fit residues: 24.1428 Evaluate side-chains 108 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 31.269 678 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 fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8333 (t0) cc_final: 0.7950 (t0) REVERT: A 289 ASP cc_start: 0.8356 (p0) cc_final: 0.8075 (p0) REVERT: B 16 CYS cc_start: 0.8034 (p) cc_final: 0.7530 (p) REVERT: B 82 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.8022 (ttt) REVERT: B 130 MET cc_start: 0.8512 (tpp) cc_final: 0.8237 (ttt) REVERT: B 175 THR cc_start: 0.9003 (p) cc_final: 0.8645 (t) REVERT: B 240 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7279 (tm-30) REVERT: D 0 GLN cc_start: 0.8305 (mm110) cc_final: 0.8085 (mm-40) outliers start: 7 outliers final: 4 residues processed: 116 average time/residue: 0.1235 time to fit residues: 19.5937 Evaluate side-chains 115 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 31 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2033 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 : 0.620 6.577 6800 Z= 0.315 Chirality : 0.042 0.178 766 Planarity : 0.004 0.045 884 Dihedral : 4.950 26.410 678 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.02 % Allowed : 12.32 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 0.010 0.001 PHE A 181 TYR 0.029 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 138 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8303 (t0) cc_final: 0.7907 (t0) REVERT: A 289 ASP cc_start: 0.8268 (p0) cc_final: 0.8015 (p0) REVERT: B 16 CYS cc_start: 0.7977 (p) cc_final: 0.7578 (p) REVERT: B 175 THR cc_start: 0.8941 (p) cc_final: 0.8559 (t) outliers start: 11 outliers final: 2 residues processed: 130 average time/residue: 0.1278 time to fit residues: 22.5148 Evaluate side-chains 115 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 55 optimal weight: 2.9990 chunk 42 optimal weight: 0.0670 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 59 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.4220 ------------------------------------------------------------------------------- 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** B 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5010 Z= 0.232 Angle : 0.646 6.448 6800 Z= 0.324 Chirality : 0.042 0.141 766 Planarity : 0.004 0.047 884 Dihedral : 4.850 23.705 678 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.10 % Allowed : 16.36 % Favored : 82.54 % 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: -1.23 (0.33), residues: 626 helix: 1.13 (0.42), residues: 152 sheet: -3.71 (0.53), residues: 64 loop : -1.11 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 31 HIS 0.005 0.001 HIS B 41 PHE 0.011 0.001 PHE B 140 TYR 0.030 0.002 TYR A 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 127 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8295 (t0) cc_final: 0.7873 (t0) REVERT: A 270 GLU cc_start: 0.7725 (tp30) cc_final: 0.7349 (tp30) REVERT: A 289 ASP cc_start: 0.8356 (p0) cc_final: 0.8066 (p0) REVERT: B 6 MET cc_start: 0.7846 (tpt) cc_final: 0.7534 (tpt) REVERT: B 16 CYS cc_start: 0.8046 (p) cc_final: 0.7664 (p) REVERT: B 83 GLN cc_start: 0.8130 (tt0) cc_final: 0.7819 (tt0) REVERT: B 119 ASN cc_start: 0.8221 (t0) cc_final: 0.7958 (t0) REVERT: B 130 MET cc_start: 0.8449 (tpp) cc_final: 0.8067 (ttt) REVERT: B 175 THR cc_start: 0.8990 (p) cc_final: 0.8528 (t) outliers start: 6 outliers final: 6 residues processed: 124 average time/residue: 0.1358 time to fit residues: 22.7237 Evaluate side-chains 121 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 271 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 19 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5010 Z= 0.188 Angle : 0.621 7.421 6800 Z= 0.306 Chirality : 0.041 0.155 766 Planarity : 0.004 0.047 884 Dihedral : 4.694 23.319 678 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.84 % Allowed : 17.28 % Favored : 80.88 % 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: 1.26 (0.43), residues: 152 sheet: -2.77 (0.52), residues: 88 loop : -1.14 (0.30), residues: 386 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 230 TYR 0.027 0.002 TYR B 161 ARG 0.008 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 139 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8268 (t0) cc_final: 0.7848 (t0) REVERT: A 270 GLU cc_start: 0.7749 (tp30) cc_final: 0.7376 (tp30) REVERT: A 276 MET cc_start: 0.8765 (tpp) cc_final: 0.8238 (mmm) REVERT: A 289 ASP cc_start: 0.8323 (p0) cc_final: 0.8013 (p0) REVERT: A 294 PHE cc_start: 0.8053 (t80) cc_final: 0.7840 (t80) REVERT: B 16 CYS cc_start: 0.8064 (p) cc_final: 0.7726 (p) REVERT: B 83 GLN cc_start: 0.8124 (tt0) cc_final: 0.7682 (tt0) REVERT: B 119 ASN cc_start: 0.8191 (t0) cc_final: 0.7896 (t0) REVERT: B 175 THR cc_start: 0.8973 (p) cc_final: 0.8536 (t) REVERT: B 240 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7395 (tm-30) REVERT: B 276 MET cc_start: 0.8715 (tpp) cc_final: 0.8185 (mmm) outliers start: 10 outliers final: 7 residues processed: 135 average time/residue: 0.1451 time to fit residues: 25.9659 Evaluate side-chains 120 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 271 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 6.9990 chunk 14 optimal weight: 0.0970 chunk 59 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2953 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= 0.191 Angle : 0.642 8.497 6800 Z= 0.314 Chirality : 0.042 0.191 766 Planarity : 0.004 0.048 884 Dihedral : 4.670 25.085 678 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.47 % Allowed : 19.30 % Favored : 79.23 % 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: -1.07 (0.33), residues: 626 helix: 1.32 (0.42), residues: 154 sheet: -3.34 (0.53), residues: 64 loop : -1.10 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 31 HIS 0.007 0.001 HIS A 164 PHE 0.010 0.001 PHE B 140 TYR 0.024 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 121 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8296 (t0) cc_final: 0.7874 (t0) REVERT: A 270 GLU cc_start: 0.7744 (tp30) cc_final: 0.7443 (tp30) REVERT: A 276 MET cc_start: 0.8767 (tpp) cc_final: 0.8231 (mmm) REVERT: B 16 CYS cc_start: 0.8191 (p) cc_final: 0.7786 (p) REVERT: B 54 TYR cc_start: 0.7633 (m-80) cc_final: 0.7425 (m-80) REVERT: B 119 ASN cc_start: 0.8186 (t0) cc_final: 0.7916 (t0) REVERT: B 130 MET cc_start: 0.8382 (tpp) cc_final: 0.7846 (ttt) REVERT: B 175 THR cc_start: 0.8982 (p) cc_final: 0.8519 (t) outliers start: 8 outliers final: 6 residues processed: 119 average time/residue: 0.1272 time to fit residues: 20.6842 Evaluate side-chains 115 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 271 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3147 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= 0.179 Angle : 0.643 8.670 6800 Z= 0.315 Chirality : 0.042 0.159 766 Planarity : 0.004 0.048 884 Dihedral : 4.644 24.962 678 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.47 % Allowed : 20.96 % Favored : 77.57 % 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: -1.14 (0.33), residues: 626 helix: 1.29 (0.42), residues: 154 sheet: -3.42 (0.53), residues: 74 loop : -1.07 (0.29), 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 0.010 0.001 PHE B 230 TYR 0.027 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 130 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8262 (t0) cc_final: 0.7823 (t0) REVERT: A 270 GLU cc_start: 0.7742 (tp30) cc_final: 0.7460 (tp30) REVERT: A 276 MET cc_start: 0.8745 (tpp) cc_final: 0.8448 (mmm) REVERT: A 289 ASP cc_start: 0.8294 (p0) cc_final: 0.8058 (p0) REVERT: C 0 GLN cc_start: 0.7995 (mp10) cc_final: 0.7473 (mp10) REVERT: B 16 CYS cc_start: 0.8131 (p) cc_final: 0.7786 (p) REVERT: B 119 ASN cc_start: 0.8180 (t0) cc_final: 0.7906 (t0) REVERT: B 130 MET cc_start: 0.8312 (tpp) cc_final: 0.8014 (ttt) REVERT: B 175 THR cc_start: 0.8962 (p) cc_final: 0.8494 (t) outliers start: 8 outliers final: 7 residues processed: 126 average time/residue: 0.1503 time to fit residues: 24.7551 Evaluate side-chains 123 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 271 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.0030 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5010 Z= 0.192 Angle : 0.655 10.258 6800 Z= 0.317 Chirality : 0.042 0.162 766 Planarity : 0.004 0.048 884 Dihedral : 4.634 24.884 678 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.84 % Allowed : 21.14 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.18 (0.33), residues: 626 helix: 1.17 (0.42), residues: 154 sheet: -3.34 (0.53), residues: 74 loop : -1.07 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 31 HIS 0.005 0.001 HIS B 41 PHE 0.010 0.001 PHE B 140 TYR 0.025 0.002 TYR B 161 ARG 0.005 0.000 ARG A 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 131 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8245 (t0) cc_final: 0.7760 (t0) REVERT: A 175 THR cc_start: 0.8925 (p) cc_final: 0.8722 (p) REVERT: A 270 GLU cc_start: 0.7728 (tp30) cc_final: 0.7444 (tp30) REVERT: A 276 MET cc_start: 0.8748 (tpp) cc_final: 0.8445 (mmm) REVERT: A 289 ASP cc_start: 0.8304 (p0) cc_final: 0.8099 (p0) REVERT: A 294 PHE cc_start: 0.8063 (t80) cc_final: 0.7835 (t80) REVERT: C 0 GLN cc_start: 0.7899 (mp10) cc_final: 0.7362 (mp10) REVERT: B 6 MET cc_start: 0.6687 (tpt) cc_final: 0.6122 (tpt) REVERT: B 16 CYS cc_start: 0.8206 (p) cc_final: 0.7858 (p) REVERT: B 119 ASN cc_start: 0.8200 (t0) cc_final: 0.7932 (t0) REVERT: B 130 MET cc_start: 0.8322 (tpp) cc_final: 0.7687 (ttt) REVERT: B 175 THR cc_start: 0.8987 (p) cc_final: 0.8501 (t) REVERT: B 279 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7699 (ptt180) REVERT: D 4 ARG cc_start: 0.7710 (ptm160) cc_final: 0.7495 (ptm-80) outliers start: 10 outliers final: 6 residues processed: 127 average time/residue: 0.1529 time to fit residues: 25.6103 Evaluate side-chains 121 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 45 THR Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 271 LEU 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 24 optimal weight: 0.0470 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- 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 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5010 Z= 0.178 Angle : 0.644 11.162 6800 Z= 0.315 Chirality : 0.042 0.172 766 Planarity : 0.004 0.048 884 Dihedral : 4.599 21.896 678 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.65 % Allowed : 22.24 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.33), residues: 626 helix: 1.16 (0.42), residues: 154 sheet: -3.32 (0.53), residues: 74 loop : -1.02 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 31 HIS 0.005 0.001 HIS B 41 PHE 0.010 0.001 PHE B 230 TYR 0.023 0.003 TYR B 161 ARG 0.007 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 129 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8158 (t0) cc_final: 0.7817 (t0) REVERT: A 182 TYR cc_start: 0.8165 (m-80) cc_final: 0.7905 (m-80) REVERT: A 270 GLU cc_start: 0.7714 (tp30) cc_final: 0.7445 (tp30) REVERT: A 276 MET cc_start: 0.8738 (tpp) cc_final: 0.8432 (mmm) REVERT: A 289 ASP cc_start: 0.8354 (p0) cc_final: 0.8128 (p0) REVERT: C 0 GLN cc_start: 0.7849 (mp10) cc_final: 0.7263 (mp10) REVERT: B 6 MET cc_start: 0.6497 (tpt) cc_final: 0.5353 (tpt) REVERT: B 16 CYS cc_start: 0.8360 (p) cc_final: 0.8039 (p) REVERT: B 119 ASN cc_start: 0.8197 (t0) cc_final: 0.7931 (t0) REVERT: B 175 THR cc_start: 0.8957 (p) cc_final: 0.8475 (t) outliers start: 9 outliers final: 6 residues processed: 125 average time/residue: 0.1367 time to fit residues: 23.0186 Evaluate side-chains 120 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 45 THR Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 271 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 HIS ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5010 Z= 0.199 Angle : 0.664 10.287 6800 Z= 0.320 Chirality : 0.042 0.164 766 Planarity : 0.004 0.048 884 Dihedral : 4.638 21.072 678 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.10 % Allowed : 24.63 % Favored : 74.26 % 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: -1.13 (0.33), residues: 626 helix: 1.11 (0.42), residues: 154 sheet: -3.23 (0.54), residues: 74 loop : -1.01 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 31 HIS 0.006 0.001 HIS A 164 PHE 0.011 0.001 PHE B 150 TYR 0.023 0.003 TYR B 161 ARG 0.006 0.001 ARG D 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 131 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8111 (t0) cc_final: 0.7771 (t0) REVERT: A 182 TYR cc_start: 0.8251 (m-80) cc_final: 0.7925 (m-80) REVERT: A 270 GLU cc_start: 0.7718 (tp30) cc_final: 0.7448 (tp30) REVERT: A 276 MET cc_start: 0.8722 (tpp) cc_final: 0.8137 (mmm) REVERT: A 289 ASP cc_start: 0.8367 (p0) cc_final: 0.8055 (p0) REVERT: C 0 GLN cc_start: 0.7791 (mp10) cc_final: 0.7338 (mp10) REVERT: B 6 MET cc_start: 0.6456 (tpt) cc_final: 0.5344 (tpt) REVERT: B 16 CYS cc_start: 0.8495 (p) cc_final: 0.8172 (p) REVERT: B 26 THR cc_start: 0.7960 (m) cc_final: 0.7691 (m) REVERT: B 119 ASN cc_start: 0.8263 (t0) cc_final: 0.8019 (t0) REVERT: B 130 MET cc_start: 0.8317 (tpp) cc_final: 0.7795 (ttt) REVERT: B 175 THR cc_start: 0.8948 (p) cc_final: 0.8461 (t) REVERT: B 264 MET cc_start: 0.5901 (ptm) cc_final: 0.5512 (ttp) outliers start: 6 outliers final: 6 residues processed: 129 average time/residue: 0.1680 time to fit residues: 27.6187 Evaluate side-chains 116 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 265 CYS 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 271 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.0970 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 HIS ** 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** A 299 GLN ** B 172 HIS ** 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 = 0.3857 r_free = 0.3857 target = 0.136689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.117094 restraints weight = 8405.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.121510 restraints weight = 4090.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.124481 restraints weight = 2541.234| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5010 Z= 0.187 Angle : 0.670 11.472 6800 Z= 0.322 Chirality : 0.042 0.180 766 Planarity : 0.005 0.059 884 Dihedral : 4.594 21.099 678 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.10 % Allowed : 25.18 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.33), residues: 626 helix: 1.16 (0.42), residues: 154 sheet: -2.93 (0.48), residues: 98 loop : -0.97 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 31 HIS 0.005 0.001 HIS B 41 PHE 0.011 0.001 PHE B 140 TYR 0.022 0.003 TYR B 161 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: 1415.79 seconds wall clock time: 25 minutes 57.18 seconds (1557.18 seconds total)