Starting phenix.real_space_refine on Mon Feb 10 22:26:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7exa_31367/02_2025/7exa_31367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7exa_31367/02_2025/7exa_31367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7exa_31367/02_2025/7exa_31367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7exa_31367/02_2025/7exa_31367.map" model { file = "/net/cci-nas-00/data/ceres_data/7exa_31367/02_2025/7exa_31367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7exa_31367/02_2025/7exa_31367.cif" } resolution = 2.9 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= 0.007 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 19 5.16 5 C 1942 2.51 5 N 530 2.21 5 O 591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3088 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2968 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 4.36, per 1000 atoms: 1.41 Number of scatterers: 3088 At special positions: 0 Unit cell: (91.74, 66.66, 79.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 6 15.00 O 591 8.00 N 530 7.00 C 1942 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: 0.80 Conformation dependent library (CDL) restraints added in 364.6 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 698 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 1 sheets defined 69.5% alpha, 3.7% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 Processing helix chain 'A' and resid 44 through 61 Processing helix chain 'A' and resid 65 through 78 Processing helix chain 'A' and resid 83 through 92 removed outlier: 4.289A pdb=" N LEU A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.553A pdb=" N GLY A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 179 removed outlier: 3.582A pdb=" N PHE A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 202 removed outlier: 4.202A pdb=" N ASP A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.639A pdb=" N SER A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 242 Processing helix chain 'A' and resid 248 through 262 removed outlier: 3.655A pdb=" N MET A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.770A pdb=" N GLY A 307 " --> pdb=" O TYR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 325 through 328 Processing helix chain 'A' and resid 329 through 344 removed outlier: 3.653A pdb=" N VAL A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 358 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.275A pdb=" N VAL A 35 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N CYS A 102 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL A 37 " --> pdb=" O CYS A 102 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE A 104 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL A 39 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLY A 106 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 115 " --> pdb=" O ASP A 105 " (cutoff:3.500A) 167 hydrogen bonds defined for protein. 474 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 697 1.33 - 1.45: 697 1.45 - 1.57: 1725 1.57 - 1.69: 11 1.69 - 1.81: 31 Bond restraints: 3161 Sorted by residual: bond pdb=" N THR A 145 " pdb=" CA THR A 145 " ideal model delta sigma weight residual 1.453 1.487 -0.033 9.20e-03 1.18e+04 1.32e+01 bond pdb=" N GLN A 187 " pdb=" CA GLN A 187 " ideal model delta sigma weight residual 1.455 1.489 -0.034 9.60e-03 1.09e+04 1.25e+01 bond pdb=" N ILE A 26 " pdb=" CA ILE A 26 " ideal model delta sigma weight residual 1.462 1.496 -0.035 1.01e-02 9.80e+03 1.18e+01 bond pdb=" N LEU A 79 " pdb=" CA LEU A 79 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.04e-02 9.25e+03 9.99e+00 bond pdb=" N VAL A 39 " pdb=" CA VAL A 39 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.56e+00 ... (remaining 3156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 3694 1.77 - 3.53: 545 3.53 - 5.30: 56 5.30 - 7.07: 5 7.07 - 8.83: 4 Bond angle restraints: 4304 Sorted by residual: angle pdb=" C4' U B 23 " pdb=" C3' U B 23 " pdb=" O3' U B 23 " ideal model delta sigma weight residual 113.00 121.83 -8.83 1.50e+00 4.44e-01 3.47e+01 angle pdb=" C4' U B 24 " pdb=" C3' U B 24 " pdb=" O3' U B 24 " ideal model delta sigma weight residual 113.00 121.10 -8.10 1.50e+00 4.44e-01 2.91e+01 angle pdb=" C4' U B 20 " pdb=" C3' U B 20 " pdb=" O3' U B 20 " ideal model delta sigma weight residual 113.00 120.61 -7.61 1.50e+00 4.44e-01 2.57e+01 angle pdb=" CA GLY A 244 " pdb=" C GLY A 244 " pdb=" O GLY A 244 " ideal model delta sigma weight residual 122.28 118.38 3.90 1.00e+00 1.00e+00 1.52e+01 angle pdb=" O2' U B 20 " pdb=" C2' U B 20 " pdb=" C1' U B 20 " ideal model delta sigma weight residual 108.40 102.64 5.76 1.50e+00 4.44e-01 1.47e+01 ... (remaining 4299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 1688 17.89 - 35.79: 185 35.79 - 53.68: 40 53.68 - 71.58: 13 71.58 - 89.47: 5 Dihedral angle restraints: 1931 sinusoidal: 839 harmonic: 1092 Sorted by residual: dihedral pdb=" C5' U B 25 " pdb=" C4' U B 25 " pdb=" C3' U B 25 " pdb=" O3' U B 25 " ideal model delta sinusoidal sigma weight residual 147.00 106.23 40.77 1 8.00e+00 1.56e-02 3.64e+01 dihedral pdb=" C4' U B 25 " pdb=" C3' U B 25 " pdb=" C2' U B 25 " pdb=" C1' U B 25 " ideal model delta sinusoidal sigma weight residual -35.00 0.49 -35.49 1 8.00e+00 1.56e-02 2.79e+01 dihedral pdb=" O4' U B 25 " pdb=" C4' U B 25 " pdb=" C3' U B 25 " pdb=" C2' U B 25 " ideal model delta sinusoidal sigma weight residual 24.00 -11.43 35.43 1 8.00e+00 1.56e-02 2.78e+01 ... (remaining 1928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 294 0.052 - 0.105: 120 0.105 - 0.157: 40 0.157 - 0.209: 14 0.209 - 0.261: 12 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA LEU A 90 " pdb=" N LEU A 90 " pdb=" C LEU A 90 " pdb=" CB LEU A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ILE A 26 " pdb=" N ILE A 26 " pdb=" C ILE A 26 " pdb=" CB ILE A 26 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C3' U B 23 " pdb=" C4' U B 23 " pdb=" O3' U B 23 " pdb=" C2' U B 23 " both_signs ideal model delta sigma weight residual False -2.48 -2.23 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 477 not shown) Planarity restraints: 543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 277 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C LEU A 277 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU A 277 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY A 278 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 24 " -0.020 2.00e-02 2.50e+03 1.21e-02 3.30e+00 pdb=" N1 U B 24 " 0.030 2.00e-02 2.50e+03 pdb=" C2 U B 24 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U B 24 " -0.000 2.00e-02 2.50e+03 pdb=" N3 U B 24 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U B 24 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U B 24 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U B 24 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 24 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 314 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" C ALA A 314 " 0.030 2.00e-02 2.50e+03 pdb=" O ALA A 314 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 315 " -0.010 2.00e-02 2.50e+03 ... (remaining 540 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 16 2.57 - 3.15: 2400 3.15 - 3.73: 4705 3.73 - 4.32: 6964 4.32 - 4.90: 11041 Nonbonded interactions: 25126 Sorted by model distance: nonbonded pdb=" O LYS A 180 " pdb=" O ALA A 184 " model vdw 1.984 3.040 nonbonded pdb=" OG SER A 94 " pdb=" OE1 GLN A 231 " model vdw 2.252 3.040 nonbonded pdb=" O SER A 61 " pdb=" NH2 ARG A 69 " model vdw 2.265 3.120 nonbonded pdb=" OD1 ASN A 63 " pdb=" OD2 ASP A 136 " model vdw 2.385 3.040 nonbonded pdb=" O ALA A 64 " pdb=" NH1 ARG A 69 " model vdw 2.394 3.120 ... (remaining 25121 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: 5.830 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: 0.300 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.260 Find NCS groups from input model: 0.050 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:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.010 0.042 3161 Z= 0.684 Angle : 1.219 8.833 4304 Z= 0.894 Chirality : 0.074 0.261 480 Planarity : 0.005 0.030 543 Dihedral : 16.181 89.470 1233 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.60 % Allowed : 9.94 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.40), residues: 372 helix: -0.46 (0.31), residues: 223 sheet: 0.89 (1.43), residues: 14 loop : 0.20 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 175 HIS 0.003 0.001 HIS A 68 PHE 0.016 0.003 PHE A 289 TYR 0.022 0.003 TYR A 361 ARG 0.003 0.001 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.323 Fit side-chains REVERT: A 6 LYS cc_start: 0.8325 (mttt) cc_final: 0.8024 (mttp) REVERT: A 65 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7552 (mtp180) REVERT: A 88 ILE cc_start: 0.7996 (mm) cc_final: 0.7723 (mm) REVERT: A 214 GLU cc_start: 0.6853 (mp0) cc_final: 0.6228 (mm-30) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 1.6592 time to fit residues: 103.2520 Evaluate side-chains 43 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 248 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 0.0770 chunk 18 optimal weight: 0.0000 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.6148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 63 ASN A 121 ASN A 212 GLN A 238 GLN A 346 GLN A 373 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.132401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.111617 restraints weight = 3013.481| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.01 r_work: 0.2877 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3161 Z= 0.186 Angle : 0.528 4.968 4304 Z= 0.284 Chirality : 0.040 0.192 480 Planarity : 0.004 0.034 543 Dihedral : 9.706 60.381 521 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.88 % Allowed : 12.18 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.45), residues: 372 helix: 1.46 (0.36), residues: 220 sheet: 1.37 (1.46), residues: 14 loop : 1.15 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 175 HIS 0.003 0.001 HIS A 68 PHE 0.012 0.001 PHE A 289 TYR 0.015 0.001 TYR A 361 ARG 0.004 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.312 Fit side-chains REVERT: A 6 LYS cc_start: 0.8515 (mttt) cc_final: 0.8229 (mttt) REVERT: A 208 ARG cc_start: 0.7860 (ttt-90) cc_final: 0.7173 (ttp-170) REVERT: A 214 GLU cc_start: 0.7009 (mp0) cc_final: 0.6436 (tp30) outliers start: 9 outliers final: 1 residues processed: 50 average time/residue: 1.9012 time to fit residues: 96.8673 Evaluate side-chains 50 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 0.0370 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 68 HIS A 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.133308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.112308 restraints weight = 3051.071| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.04 r_work: 0.2873 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3161 Z= 0.168 Angle : 0.484 4.790 4304 Z= 0.258 Chirality : 0.039 0.189 480 Planarity : 0.004 0.032 543 Dihedral : 8.975 60.335 516 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.56 % Allowed : 13.14 % Favored : 84.29 % 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: 2.32 (0.44), residues: 372 helix: 1.83 (0.36), residues: 220 sheet: 1.75 (1.46), residues: 14 loop : 1.25 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 175 HIS 0.002 0.001 HIS A 68 PHE 0.010 0.001 PHE A 163 TYR 0.014 0.001 TYR A 361 ARG 0.002 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.356 Fit side-chains REVERT: A 6 LYS cc_start: 0.8484 (mttt) cc_final: 0.8210 (mttt) REVERT: A 208 ARG cc_start: 0.7884 (ttt-90) cc_final: 0.7192 (ttp-170) REVERT: A 214 GLU cc_start: 0.6997 (mp0) cc_final: 0.6426 (tp30) outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 1.6380 time to fit residues: 103.7005 Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.133212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.114164 restraints weight = 3080.568| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.03 r_work: 0.2826 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3161 Z= 0.163 Angle : 0.474 5.059 4304 Z= 0.251 Chirality : 0.038 0.191 480 Planarity : 0.003 0.031 543 Dihedral : 8.863 60.310 516 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 3.21 % Allowed : 13.78 % Favored : 83.01 % 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: 2.47 (0.44), residues: 372 helix: 1.99 (0.36), residues: 220 sheet: 2.12 (1.49), residues: 14 loop : 1.20 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 281 HIS 0.001 0.000 HIS A 149 PHE 0.010 0.001 PHE A 163 TYR 0.014 0.001 TYR A 361 ARG 0.004 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.316 Fit side-chains REVERT: A 6 LYS cc_start: 0.8491 (mttt) cc_final: 0.8216 (mttp) REVERT: A 214 GLU cc_start: 0.7056 (mp0) cc_final: 0.6606 (tp30) REVERT: A 317 GLU cc_start: 0.7659 (pt0) cc_final: 0.7395 (mt-10) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 1.7153 time to fit residues: 92.8022 Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.128321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.107283 restraints weight = 3105.065| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 0.97 r_work: 0.2736 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3161 Z= 0.283 Angle : 0.574 6.478 4304 Z= 0.299 Chirality : 0.042 0.193 480 Planarity : 0.004 0.035 543 Dihedral : 9.219 60.329 516 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.49 % Allowed : 12.50 % Favored : 83.01 % 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 (0.43), residues: 372 helix: 1.70 (0.35), residues: 220 sheet: 2.43 (1.50), residues: 14 loop : 0.94 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 281 HIS 0.001 0.000 HIS A 87 PHE 0.014 0.002 PHE A 289 TYR 0.018 0.002 TYR A 361 ARG 0.004 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.337 Fit side-chains REVERT: A 6 LYS cc_start: 0.8509 (mttt) cc_final: 0.8242 (mttp) REVERT: A 214 GLU cc_start: 0.7076 (mp0) cc_final: 0.6563 (tp30) REVERT: A 317 GLU cc_start: 0.7773 (pt0) cc_final: 0.7492 (mt-10) outliers start: 14 outliers final: 8 residues processed: 54 average time/residue: 1.6646 time to fit residues: 91.8188 Evaluate side-chains 48 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 35 optimal weight: 0.0170 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 overall best weight: 1.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.133596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.117066 restraints weight = 3124.865| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 0.68 r_work: 0.2895 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3161 Z= 0.145 Angle : 0.456 4.602 4304 Z= 0.243 Chirality : 0.038 0.194 480 Planarity : 0.003 0.031 543 Dihedral : 8.785 60.241 516 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 3.21 % Allowed : 13.14 % Favored : 83.65 % 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: 2.46 (0.44), residues: 372 helix: 2.01 (0.36), residues: 220 sheet: 2.42 (1.54), residues: 14 loop : 1.09 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 175 HIS 0.001 0.000 HIS A 149 PHE 0.009 0.001 PHE A 163 TYR 0.014 0.001 TYR A 361 ARG 0.003 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.385 Fit side-chains REVERT: A 41 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7714 (t0) REVERT: A 214 GLU cc_start: 0.7165 (mp0) cc_final: 0.6630 (tp30) REVERT: A 317 GLU cc_start: 0.7802 (pt0) cc_final: 0.7527 (mt-10) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 1.7338 time to fit residues: 92.0794 Evaluate side-chains 50 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 0.0370 chunk 7 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.135582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.118875 restraints weight = 3063.993| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 0.70 r_work: 0.2925 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3161 Z= 0.133 Angle : 0.437 4.565 4304 Z= 0.232 Chirality : 0.038 0.188 480 Planarity : 0.003 0.032 543 Dihedral : 8.628 60.159 516 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.88 % Allowed : 13.78 % Favored : 83.33 % 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: 2.67 (0.44), residues: 372 helix: 2.21 (0.36), residues: 220 sheet: 2.52 (1.56), residues: 14 loop : 1.13 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 281 HIS 0.001 0.000 HIS A 149 PHE 0.008 0.001 PHE A 163 TYR 0.013 0.001 TYR A 361 ARG 0.003 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.320 Fit side-chains REVERT: A 41 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7745 (t0) REVERT: A 44 ASN cc_start: 0.6552 (m-40) cc_final: 0.5770 (t0) REVERT: A 214 GLU cc_start: 0.7167 (mp0) cc_final: 0.6620 (tp30) REVERT: A 274 LYS cc_start: 0.8926 (ttmp) cc_final: 0.8726 (ttmm) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 1.6639 time to fit residues: 85.0224 Evaluate side-chains 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 33 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.132343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.111291 restraints weight = 3110.138| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.05 r_work: 0.2867 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3161 Z= 0.180 Angle : 0.479 4.785 4304 Z= 0.252 Chirality : 0.039 0.189 480 Planarity : 0.003 0.031 543 Dihedral : 8.766 60.196 516 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.21 % Allowed : 14.42 % Favored : 82.37 % 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: 2.58 (0.44), residues: 372 helix: 2.11 (0.35), residues: 220 sheet: 2.54 (1.55), residues: 14 loop : 1.14 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 281 HIS 0.001 0.000 HIS A 87 PHE 0.011 0.001 PHE A 270 TYR 0.015 0.001 TYR A 361 ARG 0.003 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.404 Fit side-chains REVERT: A 6 LYS cc_start: 0.8489 (mttt) cc_final: 0.8223 (mttp) REVERT: A 41 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7696 (t0) REVERT: A 214 GLU cc_start: 0.7044 (mp0) cc_final: 0.6507 (tp30) outliers start: 10 outliers final: 7 residues processed: 58 average time/residue: 1.5019 time to fit residues: 89.1999 Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.134686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.115134 restraints weight = 3069.732| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 0.97 r_work: 0.2894 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3161 Z= 0.138 Angle : 0.441 4.618 4304 Z= 0.233 Chirality : 0.037 0.190 480 Planarity : 0.003 0.032 543 Dihedral : 8.624 60.151 516 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 2.56 % Allowed : 15.38 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.44), residues: 372 helix: 2.20 (0.36), residues: 220 sheet: 2.56 (1.56), residues: 14 loop : 1.20 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 281 HIS 0.001 0.000 HIS A 87 PHE 0.009 0.001 PHE A 163 TYR 0.014 0.001 TYR A 361 ARG 0.003 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.294 Fit side-chains REVERT: A 41 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7736 (t0) REVERT: A 44 ASN cc_start: 0.6543 (m-40) cc_final: 0.5731 (t0) REVERT: A 214 GLU cc_start: 0.7063 (mp0) cc_final: 0.6545 (tp30) REVERT: A 253 MET cc_start: 0.8399 (ttm) cc_final: 0.8188 (ttp) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 1.6916 time to fit residues: 88.0389 Evaluate side-chains 51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 35 optimal weight: 0.0070 chunk 28 optimal weight: 7.9990 overall best weight: 3.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.129199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.108449 restraints weight = 3061.094| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 0.97 r_work: 0.2719 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3161 Z= 0.269 Angle : 0.552 5.657 4304 Z= 0.288 Chirality : 0.041 0.192 480 Planarity : 0.004 0.030 543 Dihedral : 9.061 60.240 516 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.88 % Allowed : 15.06 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.43), residues: 372 helix: 1.85 (0.35), residues: 220 sheet: 2.60 (1.54), residues: 14 loop : 1.00 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP A 281 HIS 0.001 0.001 HIS A 87 PHE 0.014 0.002 PHE A 289 TYR 0.019 0.002 TYR A 360 ARG 0.003 0.000 ARG A 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.380 Fit side-chains REVERT: A 6 LYS cc_start: 0.8550 (mttt) cc_final: 0.8287 (mttp) REVERT: A 41 ASN cc_start: 0.8038 (OUTLIER) cc_final: 0.7650 (t0) REVERT: A 214 GLU cc_start: 0.7102 (mp0) cc_final: 0.6571 (tp30) outliers start: 9 outliers final: 7 residues processed: 53 average time/residue: 1.6394 time to fit residues: 88.8118 Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 28 optimal weight: 0.0570 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 149 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.137513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.119119 restraints weight = 3106.935| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.46 r_work: 0.2956 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3161 Z= 0.124 Angle : 0.428 4.436 4304 Z= 0.228 Chirality : 0.037 0.197 480 Planarity : 0.003 0.034 543 Dihedral : 8.582 60.123 516 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.92 % Allowed : 16.35 % Favored : 81.73 % 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: 2.57 (0.44), residues: 372 helix: 2.13 (0.35), residues: 220 sheet: 2.39 (1.56), residues: 14 loop : 1.09 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 281 HIS 0.001 0.000 HIS A 149 PHE 0.008 0.001 PHE A 163 TYR 0.013 0.001 TYR A 361 ARG 0.003 0.000 ARG A 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3210.24 seconds wall clock time: 57 minutes 20.42 seconds (3440.42 seconds total)