Starting phenix.real_space_refine on Mon Feb 10 20:31:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlx_36407/02_2025/8jlx_36407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlx_36407/02_2025/8jlx_36407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jlx_36407/02_2025/8jlx_36407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlx_36407/02_2025/8jlx_36407.map" model { file = "/net/cci-nas-00/data/ceres_data/8jlx_36407/02_2025/8jlx_36407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlx_36407/02_2025/8jlx_36407.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 1417 2.51 5 N 382 2.21 5 O 456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2277 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 539 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 5, 'TRANS': 63} Chain breaks: 1 Chain: "H" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 907 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Time building chain proxies: 2.89, per 1000 atoms: 1.27 Number of scatterers: 2277 At special positions: 0 Unit cell: (52.25, 69.35, 89.3, 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 22 16.00 O 456 8.00 N 382 7.00 C 1417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A1165 " - pdb=" SG CYS A1198 " distance=2.03 Simple disulfide: pdb=" SG CYS A1169 " - pdb=" SG CYS A1205 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1207 " distance=2.03 Simple disulfide: pdb=" SG CYS A1175 " - pdb=" SG CYS A1180 " distance=2.03 Simple disulfide: pdb=" SG CYS A1193 " - pdb=" SG CYS A1360 " distance=2.03 Simple disulfide: pdb=" SG CYS A1208 " - pdb=" SG CYS A1368 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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: 0.56 Conformation dependent library (CDL) restraints added in 284.2 milliseconds 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 532 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 4.8% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.711A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.703A pdb=" N ILE L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1162 through 1164 Processing sheet with id=AA2, first strand: chain 'A' and resid 1356 through 1359 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.071A pdb=" N ALA H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL H 50 " --> pdb=" O THR H 34 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.737A pdb=" N CYS H 96 " --> pdb=" O TRP H 107 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TRP H 107 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASN H 98 " --> pdb=" O ASP H 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.450A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 198 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: 0.65 Time building geometry restraints manager: 0.67 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: 723 1.34 - 1.46: 629 1.46 - 1.58: 955 1.58 - 1.70: 0 1.70 - 1.82: 27 Bond restraints: 2334 Sorted by residual: bond pdb=" CB CYS A1207 " pdb=" SG CYS A1207 " ideal model delta sigma weight residual 1.808 1.775 0.033 3.30e-02 9.18e+02 1.01e+00 bond pdb=" CB CYS A1368 " pdb=" SG CYS A1368 " ideal model delta sigma weight residual 1.808 1.776 0.032 3.30e-02 9.18e+02 9.58e-01 bond pdb=" C THR L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.352 -0.019 2.34e-02 1.83e+03 6.32e-01 bond pdb=" CG GLU H 82 " pdb=" CD GLU H 82 " ideal model delta sigma weight residual 1.516 1.497 0.019 2.50e-02 1.60e+03 5.82e-01 bond pdb=" CB CYS A1208 " pdb=" SG CYS A1208 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.32e-01 ... (remaining 2329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 2922 1.23 - 2.45: 204 2.45 - 3.68: 29 3.68 - 4.90: 14 4.90 - 6.13: 4 Bond angle restraints: 3173 Sorted by residual: angle pdb=" N THR L 7 " pdb=" CA THR L 7 " pdb=" C THR L 7 " ideal model delta sigma weight residual 109.81 115.61 -5.80 2.21e+00 2.05e-01 6.90e+00 angle pdb=" C ASP A1364 " pdb=" N TRP A1365 " pdb=" CA TRP A1365 " ideal model delta sigma weight residual 121.80 127.09 -5.29 2.44e+00 1.68e-01 4.70e+00 angle pdb=" CA THR L 7 " pdb=" C THR L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 118.44 121.84 -3.40 1.59e+00 3.96e-01 4.56e+00 angle pdb=" N PRO H 14 " pdb=" CA PRO H 14 " pdb=" C PRO H 14 " ideal model delta sigma weight residual 110.50 113.83 -3.33 1.57e+00 4.06e-01 4.49e+00 angle pdb=" CA CYS A1368 " pdb=" CB CYS A1368 " pdb=" SG CYS A1368 " ideal model delta sigma weight residual 114.40 119.26 -4.86 2.30e+00 1.89e-01 4.47e+00 ... (remaining 3168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 1233 16.88 - 33.76: 107 33.76 - 50.63: 24 50.63 - 67.51: 4 67.51 - 84.38: 8 Dihedral angle restraints: 1376 sinusoidal: 537 harmonic: 839 Sorted by residual: dihedral pdb=" CB CYS A1175 " pdb=" SG CYS A1175 " pdb=" SG CYS A1180 " pdb=" CB CYS A1180 " ideal model delta sinusoidal sigma weight residual -86.00 -15.17 -70.83 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS A1208 " pdb=" SG CYS A1208 " pdb=" SG CYS A1368 " pdb=" CB CYS A1368 " ideal model delta sinusoidal sigma weight residual 93.00 162.79 -69.79 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS A1169 " pdb=" SG CYS A1169 " pdb=" SG CYS A1205 " pdb=" CB CYS A1205 " ideal model delta sinusoidal sigma weight residual 93.00 41.08 51.92 1 1.00e+01 1.00e-02 3.68e+01 ... (remaining 1373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 243 0.045 - 0.091: 68 0.091 - 0.136: 25 0.136 - 0.182: 2 0.182 - 0.227: 2 Chirality restraints: 340 Sorted by residual: chirality pdb=" CB ILE H 51 " pdb=" CA ILE H 51 " pdb=" CG1 ILE H 51 " pdb=" CG2 ILE H 51 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA THR L 7 " pdb=" N THR L 7 " pdb=" C THR L 7 " pdb=" CB THR L 7 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 337 not shown) Planarity restraints: 402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR L 7 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO L 8 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO L 59 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A1160 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO A1161 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A1161 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1161 " -0.017 5.00e-02 4.00e+02 ... (remaining 399 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 442 2.78 - 3.31: 2014 3.31 - 3.84: 3555 3.84 - 4.37: 4331 4.37 - 4.90: 7602 Nonbonded interactions: 17944 Sorted by model distance: nonbonded pdb=" NE2 GLN H 6 " pdb=" O TYR H 94 " model vdw 2.247 3.120 nonbonded pdb=" O VAL H 50 " pdb=" OG1 THR H 58 " model vdw 2.258 3.040 nonbonded pdb=" NE1 TRP A1197 " pdb=" OD2 ASP H 31 " model vdw 2.302 3.120 nonbonded pdb=" O PRO L 8 " pdb=" OG1 THR L 102 " model vdw 2.308 3.040 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.320 3.040 ... (remaining 17939 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.270 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2334 Z= 0.280 Angle : 0.746 6.127 3173 Z= 0.397 Chirality : 0.050 0.227 340 Planarity : 0.005 0.057 402 Dihedral : 14.315 84.384 820 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.47), residues: 285 helix: None (None), residues: 0 sheet: -0.85 (0.42), residues: 141 loop : -2.20 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1199 HIS 0.002 0.001 HIS L 55 PHE 0.005 0.001 PHE L 87 TYR 0.015 0.002 TYR A1358 ARG 0.004 0.001 ARG H 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.6809 (mt0) cc_final: 0.6563 (mt0) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 1.0091 time to fit residues: 60.1294 Evaluate side-chains 41 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 GLN L 6 GLN L 34 ASN L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.184262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.168545 restraints weight = 2895.786| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.88 r_work: 0.3848 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2334 Z= 0.300 Angle : 0.735 6.868 3173 Z= 0.387 Chirality : 0.049 0.196 340 Planarity : 0.006 0.058 402 Dihedral : 5.727 21.615 319 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 5.88 % Allowed : 14.90 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.48), residues: 285 helix: None (None), residues: 0 sheet: -0.78 (0.41), residues: 149 loop : -2.07 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.001 0.001 HIS L 55 PHE 0.005 0.001 PHE L 87 TYR 0.018 0.002 TYR A1358 ARG 0.007 0.001 ARG A1192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.7303 (mt0) cc_final: 0.7041 (mt0) REVERT: L 38 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7558 (tt0) outliers start: 15 outliers final: 7 residues processed: 58 average time/residue: 0.9302 time to fit residues: 55.4968 Evaluate side-chains 48 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN H 109 GLN L 34 ASN L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.186070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.170293 restraints weight = 2858.312| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.90 r_work: 0.3823 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2334 Z= 0.243 Angle : 0.692 7.197 3173 Z= 0.362 Chirality : 0.047 0.178 340 Planarity : 0.005 0.052 402 Dihedral : 5.500 20.845 319 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 5.88 % Allowed : 18.82 % Favored : 75.29 % 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: -1.98 (0.49), residues: 285 helix: None (None), residues: 0 sheet: -0.68 (0.42), residues: 146 loop : -2.00 (0.52), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 36 HIS 0.001 0.000 HIS L 55 PHE 0.004 0.001 PHE L 98 TYR 0.016 0.002 TYR A1358 ARG 0.008 0.001 ARG H 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: H 82 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7462 (mm-30) REVERT: L 38 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7607 (tt0) outliers start: 15 outliers final: 5 residues processed: 58 average time/residue: 0.9758 time to fit residues: 58.0505 Evaluate side-chains 48 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 44 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 GLN L 3 GLN L 6 GLN L 34 ASN L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.184969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.169220 restraints weight = 2882.804| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.91 r_work: 0.3853 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2334 Z= 0.226 Angle : 0.676 7.188 3173 Z= 0.353 Chirality : 0.047 0.214 340 Planarity : 0.005 0.046 402 Dihedral : 5.353 20.342 319 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 6.67 % Allowed : 18.43 % Favored : 74.90 % 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: -1.96 (0.49), residues: 285 helix: None (None), residues: 0 sheet: -0.68 (0.42), residues: 146 loop : -1.98 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.001 0.000 HIS L 55 PHE 0.006 0.001 PHE L 87 TYR 0.015 0.002 TYR A1358 ARG 0.009 0.001 ARG H 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7602 (tt0) outliers start: 17 outliers final: 8 residues processed: 56 average time/residue: 0.8628 time to fit residues: 49.8654 Evaluate side-chains 49 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 44 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.0870 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN H 109 GLN L 3 GLN L 34 ASN L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.185535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.170122 restraints weight = 2891.109| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 1.90 r_work: 0.3829 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2334 Z= 0.225 Angle : 0.692 7.158 3173 Z= 0.359 Chirality : 0.047 0.173 340 Planarity : 0.005 0.040 402 Dihedral : 5.344 20.116 319 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 6.27 % Allowed : 20.39 % Favored : 73.33 % 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: -1.99 (0.48), residues: 285 helix: None (None), residues: 0 sheet: -0.64 (0.43), residues: 140 loop : -2.03 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.001 0.000 HIS L 55 PHE 0.005 0.001 PHE L 87 TYR 0.014 0.002 TYR A1358 ARG 0.010 0.001 ARG H 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7587 (tt0) outliers start: 16 outliers final: 8 residues processed: 58 average time/residue: 0.8945 time to fit residues: 53.4486 Evaluate side-chains 51 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 44 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 22 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.185146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.169834 restraints weight = 2847.597| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 1.87 r_work: 0.3844 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2334 Z= 0.260 Angle : 0.706 7.208 3173 Z= 0.368 Chirality : 0.047 0.170 340 Planarity : 0.005 0.044 402 Dihedral : 5.454 20.145 319 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 6.27 % Allowed : 22.75 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.48), residues: 285 helix: None (None), residues: 0 sheet: -0.75 (0.43), residues: 140 loop : -2.05 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A1199 HIS 0.001 0.001 HIS L 55 PHE 0.005 0.001 PHE L 87 TYR 0.015 0.002 TYR A1358 ARG 0.012 0.002 ARG H 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7579 (tt0) outliers start: 16 outliers final: 8 residues processed: 55 average time/residue: 0.7724 time to fit residues: 44.0764 Evaluate side-chains 50 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 44 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.185351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.170184 restraints weight = 2910.314| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.89 r_work: 0.3861 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2334 Z= 0.243 Angle : 0.720 7.156 3173 Z= 0.378 Chirality : 0.046 0.169 340 Planarity : 0.005 0.050 402 Dihedral : 5.447 21.437 319 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 6.67 % Allowed : 23.53 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.48), residues: 285 helix: None (None), residues: 0 sheet: -0.72 (0.43), residues: 140 loop : -2.10 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 36 HIS 0.001 0.000 HIS H 41 PHE 0.004 0.001 PHE L 87 TYR 0.015 0.002 TYR A1358 ARG 0.013 0.001 ARG H 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: H 82 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7440 (mm-30) REVERT: L 38 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7559 (tt0) outliers start: 17 outliers final: 8 residues processed: 55 average time/residue: 0.7298 time to fit residues: 41.5742 Evaluate side-chains 48 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 44 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 11 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.186394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.171300 restraints weight = 2952.003| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.88 r_work: 0.3866 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2334 Z= 0.223 Angle : 0.708 7.449 3173 Z= 0.370 Chirality : 0.047 0.283 340 Planarity : 0.005 0.055 402 Dihedral : 5.403 20.481 319 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 5.49 % Allowed : 24.31 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.49), residues: 285 helix: None (None), residues: 0 sheet: -0.66 (0.43), residues: 140 loop : -2.10 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1199 HIS 0.001 0.000 HIS L 55 PHE 0.005 0.001 PHE L 87 TYR 0.014 0.002 TYR A1358 ARG 0.014 0.002 ARG H 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 1192 ARG cc_start: 0.6252 (ttp-110) cc_final: 0.6010 (mtp85) REVERT: H 82 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7437 (mm-30) REVERT: L 38 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7534 (tt0) outliers start: 14 outliers final: 9 residues processed: 53 average time/residue: 0.7007 time to fit residues: 38.5600 Evaluate side-chains 50 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 44 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.183397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.168525 restraints weight = 2849.689| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.84 r_work: 0.3846 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2334 Z= 0.299 Angle : 0.742 7.411 3173 Z= 0.389 Chirality : 0.049 0.258 340 Planarity : 0.005 0.046 402 Dihedral : 5.692 20.068 319 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 5.10 % Allowed : 24.31 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.48), residues: 285 helix: None (None), residues: 0 sheet: -0.82 (0.43), residues: 140 loop : -2.19 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1185 HIS 0.001 0.001 HIS L 55 PHE 0.005 0.001 PHE L 87 TYR 0.016 0.002 TYR A1358 ARG 0.011 0.001 ARG A1192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 1192 ARG cc_start: 0.6307 (ttp-110) cc_final: 0.6070 (mtp85) REVERT: L 38 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7501 (tt0) outliers start: 13 outliers final: 10 residues processed: 52 average time/residue: 0.7835 time to fit residues: 42.2148 Evaluate side-chains 51 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 44 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.0370 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.0060 chunk 13 optimal weight: 0.5980 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.189308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.174112 restraints weight = 2885.702| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.88 r_work: 0.3903 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2334 Z= 0.181 Angle : 0.682 7.438 3173 Z= 0.355 Chirality : 0.046 0.227 340 Planarity : 0.005 0.061 402 Dihedral : 5.249 20.083 319 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.31 % Allowed : 25.10 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.49), residues: 285 helix: None (None), residues: 0 sheet: -0.65 (0.42), residues: 145 loop : -2.01 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1199 HIS 0.001 0.000 HIS H 35 PHE 0.004 0.001 PHE L 87 TYR 0.011 0.001 TYR L 86 ARG 0.015 0.002 ARG H 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 1192 ARG cc_start: 0.6188 (ttp-110) cc_final: 0.5983 (mtp85) REVERT: H 82 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7199 (mm-30) REVERT: L 38 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7480 (tt0) outliers start: 11 outliers final: 8 residues processed: 53 average time/residue: 0.7023 time to fit residues: 38.6531 Evaluate side-chains 49 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 44 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 0.0670 chunk 20 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.188664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.173251 restraints weight = 2833.801| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.92 r_work: 0.3892 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2334 Z= 0.211 Angle : 0.685 7.307 3173 Z= 0.360 Chirality : 0.046 0.222 340 Planarity : 0.005 0.043 402 Dihedral : 5.419 20.289 319 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.31 % Allowed : 25.10 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.49), residues: 285 helix: None (None), residues: 0 sheet: -0.65 (0.42), residues: 145 loop : -1.97 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1199 HIS 0.001 0.000 HIS H 41 PHE 0.005 0.001 PHE L 87 TYR 0.012 0.002 TYR A1358 ARG 0.010 0.001 ARG A1192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2315.58 seconds wall clock time: 41 minutes 28.39 seconds (2488.39 seconds total)