Starting phenix.real_space_refine on Mon Sep 23 12:27:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8e_29846/09_2024/8g8e_29846.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8e_29846/09_2024/8g8e_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8e_29846/09_2024/8g8e_29846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8e_29846/09_2024/8g8e_29846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8e_29846/09_2024/8g8e_29846.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8e_29846/09_2024/8g8e_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): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 2.52, per 1000 atoms: 1.02 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: 1.49 Conformation dependent library (CDL) restraints added in 588.1 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: 1.09 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: 1.00 Time building geometry restraints manager: 0.79 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.320 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.570 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.210 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: 0.2309 time to fit residues: 11.8185 Evaluate side-chains 27 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 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 fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 187 PHE cc_start: 0.5909 (t80) cc_final: 0.5706 (t80) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1665 time to fit residues: 5.4750 Evaluate side-chains 23 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.3453 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 : 0.608 5.663 3822 Z= 0.366 Chirality : 0.033 0.151 430 Planarity : 0.004 0.036 263 Dihedral : 30.637 149.876 865 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.79 % Allowed : 7.87 % 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: 0.42 (0.71), residues: 136 helix: 0.80 (0.49), residues: 110 sheet: None (None), residues: 0 loop : -1.74 (1.10), 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 0.023 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 25 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.1417 time to fit residues: 4.2032 Evaluate side-chains 21 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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: 0.9990 chunk 17 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 0.0270 chunk 10 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5040 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2636 Z= 0.169 Angle : 0.604 4.961 3822 Z= 0.364 Chirality : 0.034 0.142 430 Planarity : 0.003 0.019 263 Dihedral : 30.661 150.754 865 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: 0.26 (0.71), residues: 136 helix: 0.56 (0.50), residues: 111 sheet: None (None), residues: 0 loop : -1.14 (1.09), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.007 TRP X 277 HIS 0.001 0.000 HIS X 262 PHE 0.019 0.002 PHE X 278 TYR 0.000 0.000 TYR X 162 ARG 0.004 0.000 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 27 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1390 time to fit residues: 4.6122 Evaluate side-chains 20 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.4491 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= 0.172 Angle : 0.596 5.350 3822 Z= 0.359 Chirality : 0.033 0.135 430 Planarity : 0.003 0.017 263 Dihedral : 30.697 151.078 865 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 5.51 % 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: 0.51 (0.70), residues: 136 helix: 0.77 (0.50), residues: 110 sheet: None (None), residues: 0 loop : -1.20 (0.98), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.007 TRP X 277 HIS 0.001 0.000 HIS X 262 PHE 0.019 0.002 PHE X 278 TYR 0.001 0.001 TYR X 162 ARG 0.003 0.000 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 26 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1436 time to fit residues: 4.5806 Evaluate side-chains 20 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.0040 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.4711 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 4.740 3822 Z= 0.361 Chirality : 0.033 0.138 430 Planarity : 0.003 0.023 263 Dihedral : 30.700 151.420 865 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.67 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: 0.13 (0.70), residues: 136 helix: 0.51 (0.50), residues: 110 sheet: None (None), residues: 0 loop : -1.34 (0.94), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP X 277 HIS 0.000 0.000 HIS X 262 PHE 0.020 0.002 PHE X 278 TYR 0.001 0.000 TYR X 162 ARG 0.002 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 24 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 187 PHE cc_start: 0.6164 (t80) cc_final: 0.5742 (t80) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1441 time to fit residues: 4.2368 Evaluate side-chains 18 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.5172 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= 0.190 Angle : 0.620 5.442 3822 Z= 0.376 Chirality : 0.034 0.146 430 Planarity : 0.004 0.018 263 Dihedral : 30.831 151.690 865 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.63 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: -0.31 (0.70), residues: 136 helix: 0.23 (0.50), residues: 110 sheet: None (None), residues: 0 loop : -1.65 (0.90), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP X 207 HIS 0.001 0.001 HIS X 262 PHE 0.027 0.003 PHE X 278 TYR 0.003 0.001 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.192 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1423 time to fit residues: 4.3529 Evaluate side-chains 18 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 0.0060 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.5300 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= 0.187 Angle : 0.613 5.826 3822 Z= 0.373 Chirality : 0.034 0.147 430 Planarity : 0.003 0.016 263 Dihedral : 30.882 151.707 865 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.63 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: -0.35 (0.70), residues: 136 helix: 0.33 (0.51), residues: 108 sheet: None (None), residues: 0 loop : -2.16 (0.84), residues: 28 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP X 277 HIS 0.001 0.001 HIS X 262 PHE 0.021 0.002 PHE X 278 TYR 0.003 0.001 TYR X 162 ARG 0.005 0.001 ARG X 232 *********************** 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 25 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: X 187 PHE cc_start: 0.6290 (t80) cc_final: 0.5827 (t80) REVERT: X 213 ASN cc_start: 0.7098 (p0) cc_final: 0.6732 (p0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1441 time to fit residues: 4.3927 Evaluate side-chains 17 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.5661 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= 0.197 Angle : 0.619 6.109 3822 Z= 0.375 Chirality : 0.034 0.152 430 Planarity : 0.004 0.025 263 Dihedral : 30.963 152.015 865 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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: -0.27 (0.70), residues: 136 helix: 0.30 (0.51), residues: 109 sheet: None (None), residues: 0 loop : -1.80 (0.84), residues: 27 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.007 TRP X 207 HIS 0.001 0.001 HIS X 262 PHE 0.022 0.002 PHE X 278 TYR 0.003 0.001 TYR X 162 ARG 0.005 0.001 ARG X 232 *********************** 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 fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1447 time to fit residues: 4.3201 Evaluate side-chains 19 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.5622 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= 0.192 Angle : 0.606 5.009 3822 Z= 0.367 Chirality : 0.034 0.126 430 Planarity : 0.004 0.022 263 Dihedral : 31.004 152.037 865 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.54 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: 0.06 (0.69), residues: 136 helix: 0.51 (0.50), residues: 110 sheet: None (None), residues: 0 loop : -1.65 (0.88), 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 0.023 0.002 PHE X 278 TYR 0.003 0.001 TYR X 162 ARG 0.005 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 fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1372 time to fit residues: 4.0486 Evaluate side-chains 17 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.0020 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7990 ------------------------------------------------------------------------------- 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 = 0.2793 r_free = 0.2793 target = 0.029370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.022377 restraints weight = 32668.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.023485 restraints weight = 14518.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.024202 restraints weight = 8526.597| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2636 Z= 0.184 Angle : 0.608 5.007 3822 Z= 0.366 Chirality : 0.034 0.134 430 Planarity : 0.004 0.021 263 Dihedral : 31.034 152.025 865 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.08 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: -0.05 (0.69), residues: 136 helix: 0.43 (0.50), residues: 110 sheet: None (None), residues: 0 loop : -1.67 (0.88), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.007 TRP X 207 HIS 0.001 0.001 HIS X 262 PHE 0.024 0.002 PHE X 278 TYR 0.002 0.001 TYR X 162 ARG 0.004 0.001 ARG X 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 936.29 seconds wall clock time: 17 minutes 25.62 seconds (1045.62 seconds total)