Starting phenix.real_space_refine (version: dev) on Fri Feb 17 21:02:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jc3_9793/02_2023/6jc3_9793.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jc3_9793/02_2023/6jc3_9793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jc3_9793/02_2023/6jc3_9793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jc3_9793/02_2023/6jc3_9793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jc3_9793/02_2023/6jc3_9793.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jc3_9793/02_2023/6jc3_9793.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3154 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 222": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 3154 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3034 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 378} Chain breaks: 1 Chain: "N" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 2.81, per 1000 atoms: 0.89 Number of scatterers: 3154 At special positions: 0 Unit cell: (74.25, 87.75, 89.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 6 15.00 O 631 8.00 N 545 7.00 C 1953 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 - 3.50 Amino acid : False - 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: 1.50 Conformation dependent library (CDL) restraints added in 601.8 milliseconds 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 732 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 67.3% alpha, 0.0% beta 0 base pairs and 3 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 4.069A pdb=" N ALA A 14 " --> pdb=" O GLN A 10 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 60 Processing helix chain 'A' and resid 65 through 79 removed outlier: 3.539A pdb=" N ARG A 69 " --> pdb=" O ASN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.786A pdb=" N PHE A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N MET A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.786A pdb=" N VAL A 150 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU A 151 " --> pdb=" O ALA A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 151' Processing helix chain 'A' and resid 157 through 175 removed outlier: 3.986A pdb=" N THR A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.648A pdb=" N TYR A 207 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 208 " --> pdb=" O LYS A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 208' Processing helix chain 'A' and resid 210 through 224 Processing helix chain 'A' and resid 224 through 241 removed outlier: 4.082A pdb=" N ARG A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.525A pdb=" N ASN A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TYR A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 287 through 303 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 316 through 323 removed outlier: 3.922A pdb=" N GLN A 319 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 356 through 369 removed outlier: 3.849A pdb=" N TRP A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 Processing helix chain 'A' and resid 385 through 397 159 hydrogen bonds defined for protein. 459 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 3 stacking parallelities Total time for adding SS restraints: 0.74 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 566 1.32 - 1.45: 863 1.45 - 1.57: 1740 1.57 - 1.70: 11 1.70 - 1.83: 34 Bond restraints: 3214 Sorted by residual: bond pdb=" CA MET A 129 " pdb=" C MET A 129 " ideal model delta sigma weight residual 1.524 1.485 0.039 1.27e-02 6.20e+03 9.42e+00 bond pdb=" CA GLU A 184 " pdb=" C GLU A 184 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.32e-02 5.74e+03 8.65e+00 bond pdb=" N THR A 185 " pdb=" CA THR A 185 " ideal model delta sigma weight residual 1.462 1.425 0.037 1.26e-02 6.30e+03 8.51e+00 bond pdb=" CA PHE A 350 " pdb=" CB PHE A 350 " ideal model delta sigma weight residual 1.535 1.447 0.088 3.03e-02 1.09e+03 8.40e+00 bond pdb=" N PHE A 114 " pdb=" CA PHE A 114 " ideal model delta sigma weight residual 1.462 1.424 0.037 1.35e-02 5.49e+03 7.57e+00 ... (remaining 3209 not shown) Histogram of bond angle deviations from ideal: 96.30 - 103.87: 65 103.87 - 111.45: 1324 111.45 - 119.02: 1273 119.02 - 126.59: 1670 126.59 - 134.16: 32 Bond angle restraints: 4364 Sorted by residual: angle pdb=" N MET A 129 " pdb=" CA MET A 129 " pdb=" C MET A 129 " ideal model delta sigma weight residual 111.07 96.30 14.77 1.07e+00 8.73e-01 1.90e+02 angle pdb=" CA ARG A 124 " pdb=" C ARG A 124 " pdb=" N ALA A 125 " ideal model delta sigma weight residual 117.63 106.48 11.15 1.25e+00 6.40e-01 7.95e+01 angle pdb=" N LEU A 282 " pdb=" CA LEU A 282 " pdb=" C LEU A 282 " ideal model delta sigma weight residual 111.28 101.96 9.32 1.09e+00 8.42e-01 7.31e+01 angle pdb=" N ARG A 127 " pdb=" CA ARG A 127 " pdb=" C ARG A 127 " ideal model delta sigma weight residual 111.14 119.82 -8.68 1.08e+00 8.57e-01 6.47e+01 angle pdb=" N GLN A 319 " pdb=" CA GLN A 319 " pdb=" C GLN A 319 " ideal model delta sigma weight residual 111.28 102.76 8.52 1.09e+00 8.42e-01 6.11e+01 ... (remaining 4359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 1659 15.35 - 30.71: 217 30.71 - 46.06: 53 46.06 - 61.41: 15 61.41 - 76.77: 4 Dihedral angle restraints: 1948 sinusoidal: 813 harmonic: 1135 Sorted by residual: dihedral pdb=" CA ASN A 41 " pdb=" C ASN A 41 " pdb=" N SER A 42 " pdb=" CA SER A 42 " ideal model delta harmonic sigma weight residual -180.00 -155.72 -24.28 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA LEU A 264 " pdb=" C LEU A 264 " pdb=" N THR A 265 " pdb=" CA THR A 265 " ideal model delta harmonic sigma weight residual -180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" N GLN A 113 " pdb=" C GLN A 113 " pdb=" CA GLN A 113 " pdb=" CB GLN A 113 " ideal model delta harmonic sigma weight residual 122.80 133.67 -10.87 0 2.50e+00 1.60e-01 1.89e+01 ... (remaining 1945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 439 0.100 - 0.200: 54 0.200 - 0.300: 4 0.300 - 0.400: 1 0.400 - 0.500: 1 Chirality restraints: 499 Sorted by residual: chirality pdb=" CA GLN A 113 " pdb=" N GLN A 113 " pdb=" C GLN A 113 " pdb=" CB GLN A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" CA PRO A 112 " pdb=" N PRO A 112 " pdb=" C PRO A 112 " pdb=" CB PRO A 112 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA GLN A 319 " pdb=" N GLN A 319 " pdb=" C GLN A 319 " pdb=" CB GLN A 319 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 496 not shown) Planarity restraints: 549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 124 " -0.024 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C ARG A 124 " 0.089 2.00e-02 2.50e+03 pdb=" O ARG A 124 " -0.036 2.00e-02 2.50e+03 pdb=" N ALA A 125 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 143 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.48e+00 pdb=" N PRO A 144 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U N 38 " 0.027 2.00e-02 2.50e+03 1.45e-02 4.75e+00 pdb=" N1 U N 38 " -0.032 2.00e-02 2.50e+03 pdb=" C2 U N 38 " -0.005 2.00e-02 2.50e+03 pdb=" O2 U N 38 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U N 38 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U N 38 " 0.007 2.00e-02 2.50e+03 pdb=" O4 U N 38 " 0.004 2.00e-02 2.50e+03 pdb=" C5 U N 38 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U N 38 " -0.003 2.00e-02 2.50e+03 ... (remaining 546 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 11 2.19 - 2.87: 1312 2.87 - 3.54: 4378 3.54 - 4.22: 6957 4.22 - 4.90: 10890 Nonbonded interactions: 23548 Sorted by model distance: nonbonded pdb=" CD2 LEU A 314 " pdb=" OD1 ASP A 316 " model vdw 1.512 3.460 nonbonded pdb=" NE2 GLN A 319 " pdb=" N MET A 320 " model vdw 1.625 3.200 nonbonded pdb=" CE1 PHE A 107 " pdb=" CA PHE A 114 " model vdw 1.904 3.770 nonbonded pdb=" O ASP A 318 " pdb=" OG SER A 321 " model vdw 1.999 2.440 nonbonded pdb=" CG MET A 180 " pdb=" OE2 GLU A 184 " model vdw 2.001 3.440 ... (remaining 23543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 19 5.16 5 C 1953 2.51 5 N 545 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 5.660 Check model and map are aligned: 0.040 Process input model: 14.980 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.088 3214 Z= 0.693 Angle : 1.350 14.766 4364 Z= 0.820 Chirality : 0.069 0.500 499 Planarity : 0.008 0.064 549 Dihedral : 15.565 76.766 1216 Min Nonbonded Distance : 1.512 Molprobity Statistics. All-atom Clashscore : 30.30 Ramachandran Plot: Outliers : 0.78 % Allowed : 10.08 % Favored : 89.15 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.55 % 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: -4.39 (0.35), residues: 387 helix: -3.13 (0.24), residues: 208 sheet: -2.62 (1.32), residues: 10 loop : -2.47 (0.46), residues: 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 138 average time/residue: 0.2206 time to fit residues: 34.6820 Evaluate side-chains 73 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0428 time to fit residues: 0.9695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 87 HIS A 218 GLN A 276 ASN A 292 GLN A 296 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 3214 Z= 0.194 Angle : 0.653 11.019 4364 Z= 0.339 Chirality : 0.041 0.152 499 Planarity : 0.005 0.043 549 Dihedral : 8.227 56.352 499 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.31 % 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: -1.77 (0.39), residues: 387 helix: -0.55 (0.30), residues: 234 sheet: -2.05 (1.36), residues: 10 loop : -2.05 (0.53), residues: 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.1663 time to fit residues: 16.4940 Evaluate side-chains 55 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.324 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.003 0.030 3214 Z= 0.161 Angle : 0.586 9.205 4364 Z= 0.297 Chirality : 0.039 0.138 499 Planarity : 0.004 0.030 549 Dihedral : 7.695 53.819 499 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 0.31 % 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: -0.18 (0.43), residues: 387 helix: 0.89 (0.33), residues: 233 sheet: -1.48 (1.68), residues: 10 loop : -1.70 (0.53), residues: 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.1480 time to fit residues: 11.9953 Evaluate side-chains 52 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 16 optimal weight: 0.3980 chunk 23 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 0.0570 chunk 31 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 3214 Z= 0.241 Angle : 0.641 9.234 4364 Z= 0.328 Chirality : 0.040 0.152 499 Planarity : 0.004 0.025 549 Dihedral : 7.842 58.645 499 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer Outliers : 0.00 % 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: 0.30 (0.43), residues: 387 helix: 1.30 (0.34), residues: 234 sheet: -1.35 (1.86), residues: 10 loop : -1.58 (0.51), residues: 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1348 time to fit residues: 9.7674 Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3214 Z= 0.175 Angle : 0.606 8.552 4364 Z= 0.303 Chirality : 0.040 0.187 499 Planarity : 0.003 0.023 549 Dihedral : 7.628 56.923 499 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 0.00 % 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: 0.51 (0.43), residues: 387 helix: 1.48 (0.34), residues: 235 sheet: -1.08 (1.97), residues: 10 loop : -1.56 (0.50), residues: 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1462 time to fit residues: 9.4888 Evaluate side-chains 39 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 27 optimal weight: 0.0770 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 296 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.6884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 3214 Z= 0.134 Angle : 0.562 6.921 4364 Z= 0.279 Chirality : 0.038 0.172 499 Planarity : 0.003 0.023 549 Dihedral : 7.301 56.818 499 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.00 % 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: 0.69 (0.44), residues: 387 helix: 1.60 (0.34), residues: 245 sheet: -0.96 (1.94), residues: 10 loop : -1.67 (0.51), residues: 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1436 time to fit residues: 10.1245 Evaluate side-chains 41 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.7187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3214 Z= 0.206 Angle : 0.603 9.851 4364 Z= 0.301 Chirality : 0.040 0.169 499 Planarity : 0.003 0.027 549 Dihedral : 7.558 58.837 499 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 0.00 % 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: 0.88 (0.44), residues: 387 helix: 1.79 (0.35), residues: 243 sheet: -0.86 (1.86), residues: 10 loop : -1.64 (0.50), residues: 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1539 time to fit residues: 9.6294 Evaluate side-chains 41 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.7333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 3214 Z= 0.137 Angle : 0.565 7.968 4364 Z= 0.276 Chirality : 0.039 0.165 499 Planarity : 0.003 0.028 549 Dihedral : 7.264 58.121 499 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 0.00 % 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: 0.97 (0.45), residues: 387 helix: 1.85 (0.35), residues: 245 sheet: -0.55 (1.87), residues: 10 loop : -1.67 (0.51), residues: 132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1414 time to fit residues: 9.7367 Evaluate side-chains 39 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 20.0000 chunk 34 optimal weight: 0.0270 chunk 23 optimal weight: 0.0270 chunk 37 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.9698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.7503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 3214 Z= 0.134 Angle : 0.569 7.467 4364 Z= 0.279 Chirality : 0.039 0.164 499 Planarity : 0.003 0.031 549 Dihedral : 7.161 57.758 499 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.00 % 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: 0.97 (0.45), residues: 387 helix: 1.81 (0.35), residues: 245 sheet: -0.23 (1.91), residues: 10 loop : -1.61 (0.51), residues: 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1494 time to fit residues: 10.0445 Evaluate side-chains 42 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.0040 chunk 30 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.7629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 3214 Z= 0.134 Angle : 0.583 7.305 4364 Z= 0.285 Chirality : 0.039 0.172 499 Planarity : 0.003 0.032 549 Dihedral : 7.074 58.023 499 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.00 % 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: 0.94 (0.44), residues: 387 helix: 1.77 (0.34), residues: 245 sheet: -0.23 (1.82), residues: 10 loop : -1.57 (0.51), residues: 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1316 time to fit residues: 9.0249 Evaluate side-chains 42 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.326 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3109 r_free = 0.3109 target = 0.066877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.057214 restraints weight = 15077.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.058942 restraints weight = 9131.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.060067 restraints weight = 6181.298| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.7846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 3214 Z= 0.255 Angle : 0.687 10.455 4364 Z= 0.346 Chirality : 0.042 0.155 499 Planarity : 0.004 0.034 549 Dihedral : 7.752 61.746 499 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 0.00 % 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: 0.86 (0.44), residues: 387 helix: 1.70 (0.34), residues: 243 sheet: -0.42 (1.78), residues: 10 loop : -1.53 (0.51), residues: 134 =============================================================================== Job complete usr+sys time: 1010.25 seconds wall clock time: 19 minutes 8.63 seconds (1148.63 seconds total)