Starting phenix.real_space_refine on Mon Feb 10 20:47:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8e_29846/02_2025/8g8e_29846.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8e_29846/02_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_29846/02_2025/8g8e_29846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8e_29846/02_2025/8g8e_29846.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8e_29846/02_2025/8g8e_29846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8e_29846/02_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-5592/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: 2.44, per 1000 atoms: 0.99 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: 1.94 Conformation dependent library (CDL) restraints added in 256.5 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: 0.98 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: 0.80 Time building geometry restraints manager: 0.84 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: 0.670 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.760 Find NCS groups from input model: 0.020 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.540 ------------------------------------------------------------------------------- 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 : 0.198 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: 0.2300 time to fit residues: 11.7530 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 : 0.188 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.2835 r_free = 0.2835 target = 0.031123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.023393 restraints weight = 28783.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.024464 restraints weight = 15091.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.025157 restraints weight = 9707.924| |-----------------------------------------------------------------------------| r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2636 Z= 0.193 Angle : 0.608 5.941 3822 Z= 0.363 Chirality : 0.033 0.114 430 Planarity : 0.005 0.035 263 Dihedral : 30.563 149.721 865 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: 0.30 (0.72), residues: 136 helix: 0.71 (0.50), residues: 110 sheet: None (None), residues: 0 loop : -1.71 (1.19), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP X 277 HIS 0.002 0.001 HIS X 262 PHE 0.028 0.003 PHE X 278 TYR 0.001 0.000 TYR X 162 ARG 0.005 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 28 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 147 GLU cc_start: 0.9429 (tt0) cc_final: 0.9216 (mt-10) REVERT: X 278 PHE cc_start: 0.9809 (m-80) cc_final: 0.9173 (m-80) REVERT: X 280 ASN cc_start: 0.9495 (m110) cc_final: 0.9274 (p0) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1712 time to fit residues: 5.6459 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 : 0.184 ------------------------------------------------------------------------------- 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: 0.5980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.2808 r_free = 0.2808 target = 0.030706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.023504 restraints weight = 29315.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.024515 restraints weight = 15364.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.025193 restraints weight = 9846.646| |-----------------------------------------------------------------------------| r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2636 Z= 0.185 Angle : 0.599 7.539 3822 Z= 0.357 Chirality : 0.032 0.161 430 Planarity : 0.004 0.027 263 Dihedral : 30.655 149.871 865 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.72), residues: 136 helix: 0.81 (0.50), residues: 110 sheet: None (None), residues: 0 loop : -1.68 (1.12), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.005 TRP X 277 HIS 0.002 0.001 HIS X 262 PHE 0.019 0.002 PHE X 278 TYR 0.001 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 24 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 197 MET cc_start: 0.9558 (mmp) cc_final: 0.9356 (mmm) REVERT: X 246 GLU cc_start: 0.9440 (mm-30) cc_final: 0.9234 (mm-30) REVERT: X 278 PHE cc_start: 0.9708 (m-80) cc_final: 0.9305 (m-80) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1393 time to fit residues: 4.1226 Evaluate side-chains 20 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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: 0.9990 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.2760 r_free = 0.2760 target = 0.029022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.021544 restraints weight = 30040.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.022580 restraints weight = 15597.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.023264 restraints weight = 10020.689| |-----------------------------------------------------------------------------| r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.4131 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= 0.215 Angle : 0.611 6.684 3822 Z= 0.362 Chirality : 0.034 0.143 430 Planarity : 0.004 0.021 263 Dihedral : 30.791 150.027 865 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % 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 (0.72), residues: 136 helix: 0.60 (0.51), residues: 111 sheet: None (None), residues: 0 loop : -1.17 (1.05), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.007 TRP X 277 HIS 0.003 0.002 HIS X 262 PHE 0.013 0.002 PHE X 278 TYR 0.003 0.001 TYR X 162 ARG 0.006 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 25 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 246 GLU cc_start: 0.9484 (mm-30) cc_final: 0.9220 (mm-30) REVERT: X 278 PHE cc_start: 0.9777 (m-80) cc_final: 0.9489 (m-80) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1466 time to fit residues: 4.4246 Evaluate side-chains 20 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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: 2.9990 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.2750 r_free = 0.2750 target = 0.028799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.021431 restraints weight = 30673.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.022443 restraints weight = 15540.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.023116 restraints weight = 9835.479| |-----------------------------------------------------------------------------| r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.4590 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= 0.199 Angle : 0.592 5.523 3822 Z= 0.356 Chirality : 0.032 0.128 430 Planarity : 0.003 0.021 263 Dihedral : 30.781 150.558 865 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.72 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: 0.29 (0.70), residues: 136 helix: 0.53 (0.50), residues: 111 sheet: None (None), residues: 0 loop : -0.91 (0.98), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.005 TRP X 277 HIS 0.001 0.001 HIS X 262 PHE 0.011 0.002 PHE X 278 TYR 0.002 0.001 TYR X 162 ARG 0.005 0.001 ARG X 275 *********************** 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 24 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 166 ASP cc_start: 0.9727 (m-30) cc_final: 0.9428 (t0) REVERT: X 246 GLU cc_start: 0.9512 (mm-30) cc_final: 0.9306 (mm-30) REVERT: X 278 PHE cc_start: 0.9788 (m-80) cc_final: 0.9378 (m-80) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1383 time to fit residues: 4.0806 Evaluate side-chains 17 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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: 0.4980 chunk 17 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.2785 r_free = 0.2785 target = 0.029815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.022515 restraints weight = 31804.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.023566 restraints weight = 15563.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.024240 restraints weight = 9617.982| |-----------------------------------------------------------------------------| r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4791 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= 0.176 Angle : 0.595 5.544 3822 Z= 0.357 Chirality : 0.033 0.147 430 Planarity : 0.003 0.019 263 Dihedral : 30.765 150.954 865 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: 0.23 (0.71), residues: 136 helix: 0.57 (0.51), residues: 110 sheet: None (None), residues: 0 loop : -1.31 (0.90), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.008 TRP X 277 HIS 0.001 0.000 HIS X 262 PHE 0.010 0.002 PHE X 278 TYR 0.001 0.000 TYR X 162 ARG 0.003 0.000 ARG X 275 *********************** 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 23 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 166 ASP cc_start: 0.9756 (m-30) cc_final: 0.9482 (t0) REVERT: X 246 GLU cc_start: 0.9584 (mm-30) cc_final: 0.9349 (mm-30) REVERT: X 278 PHE cc_start: 0.9830 (m-80) cc_final: 0.9590 (m-80) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1341 time to fit residues: 3.7907 Evaluate side-chains 16 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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: 0.7980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.2784 r_free = 0.2784 target = 0.029923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.022974 restraints weight = 32001.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.024024 restraints weight = 15280.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.024711 restraints weight = 9369.107| |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4905 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= 0.176 Angle : 0.597 4.897 3822 Z= 0.361 Chirality : 0.033 0.120 430 Planarity : 0.003 0.013 263 Dihedral : 30.795 151.186 865 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: 0.14 (0.71), residues: 136 helix: 0.50 (0.50), residues: 111 sheet: None (None), residues: 0 loop : -1.33 (0.91), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP X 277 HIS 0.000 0.000 HIS X 262 PHE 0.013 0.002 PHE X 278 TYR 0.001 0.000 TYR X 162 ARG 0.003 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 25 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 246 GLU cc_start: 0.9554 (mm-30) cc_final: 0.9352 (mm-30) REVERT: X 278 PHE cc_start: 0.9793 (m-80) cc_final: 0.9420 (m-80) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1402 time to fit residues: 4.3296 Evaluate side-chains 17 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 0.0000 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- 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 = 0.2723 r_free = 0.2723 target = 0.027970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.021002 restraints weight = 33422.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.022053 restraints weight = 15329.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.022745 restraints weight = 9242.644| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.5373 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= 0.213 Angle : 0.625 6.299 3822 Z= 0.375 Chirality : 0.035 0.130 430 Planarity : 0.003 0.019 263 Dihedral : 30.904 151.059 865 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 16.13 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: 0.21 (0.70), residues: 136 helix: 0.56 (0.50), residues: 110 sheet: None (None), residues: 0 loop : -1.31 (0.91), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.008 TRP X 207 HIS 0.001 0.001 HIS X 262 PHE 0.010 0.001 PHE X 278 TYR 0.003 0.001 TYR X 162 ARG 0.002 0.001 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 23 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 166 ASP cc_start: 0.9762 (m-30) cc_final: 0.9437 (t0) REVERT: X 246 GLU cc_start: 0.9620 (mm-30) cc_final: 0.9416 (mm-30) REVERT: X 278 PHE cc_start: 0.9841 (m-80) cc_final: 0.9584 (m-80) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1519 time to fit residues: 4.2616 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 : 0.200 ------------------------------------------------------------------------------- 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: 0.5980 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.2714 r_free = 0.2714 target = 0.027813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.021055 restraints weight = 33308.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.022050 restraints weight = 15601.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.022701 restraints weight = 9502.385| |-----------------------------------------------------------------------------| r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.5508 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= 0.207 Angle : 0.619 5.623 3822 Z= 0.373 Chirality : 0.034 0.131 430 Planarity : 0.003 0.017 263 Dihedral : 30.924 150.961 865 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: 0.39 (0.71), residues: 136 helix: 0.71 (0.51), residues: 110 sheet: None (None), residues: 0 loop : -1.37 (0.94), residues: 26 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 0.009 0.002 PHE X 278 TYR 0.002 0.001 TYR X 162 ARG 0.002 0.000 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 23 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 166 ASP cc_start: 0.9770 (m-30) cc_final: 0.9431 (t0) REVERT: X 246 GLU cc_start: 0.9603 (mm-30) cc_final: 0.9391 (mm-30) REVERT: X 278 PHE cc_start: 0.9827 (m-80) cc_final: 0.9567 (m-80) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1508 time to fit residues: 4.1815 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 : 0.156 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.2744 r_free = 0.2744 target = 0.028309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.021591 restraints weight = 32178.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.022596 restraints weight = 14958.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.023246 restraints weight = 9103.189| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.5528 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= 0.191 Angle : 0.616 4.961 3822 Z= 0.370 Chirality : 0.035 0.122 430 Planarity : 0.003 0.017 263 Dihedral : 30.962 150.887 865 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: 0.07 (0.70), residues: 136 helix: 0.41 (0.50), residues: 111 sheet: None (None), residues: 0 loop : -1.15 (1.03), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.008 TRP X 207 HIS 0.001 0.000 HIS X 262 PHE 0.021 0.002 PHE X 278 TYR 0.003 0.001 TYR X 162 ARG 0.002 0.000 ARG X 275 ********************** 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 23 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 166 ASP cc_start: 0.9778 (m-30) cc_final: 0.9461 (t0) REVERT: X 278 PHE cc_start: 0.9807 (m-80) cc_final: 0.9514 (m-80) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1453 time to fit residues: 4.0944 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 : 0.193 ------------------------------------------------------------------------------- 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: 0.8980 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.2725 r_free = 0.2725 target = 0.028060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.021438 restraints weight = 32658.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.022424 restraints weight = 15413.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.023077 restraints weight = 9449.853| |-----------------------------------------------------------------------------| r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.5734 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= 0.201 Angle : 0.608 5.557 3822 Z= 0.364 Chirality : 0.034 0.118 430 Planarity : 0.003 0.017 263 Dihedral : 31.030 151.157 865 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: 0.36 (0.71), residues: 136 helix: 0.72 (0.51), residues: 109 sheet: None (None), residues: 0 loop : -1.48 (0.98), residues: 27 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.005 TRP X 277 HIS 0.001 0.001 HIS X 262 PHE 0.009 0.002 PHE X 278 TYR 0.002 0.001 TYR X 162 ARG 0.002 0.000 ARG X 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1229.25 seconds wall clock time: 23 minutes 1.84 seconds (1381.84 seconds total)