Starting phenix.real_space_refine on Wed Mar 5 17:22:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7exa_31367/03_2025/7exa_31367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7exa_31367/03_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_31367/03_2025/7exa_31367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7exa_31367/03_2025/7exa_31367.map" model { file = "/net/cci-nas-00/data/ceres_data/7exa_31367/03_2025/7exa_31367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7exa_31367/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.77, per 1000 atoms: 1.22 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: 0.79 Conformation dependent library (CDL) restraints added in 353.7 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: 1.08 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: 0.91 Time building geometry restraints manager: 0.90 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: 5.360 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.400 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: 0.010 Load rotamer database and sin/cos tables:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.440 ------------------------------------------------------------------------------- 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 : 0.342 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: 1.6818 time to fit residues: 104.6873 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 : 0.322 ------------------------------------------------------------------------------- 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 = 70)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.111610 restraints weight = 3013.481| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.01 r_work: 0.2877 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 : 0.340 Fit side-chains REVERT: A 6 LYS cc_start: 0.8510 (mttt) cc_final: 0.8225 (mttt) REVERT: A 208 ARG cc_start: 0.7866 (ttt-90) cc_final: 0.7182 (ttp-170) REVERT: A 214 GLU cc_start: 0.7016 (mp0) cc_final: 0.6452 (tp30) outliers start: 9 outliers final: 1 residues processed: 50 average time/residue: 1.9850 time to fit residues: 101.2492 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 : 0.331 ------------------------------------------------------------------------------- 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: 0.0970 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 overall best weight: 1.5982 ------------------------------------------------------------------------------- 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 = 0.133304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.113270 restraints weight = 3050.598| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.17 r_work: 0.2820 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2207 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= 0.170 Angle : 0.486 4.838 4304 Z= 0.258 Chirality : 0.039 0.188 480 Planarity : 0.004 0.032 543 Dihedral : 8.948 60.322 516 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.11 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: 1.74 (1.46), residues: 14 loop : 1.24 (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 270 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 : 0.344 Fit side-chains REVERT: A 6 LYS cc_start: 0.8441 (mttt) cc_final: 0.8155 (mttt) REVERT: A 208 ARG cc_start: 0.7850 (ttt-90) cc_final: 0.7194 (ttp-170) REVERT: A 214 GLU cc_start: 0.6969 (mp0) cc_final: 0.6459 (tp30) outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 1.6421 time to fit residues: 103.9722 Evaluate side-chains 53 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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: 8.9990 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.130626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.109975 restraints weight = 3122.606| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 0.94 r_work: 0.2762 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3161 Z= 0.210 Angle : 0.519 5.955 4304 Z= 0.272 Chirality : 0.040 0.192 480 Planarity : 0.004 0.032 543 Dihedral : 9.037 60.353 516 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.53 % Allowed : 13.46 % 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: 2.23 (0.44), residues: 372 helix: 1.84 (0.36), residues: 220 sheet: 2.13 (1.48), residues: 14 loop : 1.01 (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 0.002 PHE A 289 TYR 0.016 0.002 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: 11 poor density : 47 time to evaluate : 0.317 Fit side-chains REVERT: A 6 LYS cc_start: 0.8506 (mttt) cc_final: 0.8231 (mttp) REVERT: A 41 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7619 (t0) REVERT: A 208 ARG cc_start: 0.7913 (ttt-90) cc_final: 0.7219 (ttp-170) REVERT: A 214 GLU cc_start: 0.7054 (mp0) cc_final: 0.6517 (tp30) REVERT: A 317 GLU cc_start: 0.7717 (pt0) cc_final: 0.7436 (mt-10) outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 1.6723 time to fit residues: 92.3023 Evaluate side-chains 60 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.129924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.108855 restraints weight = 3072.732| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.02 r_work: 0.2840 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3161 Z= 0.219 Angle : 0.523 5.153 4304 Z= 0.274 Chirality : 0.040 0.192 480 Planarity : 0.004 0.031 543 Dihedral : 9.041 60.310 516 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.49 % Allowed : 12.18 % 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: 2.20 (0.43), residues: 372 helix: 1.82 (0.36), residues: 220 sheet: 2.29 (1.50), residues: 14 loop : 0.95 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 281 HIS 0.001 0.000 HIS A 149 PHE 0.011 0.002 PHE A 289 TYR 0.017 0.002 TYR A 361 ARG 0.003 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 66 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.337 Fit side-chains REVERT: A 6 LYS cc_start: 0.8515 (mttt) cc_final: 0.8247 (mttp) REVERT: A 41 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7641 (t0) REVERT: A 214 GLU cc_start: 0.7068 (mp0) cc_final: 0.6522 (tp30) REVERT: A 317 GLU cc_start: 0.7790 (pt0) cc_final: 0.7475 (mt-10) outliers start: 14 outliers final: 8 residues processed: 60 average time/residue: 1.4361 time to fit residues: 88.1738 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 : 0.314 ------------------------------------------------------------------------------- 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 92 ASP 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: 0.0770 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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 = 0.3355 r_free = 0.3355 target = 0.134307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.118537 restraints weight = 3139.950| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 0.64 r_work: 0.2918 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2642 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= 0.137 Angle : 0.447 4.600 4304 Z= 0.238 Chirality : 0.038 0.192 480 Planarity : 0.003 0.031 543 Dihedral : 8.719 60.225 516 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 3.85 % Allowed : 12.50 % 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: 2.56 (0.44), residues: 372 helix: 2.10 (0.36), residues: 220 sheet: 2.38 (1.55), residues: 14 loop : 1.15 (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 149 PHE 0.009 0.001 PHE A 163 TYR 0.013 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 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.340 Fit side-chains REVERT: A 41 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7710 (t0) REVERT: A 214 GLU cc_start: 0.7167 (mp0) cc_final: 0.6625 (tp30) REVERT: A 317 GLU cc_start: 0.7762 (pt0) cc_final: 0.7522 (mt-10) outliers start: 12 outliers final: 6 residues processed: 55 average time/residue: 1.7473 time to fit residues: 98.1600 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 : 0.328 ------------------------------------------------------------------------------- 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: 3.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.131360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.111225 restraints weight = 3067.955| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.00 r_work: 0.2842 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3161 Z= 0.190 Angle : 0.491 4.799 4304 Z= 0.259 Chirality : 0.039 0.191 480 Planarity : 0.004 0.030 543 Dihedral : 8.853 60.234 516 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.88 % Allowed : 14.74 % 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: 2.46 (0.43), residues: 372 helix: 2.04 (0.36), residues: 220 sheet: 2.49 (1.54), residues: 14 loop : 1.03 (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 0.002 PHE A 270 TYR 0.015 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 56 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.376 Fit side-chains REVERT: A 6 LYS cc_start: 0.8520 (mttt) cc_final: 0.8270 (mttp) REVERT: A 41 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7698 (t0) REVERT: A 214 GLU cc_start: 0.7057 (mp0) cc_final: 0.6521 (tp30) REVERT: A 317 GLU cc_start: 0.7736 (pt0) cc_final: 0.7486 (mt-10) outliers start: 9 outliers final: 6 residues processed: 53 average time/residue: 1.7008 time to fit residues: 92.1448 Evaluate side-chains 53 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 28 optimal weight: 0.0070 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.135309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.118823 restraints weight = 3081.375| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 0.69 r_work: 0.2931 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3161 Z= 0.133 Angle : 0.438 4.581 4304 Z= 0.233 Chirality : 0.038 0.192 480 Planarity : 0.003 0.032 543 Dihedral : 8.619 60.149 516 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 3.53 % Allowed : 13.78 % Favored : 82.69 % 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: 2.65 (0.44), residues: 372 helix: 2.20 (0.36), residues: 220 sheet: 2.52 (1.56), residues: 14 loop : 1.11 (0.52), 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 0.008 0.001 PHE A 163 TYR 0.013 0.001 TYR A 361 ARG 0.003 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 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 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.318 Fit side-chains REVERT: A 41 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7727 (t0) REVERT: A 214 GLU cc_start: 0.7150 (mp0) cc_final: 0.6636 (tp30) outliers start: 11 outliers final: 7 residues processed: 52 average time/residue: 1.6160 time to fit residues: 85.8196 Evaluate side-chains 51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 100 GLU 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: 6.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.138501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.121878 restraints weight = 3063.157| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 0.92 r_work: 0.2927 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3161 Z= 0.116 Angle : 0.416 4.427 4304 Z= 0.219 Chirality : 0.037 0.181 480 Planarity : 0.003 0.033 543 Dihedral : 8.491 59.992 516 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.45 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: 2.85 (0.44), residues: 372 helix: 2.35 (0.35), residues: 220 sheet: 2.64 (1.57), residues: 14 loop : 1.21 (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 87 PHE 0.008 0.001 PHE A 163 TYR 0.012 0.001 TYR A 361 ARG 0.003 0.000 ARG A 101 *********************** 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 56 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.335 Fit side-chains REVERT: A 41 ASN cc_start: 0.7984 (OUTLIER) cc_final: 0.7699 (t0) REVERT: A 44 ASN cc_start: 0.6173 (m-40) cc_final: 0.5702 (t0) REVERT: A 214 GLU cc_start: 0.7031 (mp0) cc_final: 0.6512 (mm-30) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 1.7125 time to fit residues: 96.1554 Evaluate side-chains 50 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 41 ASN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 100 GLU 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: 10.0000 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.132139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.117805 restraints weight = 2988.662| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 0.59 r_work: 0.2891 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2774 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= 0.183 Angle : 0.481 4.759 4304 Z= 0.254 Chirality : 0.039 0.187 480 Planarity : 0.003 0.031 543 Dihedral : 8.689 60.105 516 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 : 2.56 % Allowed : 15.71 % 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: 2.70 (0.44), residues: 372 helix: 2.20 (0.35), residues: 220 sheet: 2.71 (1.56), residues: 14 loop : 1.18 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 281 HIS 0.001 0.001 HIS A 149 PHE 0.011 0.001 PHE A 270 TYR 0.015 0.001 TYR A 360 ARG 0.005 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 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.351 Fit side-chains REVERT: A 6 LYS cc_start: 0.8618 (mttt) cc_final: 0.8377 (mttp) REVERT: A 41 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7783 (t0) REVERT: A 214 GLU cc_start: 0.7175 (mp0) cc_final: 0.6592 (tp30) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 1.6329 time to fit residues: 85.1016 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 : 0.279 ------------------------------------------------------------------------------- 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 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 100 GLU 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: 10.0000 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3353 r_free = 0.3353 target = 0.133818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.115389 restraints weight = 3078.373| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.26 r_work: 0.2850 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3161 Z= 0.152 Angle : 0.458 4.646 4304 Z= 0.241 Chirality : 0.038 0.190 480 Planarity : 0.003 0.032 543 Dihedral : 8.628 60.122 516 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.56 % Allowed : 15.71 % 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: 2.66 (0.44), residues: 372 helix: 2.20 (0.35), residues: 220 sheet: 2.63 (1.55), residues: 14 loop : 1.12 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 281 HIS 0.001 0.001 HIS A 149 PHE 0.009 0.001 PHE A 270 TYR 0.014 0.001 TYR A 361 ARG 0.005 0.000 ARG A 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3288.60 seconds wall clock time: 56 minutes 48.74 seconds (3408.74 seconds total)