Starting phenix.real_space_refine on Wed Mar 5 15:42:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8e_29846/03_2025/8g8e_29846.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8e_29846/03_2025/8g8e_29846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g8e_29846/03_2025/8g8e_29846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8e_29846/03_2025/8g8e_29846.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8e_29846/03_2025/8g8e_29846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8e_29846/03_2025/8g8e_29846.cif" } resolution = 4.2 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= 0.002 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 64 5.49 5 S 5 5.16 5 C 1357 2.51 5 N 453 2.21 5 O 585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 2464 Number of models: 1 Model: "" Number of chains: 3 Chain: "J" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 661 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "I" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 651 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "X" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1152 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Time building chain proxies: 2.68, per 1000 atoms: 1.09 Number of scatterers: 2464 At special positions: 0 Unit cell: (69.96, 76.32, 115.54, 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 5 16.00 P 64 15.00 O 585 8.00 N 453 7.00 C 1357 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: 0.83 Conformation dependent library (CDL) restraints added in 150.9 milliseconds 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 266 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 81.4% alpha, 0.0% beta 31 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'X' and resid 141 through 161 Processing helix chain 'X' and resid 163 through 176 Processing helix chain 'X' and resid 180 through 189 removed outlier: 3.554A pdb=" N ILE X 184 " --> pdb=" O SER X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 193 through 211 Proline residue: X 202 - end of helix Processing helix chain 'X' and resid 215 through 220 Processing helix chain 'X' and resid 238 through 249 Processing helix chain 'X' and resid 256 through 268 removed outlier: 3.681A pdb=" N HIS X 262 " --> pdb=" O GLN X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 288 removed outlier: 4.059A pdb=" N SER X 288 " --> pdb=" O LYS X 284 " (cutoff:3.500A) 76 hydrogen bonds defined for protein. 228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 0.87 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: 471 1.33 - 1.45: 884 1.45 - 1.57: 1149 1.57 - 1.69: 126 1.69 - 1.81: 6 Bond restraints: 2636 Sorted by residual: bond pdb=" CG LEU X 200 " pdb=" CD1 LEU X 200 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.28e+00 bond pdb=" C3' DA I 74 " pdb=" O3' DA I 74 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" C3' DC I 75 " pdb=" C2' DC I 75 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.13e+00 bond pdb=" C3' DC I 95 " pdb=" C2' DC I 95 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 7.98e-01 bond pdb=" CB MET X 197 " pdb=" CG MET X 197 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.79e-01 ... (remaining 2631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 3771 2.38 - 4.76: 42 4.76 - 7.14: 7 7.14 - 9.53: 1 9.53 - 11.91: 1 Bond angle restraints: 3822 Sorted by residual: angle pdb=" CB MET X 197 " pdb=" CG MET X 197 " pdb=" SD MET X 197 " ideal model delta sigma weight residual 112.70 124.61 -11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CA GLU X 238 " pdb=" CB GLU X 238 " pdb=" CG GLU X 238 " ideal model delta sigma weight residual 114.10 120.61 -6.51 2.00e+00 2.50e-01 1.06e+01 angle pdb=" C3' DT J -88 " pdb=" C2' DT J -88 " pdb=" C1' DT J -88 " ideal model delta sigma weight residual 101.60 97.55 4.05 1.50e+00 4.44e-01 7.31e+00 angle pdb=" CA MET X 197 " pdb=" CB MET X 197 " pdb=" CG MET X 197 " ideal model delta sigma weight residual 114.10 119.03 -4.93 2.00e+00 2.50e-01 6.08e+00 angle pdb=" CA LEU X 200 " pdb=" CB LEU X 200 " pdb=" CG LEU X 200 " ideal model delta sigma weight residual 116.30 124.65 -8.35 3.50e+00 8.16e-02 5.69e+00 ... (remaining 3817 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 30.43: 1083 30.43 - 60.84: 356 60.84 - 91.26: 2 91.26 - 121.68: 0 121.68 - 152.10: 2 Dihedral angle restraints: 1443 sinusoidal: 1038 harmonic: 405 Sorted by residual: dihedral pdb=" C4' DA I 74 " pdb=" C3' DA I 74 " pdb=" O3' DA I 74 " pdb=" P DC I 75 " ideal model delta sinusoidal sigma weight residual 220.00 67.90 152.10 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" C4' DG J -93 " pdb=" C3' DG J -93 " pdb=" O3' DG J -93 " pdb=" P DG J -92 " ideal model delta sinusoidal sigma weight residual 220.00 81.85 138.15 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" CA GLU X 238 " pdb=" C GLU X 238 " pdb=" N ASN X 239 " pdb=" CA ASN X 239 " ideal model delta harmonic sigma weight residual -180.00 -164.72 -15.28 0 5.00e+00 4.00e-02 9.34e+00 ... (remaining 1440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 283 0.030 - 0.060: 109 0.060 - 0.089: 26 0.089 - 0.119: 8 0.119 - 0.149: 4 Chirality restraints: 430 Sorted by residual: chirality pdb=" CG LEU X 190 " pdb=" CB LEU X 190 " pdb=" CD1 LEU X 190 " pdb=" CD2 LEU X 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA LEU X 267 " pdb=" N LEU X 267 " pdb=" C LEU X 267 " pdb=" CB LEU X 267 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CG LEU X 217 " pdb=" CB LEU X 217 " pdb=" CD1 LEU X 217 " pdb=" CD2 LEU X 217 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 427 not shown) Planarity restraints: 263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS X 254 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO X 255 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO X 255 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO X 255 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC J -80 " -0.019 2.00e-02 2.50e+03 9.43e-03 2.00e+00 pdb=" N1 DC J -80 " 0.019 2.00e-02 2.50e+03 pdb=" C2 DC J -80 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC J -80 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DC J -80 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DC J -80 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC J -80 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC J -80 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC J -80 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP X 277 " -0.011 2.00e-02 2.50e+03 8.31e-03 1.72e+00 pdb=" CG TRP X 277 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP X 277 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP X 277 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP X 277 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP X 277 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP X 277 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 277 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 277 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP X 277 " -0.000 2.00e-02 2.50e+03 ... (remaining 260 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 531 2.80 - 3.33: 2248 3.33 - 3.85: 4846 3.85 - 4.38: 5302 4.38 - 4.90: 7197 Nonbonded interactions: 20124 Sorted by model distance: nonbonded pdb=" O GLN X 155 " pdb=" OG1 THR X 159 " model vdw 2.277 3.040 nonbonded pdb=" OP2 DA J -87 " pdb=" ND2 ASN X 196 " model vdw 2.302 3.120 nonbonded pdb=" NE ARG X 157 " pdb=" OE2 GLU X 188 " model vdw 2.303 3.120 nonbonded pdb=" NH2 ARG X 157 " pdb=" OE1 GLU X 188 " model vdw 2.305 3.120 nonbonded pdb=" O LEU X 248 " pdb=" NE2 GLN X 251 " model vdw 2.308 3.120 ... (remaining 20119 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: 0.610 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.590 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2636 Z= 0.239 Angle : 0.730 11.907 3822 Z= 0.409 Chirality : 0.036 0.149 430 Planarity : 0.005 0.041 263 Dihedral : 28.395 152.096 1177 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.79 % Allowed : 18.90 % Favored : 80.31 % 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: 0.35 (0.74), residues: 136 helix: 0.74 (0.51), residues: 110 sheet: None (None), residues: 0 loop : -1.73 (1.21), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP X 277 HIS 0.001 0.001 HIS X 262 PHE 0.011 0.002 PHE X 187 TYR 0.000 0.000 TYR X 162 ARG 0.003 0.001 ARG X 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 149 PHE cc_start: 0.6098 (t80) cc_final: 0.5746 (t80) REVERT: X 273 VAL cc_start: 0.8597 (t) cc_final: 0.8031 (t) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.2245 time to fit residues: 11.5505 Evaluate side-chains 27 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 9 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.031840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.024247 restraints weight = 28234.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.025302 restraints weight = 14891.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.025991 restraints weight = 9557.404| |-----------------------------------------------------------------------------| r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2636 Z= 0.181 Angle : 0.605 6.188 3822 Z= 0.362 Chirality : 0.032 0.110 430 Planarity : 0.004 0.031 263 Dihedral : 30.539 149.786 865 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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: 0.25 (0.72), residues: 136 helix: 0.67 (0.50), residues: 110 sheet: None (None), residues: 0 loop : -1.73 (1.21), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP X 277 HIS 0.001 0.001 HIS X 262 PHE 0.031 0.003 PHE X 278 TYR 0.001 0.000 TYR X 162 ARG 0.004 0.001 ARG X 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 147 GLU cc_start: 0.9425 (tt0) cc_final: 0.9207 (mt-10) REVERT: X 181 GLN cc_start: 0.8933 (pp30) cc_final: 0.8584 (pp30) REVERT: X 278 PHE cc_start: 0.9785 (m-80) cc_final: 0.9430 (m-80) REVERT: X 280 ASN cc_start: 0.9490 (m110) cc_final: 0.9238 (p0) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1661 time to fit residues: 5.7350 Evaluate side-chains 23 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.030385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.022802 restraints weight = 29576.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.023811 restraints weight = 15678.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.024475 restraints weight = 10187.210| |-----------------------------------------------------------------------------| r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2636 Z= 0.187 Angle : 0.578 5.007 3822 Z= 0.349 Chirality : 0.031 0.115 430 Planarity : 0.004 0.024 263 Dihedral : 30.677 149.766 865 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % 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: 0.32 (0.72), residues: 136 helix: 0.73 (0.49), residues: 110 sheet: None (None), residues: 0 loop : -1.74 (1.21), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP X 277 HIS 0.002 0.001 HIS X 262 PHE 0.019 0.002 PHE X 278 TYR 0.002 0.000 TYR X 162 ARG 0.007 0.001 ARG X 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: X 197 MET cc_start: 0.9628 (mmp) cc_final: 0.9419 (mmm) REVERT: X 278 PHE cc_start: 0.9777 (m-80) cc_final: 0.9431 (m-80) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1309 time to fit residues: 4.0237 Evaluate side-chains 18 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 196 ASN ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.030583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.023234 restraints weight = 30619.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.024285 restraints weight = 15603.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.024988 restraints weight = 9865.427| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2636 Z= 0.188 Angle : 0.590 6.047 3822 Z= 0.355 Chirality : 0.032 0.121 430 Planarity : 0.004 0.022 263 Dihedral : 30.715 150.516 865 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.79 % Allowed : 4.72 % Favored : 94.49 % 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: 0.07 (0.72), residues: 136 helix: 0.43 (0.49), residues: 111 sheet: None (None), residues: 0 loop : -1.23 (1.26), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP X 277 HIS 0.001 0.001 HIS X 262 PHE 0.013 0.002 PHE X 278 TYR 0.002 0.001 TYR X 162 ARG 0.005 0.001 ARG X 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 244 ASN cc_start: 0.9599 (m110) cc_final: 0.9367 (m110) REVERT: X 246 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9262 (mm-30) REVERT: X 278 PHE cc_start: 0.9746 (m-80) cc_final: 0.9358 (m-80) outliers start: 1 outliers final: 1 residues processed: 27 average time/residue: 0.1324 time to fit residues: 4.4028 Evaluate side-chains 22 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.029411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.021935 restraints weight = 29521.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.023032 restraints weight = 14791.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.023769 restraints weight = 9228.207| |-----------------------------------------------------------------------------| r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2636 Z= 0.171 Angle : 0.583 4.997 3822 Z= 0.350 Chirality : 0.033 0.149 430 Planarity : 0.003 0.016 263 Dihedral : 30.696 151.069 865 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: 0.31 (0.74), residues: 136 helix: 0.59 (0.51), residues: 110 sheet: None (None), residues: 0 loop : -1.08 (1.20), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.007 TRP X 277 HIS 0.000 0.000 HIS X 262 PHE 0.010 0.002 PHE X 149 TYR 0.000 0.000 TYR X 162 ARG 0.004 0.001 ARG X 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 145 GLU cc_start: 0.9698 (mm-30) cc_final: 0.9394 (mm-30) REVERT: X 153 LEU cc_start: 0.9326 (mt) cc_final: 0.9116 (mt) REVERT: X 166 ASP cc_start: 0.9706 (m-30) cc_final: 0.9471 (t0) REVERT: X 196 ASN cc_start: 0.9217 (m-40) cc_final: 0.8728 (m110) REVERT: X 244 ASN cc_start: 0.9578 (m110) cc_final: 0.9372 (m110) REVERT: X 246 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9187 (mm-30) REVERT: X 278 PHE cc_start: 0.9704 (m-80) cc_final: 0.9433 (m-80) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1384 time to fit residues: 4.5754 Evaluate side-chains 24 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.029760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.022688 restraints weight = 30367.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.023764 restraints weight = 14676.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.024462 restraints weight = 9079.813| |-----------------------------------------------------------------------------| r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2636 Z= 0.174 Angle : 0.588 5.799 3822 Z= 0.350 Chirality : 0.032 0.119 430 Planarity : 0.003 0.016 263 Dihedral : 30.732 151.558 865 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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: 0.20 (0.75), residues: 136 helix: 0.46 (0.52), residues: 111 sheet: None (None), residues: 0 loop : -0.89 (1.25), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.007 TRP X 277 HIS 0.001 0.001 HIS X 262 PHE 0.008 0.001 PHE X 187 TYR 0.002 0.001 TYR X 162 ARG 0.003 0.001 ARG X 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 145 GLU cc_start: 0.9732 (mm-30) cc_final: 0.9431 (mm-30) REVERT: X 244 ASN cc_start: 0.9613 (m110) cc_final: 0.9386 (m110) REVERT: X 246 GLU cc_start: 0.9525 (mm-30) cc_final: 0.9305 (mm-30) REVERT: X 278 PHE cc_start: 0.9772 (m-80) cc_final: 0.9363 (m-80) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1363 time to fit residues: 4.3430 Evaluate side-chains 21 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 0.0980 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.029380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.022447 restraints weight = 31540.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.023515 restraints weight = 14731.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.024206 restraints weight = 8879.285| |-----------------------------------------------------------------------------| r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2636 Z= 0.171 Angle : 0.577 5.400 3822 Z= 0.348 Chirality : 0.032 0.138 430 Planarity : 0.003 0.015 263 Dihedral : 30.752 151.575 865 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -0.02 (0.74), residues: 136 helix: 0.32 (0.51), residues: 111 sheet: None (None), residues: 0 loop : -1.05 (1.16), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.005 TRP X 277 HIS 0.001 0.000 HIS X 262 PHE 0.011 0.001 PHE X 187 TYR 0.001 0.000 TYR X 162 ARG 0.002 0.000 ARG X 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: X 145 GLU cc_start: 0.9727 (mm-30) cc_final: 0.9423 (mm-30) REVERT: X 153 LEU cc_start: 0.9353 (mt) cc_final: 0.9063 (mt) REVERT: X 166 ASP cc_start: 0.9717 (m-30) cc_final: 0.9458 (t0) REVERT: X 244 ASN cc_start: 0.9598 (m110) cc_final: 0.9385 (m110) REVERT: X 246 GLU cc_start: 0.9495 (mm-30) cc_final: 0.9231 (mm-30) REVERT: X 278 PHE cc_start: 0.9750 (m-80) cc_final: 0.9471 (m-80) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1567 time to fit residues: 4.4217 Evaluate side-chains 19 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.028510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.021419 restraints weight = 33027.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.022514 restraints weight = 15075.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.023225 restraints weight = 8999.863| |-----------------------------------------------------------------------------| r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2636 Z= 0.213 Angle : 0.615 6.915 3822 Z= 0.364 Chirality : 0.034 0.142 430 Planarity : 0.003 0.016 263 Dihedral : 30.942 151.765 865 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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: -0.01 (0.72), residues: 136 helix: 0.41 (0.51), residues: 110 sheet: None (None), residues: 0 loop : -1.38 (1.00), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.008 TRP X 207 HIS 0.001 0.001 HIS X 262 PHE 0.011 0.001 PHE X 149 TYR 0.004 0.001 TYR X 162 ARG 0.002 0.000 ARG X 275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 145 GLU cc_start: 0.9776 (mm-30) cc_final: 0.9523 (mm-30) REVERT: X 147 GLU cc_start: 0.9337 (tt0) cc_final: 0.9131 (mt-10) REVERT: X 166 ASP cc_start: 0.9768 (m-30) cc_final: 0.9476 (t0) REVERT: X 246 GLU cc_start: 0.9608 (mm-30) cc_final: 0.9392 (mm-30) REVERT: X 278 PHE cc_start: 0.9843 (m-80) cc_final: 0.9583 (m-80) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1527 time to fit residues: 4.3967 Evaluate side-chains 21 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.028405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.021537 restraints weight = 32148.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.022563 restraints weight = 15307.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.023210 restraints weight = 9256.407| |-----------------------------------------------------------------------------| r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2636 Z= 0.194 Angle : 0.603 5.576 3822 Z= 0.361 Chirality : 0.034 0.142 430 Planarity : 0.003 0.019 263 Dihedral : 30.962 151.664 865 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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: -0.22 (0.70), residues: 136 helix: 0.33 (0.51), residues: 109 sheet: None (None), residues: 0 loop : -1.76 (0.94), residues: 27 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP X 277 HIS 0.001 0.001 HIS X 262 PHE 0.011 0.002 PHE X 278 TYR 0.002 0.000 TYR X 162 ARG 0.003 0.001 ARG X 275 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 145 GLU cc_start: 0.9700 (mm-30) cc_final: 0.9346 (mm-30) REVERT: X 147 GLU cc_start: 0.9402 (tt0) cc_final: 0.9148 (mt-10) REVERT: X 166 ASP cc_start: 0.9723 (m-30) cc_final: 0.9463 (t0) REVERT: X 244 ASN cc_start: 0.9561 (m110) cc_final: 0.9324 (m110) REVERT: X 278 PHE cc_start: 0.9676 (m-80) cc_final: 0.9311 (m-80) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1599 time to fit residues: 4.6037 Evaluate side-chains 19 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.028442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.021229 restraints weight = 32904.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.022275 restraints weight = 15326.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.022936 restraints weight = 9366.265| |-----------------------------------------------------------------------------| r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2636 Z= 0.219 Angle : 0.626 6.227 3822 Z= 0.369 Chirality : 0.035 0.157 430 Planarity : 0.003 0.019 263 Dihedral : 31.030 152.020 865 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.71), residues: 136 helix: 0.42 (0.51), residues: 109 sheet: None (None), residues: 0 loop : -1.70 (0.94), residues: 27 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.008 TRP X 277 HIS 0.001 0.001 HIS X 262 PHE 0.010 0.002 PHE X 149 TYR 0.002 0.001 TYR X 162 ARG 0.002 0.001 ARG X 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 145 GLU cc_start: 0.9728 (mm-30) cc_final: 0.9386 (mm-30) REVERT: X 147 GLU cc_start: 0.9418 (tt0) cc_final: 0.9165 (mt-10) REVERT: X 166 ASP cc_start: 0.9753 (m-30) cc_final: 0.9498 (t0) REVERT: X 278 PHE cc_start: 0.9735 (m-80) cc_final: 0.9383 (m-80) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1709 time to fit residues: 4.8813 Evaluate side-chains 18 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 0.0980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.028750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.021953 restraints weight = 31940.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.022945 restraints weight = 15113.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.023586 restraints weight = 9170.146| |-----------------------------------------------------------------------------| r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2636 Z= 0.173 Angle : 0.596 5.254 3822 Z= 0.358 Chirality : 0.035 0.142 430 Planarity : 0.003 0.019 263 Dihedral : 31.086 151.826 865 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -0.08 (0.72), residues: 136 helix: 0.46 (0.52), residues: 109 sheet: None (None), residues: 0 loop : -1.85 (0.91), residues: 27 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP X 277 HIS 0.001 0.001 HIS X 262 PHE 0.011 0.001 PHE X 187 TYR 0.001 0.000 TYR X 162 ARG 0.003 0.001 ARG X 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1254.26 seconds wall clock time: 22 minutes 25.43 seconds (1345.43 seconds total)