Starting phenix.real_space_refine on Tue Mar 11 16:22:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhy_24471/03_2025/7rhy_24471_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhy_24471/03_2025/7rhy_24471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rhy_24471/03_2025/7rhy_24471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhy_24471/03_2025/7rhy_24471.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhy_24471/03_2025/7rhy_24471_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhy_24471/03_2025/7rhy_24471_neut.cif" } resolution = 3.91 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= 0.001 sd= 0.055 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: 6 Type Number sf(0) Gaussians P 49 5.49 5 S 14 5.16 5 C 1968 2.51 5 N 640 2.21 5 O 722 1.98 5 H 2957 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6350 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 4789 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 7, 'TRANS': 293} Chain breaks: 1 Chain: "B" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1561 Classifications: {'DNA': 49} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 48} Time building chain proxies: 4.40, per 1000 atoms: 0.69 Number of scatterers: 6350 At special positions: 0 Unit cell: (59.5055, 74.8617, 92.1375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 49 15.00 O 722 8.00 N 640 7.00 C 1968 6.00 H 2957 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 527.7 milliseconds 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 562 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 1 sheets defined 67.4% alpha, 3.3% beta 23 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 20 through 34 removed outlier: 3.665A pdb=" N MET A 30 " --> pdb=" O ASN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 59 removed outlier: 3.595A pdb=" N MET A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 46 " --> pdb=" O TRP A 42 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 47 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.507A pdb=" N ILE A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 109 Processing helix chain 'A' and resid 110 through 127 Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.651A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 170 removed outlier: 3.553A pdb=" N ASN A 160 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 179 through 180 No H-bonds generated for 'chain 'A' and resid 179 through 180' Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.916A pdb=" N LEU A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 233 removed outlier: 4.100A pdb=" N ASP A 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 233' Processing helix chain 'A' and resid 257 through 273 removed outlier: 3.633A pdb=" N GLY A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.174A pdb=" N ALA A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 319 through 325 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 187 removed outlier: 4.177A pdb=" N MET A 193 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 209 " --> pdb=" O ILE A 197 " (cutoff:3.500A) 129 hydrogen bonds defined for protein. 384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 2953 1.03 - 1.23: 29 1.23 - 1.42: 1533 1.42 - 1.61: 1974 1.61 - 1.81: 24 Bond restraints: 6513 Sorted by residual: bond pdb=" C4' DG B 9 " pdb=" O4' DG B 9 " ideal model delta sigma weight residual 1.450 1.415 0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" N SER A 20 " pdb=" CA SER A 20 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N SER A 20 " pdb=" H SER A 20 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C2' DT B 10 " pdb=" C1' DT B 10 " ideal model delta sigma weight residual 1.525 1.497 0.028 2.00e-02 2.50e+03 1.93e+00 bond pdb=" C4' DC B 37 " pdb=" O4' DC B 37 " ideal model delta sigma weight residual 1.450 1.424 0.026 2.00e-02 2.50e+03 1.71e+00 ... (remaining 6508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 10812 1.36 - 2.72: 869 2.72 - 4.08: 52 4.08 - 5.44: 10 5.44 - 6.80: 3 Bond angle restraints: 11746 Sorted by residual: angle pdb=" C3' DC B 15 " pdb=" O3' DC B 15 " pdb=" P DA B 16 " ideal model delta sigma weight residual 120.20 125.87 -5.67 1.50e+00 4.44e-01 1.43e+01 angle pdb=" C2' DG B 9 " pdb=" C1' DG B 9 " pdb=" N9 DG B 9 " ideal model delta sigma weight residual 113.50 118.42 -4.92 1.50e+00 4.44e-01 1.07e+01 angle pdb=" C3' DT B 10 " pdb=" O3' DT B 10 " pdb=" P DA B 11 " ideal model delta sigma weight residual 120.20 125.07 -4.87 1.50e+00 4.44e-01 1.05e+01 angle pdb=" C2' DG B 14 " pdb=" C1' DG B 14 " pdb=" N9 DG B 14 " ideal model delta sigma weight residual 113.50 118.02 -4.52 1.50e+00 4.44e-01 9.10e+00 angle pdb=" C2' DT B 10 " pdb=" C1' DT B 10 " pdb=" N1 DT B 10 " ideal model delta sigma weight residual 113.50 117.70 -4.20 1.50e+00 4.44e-01 7.85e+00 ... (remaining 11741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.52: 2584 34.52 - 69.04: 281 69.04 - 103.57: 2 103.57 - 138.09: 0 138.09 - 172.61: 1 Dihedral angle restraints: 2868 sinusoidal: 1872 harmonic: 996 Sorted by residual: dihedral pdb=" CA ALA A 212 " pdb=" C ALA A 212 " pdb=" N LEU A 213 " pdb=" CA LEU A 213 " ideal model delta harmonic sigma weight residual -180.00 -154.53 -25.47 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA LYS A 211 " pdb=" C LYS A 211 " pdb=" N ALA A 212 " pdb=" CA ALA A 212 " ideal model delta harmonic sigma weight residual -180.00 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PRO A 250 " pdb=" C PRO A 250 " pdb=" N SER A 251 " pdb=" CA SER A 251 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 2865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 402 0.044 - 0.088: 106 0.088 - 0.132: 40 0.132 - 0.176: 4 0.176 - 0.220: 2 Chirality restraints: 554 Sorted by residual: chirality pdb=" C1' DT B 10 " pdb=" O4' DT B 10 " pdb=" C2' DT B 10 " pdb=" N1 DT B 10 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C3' DC B 15 " pdb=" C4' DC B 15 " pdb=" O3' DC B 15 " pdb=" C2' DC B 15 " both_signs ideal model delta sigma weight residual False -2.66 -2.47 -0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" C1' DC B 21 " pdb=" O4' DC B 21 " pdb=" C2' DC B 21 " pdb=" N1 DC B 21 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 551 not shown) Planarity restraints: 801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT B 10 " 0.041 2.00e-02 2.50e+03 4.29e-02 5.53e+01 pdb=" N1 DT B 10 " -0.119 2.00e-02 2.50e+03 pdb=" C2 DT B 10 " 0.076 2.00e-02 2.50e+03 pdb=" O2 DT B 10 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT B 10 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DT B 10 " 0.001 2.00e-02 2.50e+03 pdb=" O4 DT B 10 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DT B 10 " 0.004 2.00e-02 2.50e+03 pdb=" C7 DT B 10 " 0.009 2.00e-02 2.50e+03 pdb=" C6 DT B 10 " -0.001 2.00e-02 2.50e+03 pdb=" H3 DT B 10 " -0.009 2.00e-02 2.50e+03 pdb=" H6 DT B 10 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA B 11 " 0.039 2.00e-02 2.50e+03 2.98e-02 2.88e+01 pdb=" N9 DA B 11 " -0.088 2.00e-02 2.50e+03 pdb=" C8 DA B 11 " 0.046 2.00e-02 2.50e+03 pdb=" N7 DA B 11 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA B 11 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA B 11 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA B 11 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA B 11 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA B 11 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA B 11 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA B 11 " -0.004 2.00e-02 2.50e+03 pdb=" H8 DA B 11 " -0.005 2.00e-02 2.50e+03 pdb=" H2 DA B 11 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT B 7 " 0.028 2.00e-02 2.50e+03 2.56e-02 1.97e+01 pdb=" N1 DT B 7 " -0.073 2.00e-02 2.50e+03 pdb=" C2 DT B 7 " 0.041 2.00e-02 2.50e+03 pdb=" O2 DT B 7 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT B 7 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT B 7 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT B 7 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DT B 7 " 0.004 2.00e-02 2.50e+03 pdb=" C7 DT B 7 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DT B 7 " 0.003 2.00e-02 2.50e+03 pdb=" H3 DT B 7 " -0.004 2.00e-02 2.50e+03 pdb=" H6 DT B 7 " 0.004 2.00e-02 2.50e+03 ... (remaining 798 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 219 2.19 - 2.80: 11394 2.80 - 3.40: 15364 3.40 - 4.00: 19680 4.00 - 4.60: 30595 Nonbonded interactions: 77252 Sorted by model distance: nonbonded pdb=" H ARG A 181 " pdb=" OD2 ASP A 184 " model vdw 1.593 2.450 nonbonded pdb=" HG1 THR A 41 " pdb=" OP2 DT B 33 " model vdw 1.605 2.450 nonbonded pdb="HH21 ARG A 297 " pdb=" O ASN A 327 " model vdw 1.732 2.450 nonbonded pdb="HH12 ARG A 61 " pdb=" OD1 ASP A 70 " model vdw 1.744 2.450 nonbonded pdb=" HG SER A 287 " pdb=" OP1 DA B 36 " model vdw 1.752 2.450 ... (remaining 77247 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.100 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.620 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3556 Z= 0.257 Angle : 0.805 6.800 5012 Z= 0.511 Chirality : 0.047 0.220 554 Planarity : 0.011 0.100 474 Dihedral : 21.980 172.609 1463 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.80 % Allowed : 1.60 % Favored : 97.60 % 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: -1.06 (0.45), residues: 297 helix: -1.09 (0.33), residues: 183 sheet: 2.44 (1.61), residues: 10 loop : 0.10 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 55 HIS 0.005 0.002 HIS A 91 PHE 0.009 0.003 PHE A 64 TYR 0.010 0.004 TYR A 237 ARG 0.025 0.002 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 THR cc_start: 0.9297 (m) cc_final: 0.8995 (p) REVERT: A 308 GLU cc_start: 0.8446 (tt0) cc_final: 0.8064 (tm-30) REVERT: A 309 ILE cc_start: 0.8785 (mt) cc_final: 0.8559 (mt) REVERT: A 316 THR cc_start: 0.8645 (m) cc_final: 0.8385 (p) outliers start: 2 outliers final: 0 residues processed: 80 average time/residue: 0.5197 time to fit residues: 46.5438 Evaluate side-chains 37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106236 restraints weight = 17540.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.112371 restraints weight = 8258.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116724 restraints weight = 5145.689| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3556 Z= 0.199 Angle : 0.623 5.092 5012 Z= 0.371 Chirality : 0.037 0.126 554 Planarity : 0.004 0.030 474 Dihedral : 25.336 171.361 889 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.60 % Allowed : 10.40 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.48), residues: 297 helix: 0.36 (0.37), residues: 186 sheet: 1.52 (1.71), residues: 10 loop : 0.16 (0.63), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 42 HIS 0.003 0.001 HIS A 269 PHE 0.016 0.002 PHE A 37 TYR 0.011 0.001 TYR A 77 ARG 0.005 0.001 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TRP cc_start: 0.8691 (t-100) cc_final: 0.8290 (t-100) REVERT: A 89 GLN cc_start: 0.7797 (mt0) cc_final: 0.7575 (mt0) REVERT: A 176 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7204 (mt-10) REVERT: A 316 THR cc_start: 0.8598 (m) cc_final: 0.8380 (p) outliers start: 4 outliers final: 4 residues processed: 47 average time/residue: 0.2919 time to fit residues: 17.2233 Evaluate side-chains 42 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 323 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 4 optimal weight: 0.0470 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.104025 restraints weight = 17048.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.110013 restraints weight = 7998.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114138 restraints weight = 5054.775| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3556 Z= 0.192 Angle : 0.591 6.390 5012 Z= 0.353 Chirality : 0.037 0.117 554 Planarity : 0.004 0.031 474 Dihedral : 25.155 170.532 889 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.00 % Allowed : 12.00 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.49), residues: 297 helix: 1.03 (0.39), residues: 186 sheet: 1.11 (1.69), residues: 10 loop : 0.01 (0.62), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 42 HIS 0.002 0.001 HIS A 91 PHE 0.012 0.002 PHE A 37 TYR 0.008 0.001 TYR A 273 ARG 0.003 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7328 (mt-10) REVERT: A 316 THR cc_start: 0.8866 (m) cc_final: 0.8658 (p) outliers start: 5 outliers final: 4 residues processed: 43 average time/residue: 0.2638 time to fit residues: 14.3965 Evaluate side-chains 40 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 166 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.137251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.104932 restraints weight = 17625.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111146 restraints weight = 8089.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115252 restraints weight = 5024.947| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3556 Z= 0.177 Angle : 0.576 5.921 5012 Z= 0.344 Chirality : 0.036 0.116 554 Planarity : 0.003 0.031 474 Dihedral : 25.052 169.693 889 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.60 % Allowed : 14.40 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.50), residues: 297 helix: 1.44 (0.40), residues: 187 sheet: 0.74 (1.45), residues: 10 loop : 0.13 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 42 HIS 0.002 0.000 HIS A 269 PHE 0.008 0.002 PHE A 265 TYR 0.007 0.001 TYR A 273 ARG 0.002 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.8015 (t) REVERT: A 176 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7311 (mt-10) REVERT: A 323 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7909 (t0) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.2270 time to fit residues: 11.0358 Evaluate side-chains 38 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 323 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 22 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.137181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104842 restraints weight = 16865.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.110820 restraints weight = 7752.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.114976 restraints weight = 4848.583| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3556 Z= 0.174 Angle : 0.572 6.781 5012 Z= 0.341 Chirality : 0.036 0.117 554 Planarity : 0.003 0.032 474 Dihedral : 24.987 169.614 889 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.00 % Allowed : 14.80 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.50), residues: 297 helix: 1.82 (0.40), residues: 187 sheet: 0.96 (1.34), residues: 10 loop : 0.02 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 42 HIS 0.002 0.001 HIS A 269 PHE 0.008 0.002 PHE A 265 TYR 0.008 0.001 TYR A 273 ARG 0.003 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.418 Fit side-chains REVERT: A 48 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.8009 (t) REVERT: A 172 LEU cc_start: 0.8939 (mt) cc_final: 0.8738 (mt) REVERT: A 176 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7248 (mt-10) outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.2331 time to fit residues: 11.3890 Evaluate side-chains 38 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 166 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.137490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105182 restraints weight = 16767.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111117 restraints weight = 7709.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115185 restraints weight = 4815.742| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3556 Z= 0.168 Angle : 0.568 7.171 5012 Z= 0.338 Chirality : 0.036 0.110 554 Planarity : 0.003 0.032 474 Dihedral : 24.959 169.582 889 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.40 % Allowed : 16.40 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.50), residues: 297 helix: 1.93 (0.40), residues: 187 sheet: 0.98 (1.22), residues: 10 loop : -0.05 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 42 HIS 0.002 0.000 HIS A 269 PHE 0.007 0.001 PHE A 265 TYR 0.007 0.001 TYR A 273 ARG 0.001 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.390 Fit side-chains REVERT: A 48 VAL cc_start: 0.8267 (OUTLIER) cc_final: 0.8033 (t) REVERT: A 117 MET cc_start: 0.8693 (tpp) cc_final: 0.8489 (tpp) REVERT: A 176 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7255 (mt-10) outliers start: 6 outliers final: 4 residues processed: 38 average time/residue: 0.2301 time to fit residues: 11.4567 Evaluate side-chains 39 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 284 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.137867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105261 restraints weight = 17150.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.111263 restraints weight = 7924.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115343 restraints weight = 4954.989| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3556 Z= 0.163 Angle : 0.563 7.388 5012 Z= 0.336 Chirality : 0.036 0.110 554 Planarity : 0.003 0.032 474 Dihedral : 24.956 169.528 889 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.40 % Allowed : 17.20 % Favored : 80.40 % 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: 1.93 (0.50), residues: 297 helix: 2.05 (0.39), residues: 187 sheet: 1.04 (1.22), residues: 10 loop : -0.14 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 42 HIS 0.002 0.000 HIS A 269 PHE 0.006 0.001 PHE A 265 TYR 0.007 0.001 TYR A 273 ARG 0.001 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.8035 (t) REVERT: A 176 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7245 (mt-10) outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 0.2649 time to fit residues: 13.8031 Evaluate side-chains 41 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 284 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.136754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.104469 restraints weight = 17222.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110465 restraints weight = 7759.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114477 restraints weight = 4819.808| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3556 Z= 0.181 Angle : 0.569 7.479 5012 Z= 0.340 Chirality : 0.036 0.112 554 Planarity : 0.003 0.031 474 Dihedral : 24.982 169.448 889 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.40 % Allowed : 17.60 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.50), residues: 297 helix: 2.08 (0.40), residues: 187 sheet: 1.14 (1.25), residues: 10 loop : -0.16 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 52 HIS 0.002 0.001 HIS A 269 PHE 0.008 0.002 PHE A 265 TYR 0.008 0.001 TYR A 273 ARG 0.001 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8059 (t) outliers start: 6 outliers final: 5 residues processed: 39 average time/residue: 0.2842 time to fit residues: 14.1098 Evaluate side-chains 41 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 299 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 0.0670 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.137574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104810 restraints weight = 17181.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110749 restraints weight = 7939.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114843 restraints weight = 4990.292| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3556 Z= 0.171 Angle : 0.572 7.968 5012 Z= 0.341 Chirality : 0.036 0.113 554 Planarity : 0.003 0.032 474 Dihedral : 24.987 169.471 889 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.40 % Allowed : 17.60 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.50), residues: 297 helix: 2.15 (0.40), residues: 187 sheet: 1.19 (1.25), residues: 10 loop : -0.19 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 42 HIS 0.002 0.001 HIS A 269 PHE 0.008 0.002 PHE A 37 TYR 0.008 0.001 TYR A 273 ARG 0.001 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.8036 (t) outliers start: 6 outliers final: 5 residues processed: 39 average time/residue: 0.3279 time to fit residues: 16.3393 Evaluate side-chains 41 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.135776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.102805 restraints weight = 17344.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108988 restraints weight = 7944.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.113179 restraints weight = 4928.558| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3556 Z= 0.204 Angle : 0.601 8.398 5012 Z= 0.357 Chirality : 0.037 0.115 554 Planarity : 0.003 0.031 474 Dihedral : 25.041 169.409 889 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.40 % Allowed : 17.60 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.50), residues: 297 helix: 2.04 (0.40), residues: 187 sheet: 1.26 (1.26), residues: 10 loop : -0.30 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 52 HIS 0.002 0.001 HIS A 269 PHE 0.009 0.002 PHE A 265 TYR 0.009 0.001 TYR A 273 ARG 0.002 0.000 ARG A 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 38 average time/residue: 0.2879 time to fit residues: 13.8380 Evaluate side-chains 40 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.136987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103954 restraints weight = 17801.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.110126 restraints weight = 8169.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.114226 restraints weight = 5110.331| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3556 Z= 0.179 Angle : 0.580 8.074 5012 Z= 0.346 Chirality : 0.036 0.113 554 Planarity : 0.003 0.032 474 Dihedral : 25.038 169.538 889 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.80 % Allowed : 16.80 % Favored : 80.40 % 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: 1.92 (0.50), residues: 297 helix: 2.11 (0.40), residues: 187 sheet: 1.28 (1.25), residues: 10 loop : -0.32 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 52 HIS 0.002 0.001 HIS A 269 PHE 0.009 0.002 PHE A 37 TYR 0.009 0.001 TYR A 273 ARG 0.001 0.000 ARG A 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2824.13 seconds wall clock time: 48 minutes 39.26 seconds (2919.26 seconds total)