Starting phenix.real_space_refine on Mon Sep 23 22:34:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jc3_9793/09_2024/6jc3_9793.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jc3_9793/09_2024/6jc3_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_9793/09_2024/6jc3_9793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jc3_9793/09_2024/6jc3_9793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jc3_9793/09_2024/6jc3_9793.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jc3_9793/09_2024/6jc3_9793.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 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. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.06, per 1000 atoms: 0.97 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 348.2 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: 1.03 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: 0.79 Time building geometry restraints manager: 1.00 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: 0.00 - 2.95: 4201 2.95 - 5.91: 133 5.91 - 8.86: 18 8.86 - 11.81: 11 11.81 - 14.77: 1 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: 1669 15.35 - 30.71: 220 30.71 - 46.06: 55 46.06 - 61.41: 24 61.41 - 76.77: 4 Dihedral angle restraints: 1972 sinusoidal: 837 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 1969 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 3.040 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 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.810 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 16.287 76.766 1240 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 % Allowed : 15.17 % Favored : 81.73 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.004 TRP A 173 HIS 0.003 0.002 HIS A 87 PHE 0.023 0.003 PHE A 145 TYR 0.020 0.004 TYR A 249 ARG 0.009 0.002 ARG A 69 *********************** 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 : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8950 (tt0) cc_final: 0.8566 (pm20) REVERT: A 135 LEU cc_start: 0.8057 (mt) cc_final: 0.7491 (mt) REVERT: A 178 LYS cc_start: 0.9267 (mmtm) cc_final: 0.8874 (mppt) REVERT: A 184 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.4327 (mt-10) REVERT: A 256 ASP cc_start: 0.9568 (t70) cc_final: 0.9325 (t0) REVERT: A 258 TYR cc_start: 0.8391 (m-80) cc_final: 0.8164 (m-80) REVERT: A 278 LYS cc_start: 0.7222 (mttt) cc_final: 0.6323 (tppt) REVERT: A 282 LEU cc_start: 0.9301 (tt) cc_final: 0.8883 (mt) REVERT: A 295 LYS cc_start: 0.6852 (mttt) cc_final: 0.5860 (ptmt) REVERT: A 311 MET cc_start: 0.9183 (mtt) cc_final: 0.8907 (tpp) REVERT: A 365 GLU cc_start: 0.8539 (tp30) cc_final: 0.8275 (mt-10) outliers start: 10 outliers final: 7 residues processed: 138 average time/residue: 0.2017 time to fit residues: 31.7144 Evaluate side-chains 79 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.0060 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- 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 296 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3214 Z= 0.184 Angle : 0.647 6.212 4364 Z= 0.336 Chirality : 0.041 0.165 499 Planarity : 0.005 0.042 549 Dihedral : 10.710 59.064 523 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.88 % Favored : 95.87 % Rotamer: Outliers : 0.31 % Allowed : 3.72 % Favored : 95.98 % 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: -1.67 (0.40), residues: 387 helix: -0.50 (0.30), residues: 235 sheet: -2.08 (1.36), residues: 10 loop : -1.94 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 360 HIS 0.002 0.001 HIS A 210 PHE 0.016 0.002 PHE A 54 TYR 0.005 0.001 TYR A 310 ARG 0.006 0.001 ARG A 127 *********************** 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 87 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9509 (m-30) cc_final: 0.9302 (m-30) REVERT: A 55 CYS cc_start: 0.9601 (m) cc_final: 0.9382 (m) REVERT: A 103 GLU cc_start: 0.8997 (tt0) cc_final: 0.8471 (pm20) REVERT: A 126 GLN cc_start: 0.9442 (mm-40) cc_final: 0.9164 (pt0) REVERT: A 130 MET cc_start: 0.9390 (mmp) cc_final: 0.9153 (mmm) REVERT: A 135 LEU cc_start: 0.7602 (mt) cc_final: 0.7356 (mt) REVERT: A 173 TRP cc_start: 0.9384 (m100) cc_final: 0.8964 (m100) REVERT: A 231 LEU cc_start: 0.9518 (mt) cc_final: 0.9310 (mt) REVERT: A 241 THR cc_start: 0.7418 (m) cc_final: 0.7060 (t) REVERT: A 256 ASP cc_start: 0.9572 (t70) cc_final: 0.9184 (t70) REVERT: A 261 ASN cc_start: 0.8286 (m-40) cc_final: 0.7706 (m-40) REVERT: A 271 LEU cc_start: 0.9199 (mm) cc_final: 0.8566 (mm) REVERT: A 294 MET cc_start: 0.8978 (mmm) cc_final: 0.8727 (mmt) REVERT: A 302 ARG cc_start: 0.3236 (mtt-85) cc_final: 0.2937 (ttm170) REVERT: A 303 MET cc_start: 0.8922 (ppp) cc_final: 0.8687 (ppp) REVERT: A 337 MET cc_start: 0.8633 (ppp) cc_final: 0.8335 (ppp) REVERT: A 362 LEU cc_start: 0.9367 (tt) cc_final: 0.8912 (mm) REVERT: A 365 GLU cc_start: 0.8590 (tp30) cc_final: 0.8282 (mt-10) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1757 time to fit residues: 17.8504 Evaluate side-chains 67 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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: 5.9990 chunk 10 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 292 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3214 Z= 0.165 Angle : 0.585 7.251 4364 Z= 0.300 Chirality : 0.039 0.157 499 Planarity : 0.004 0.032 549 Dihedral : 10.242 58.970 523 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: -0.70 (0.42), residues: 387 helix: 0.46 (0.33), residues: 245 sheet: -1.43 (1.69), residues: 10 loop : -2.13 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 49 HIS 0.004 0.001 HIS A 87 PHE 0.010 0.001 PHE A 354 TYR 0.009 0.001 TYR A 258 ARG 0.004 0.000 ARG A 214 *********************** 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 79 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9390 (m-30) cc_final: 0.9174 (m-30) REVERT: A 70 GLN cc_start: 0.9586 (mt0) cc_final: 0.9115 (mt0) REVERT: A 79 SER cc_start: 0.8981 (m) cc_final: 0.8565 (m) REVERT: A 103 GLU cc_start: 0.9031 (tt0) cc_final: 0.8554 (pm20) REVERT: A 123 GLU cc_start: 0.9200 (pp20) cc_final: 0.8946 (pp20) REVERT: A 126 GLN cc_start: 0.9613 (mm-40) cc_final: 0.9330 (pt0) REVERT: A 130 MET cc_start: 0.9312 (mmp) cc_final: 0.9087 (mmp) REVERT: A 241 THR cc_start: 0.7429 (m) cc_final: 0.7134 (t) REVERT: A 256 ASP cc_start: 0.9592 (t70) cc_final: 0.9076 (t70) REVERT: A 271 LEU cc_start: 0.9126 (mm) cc_final: 0.8478 (mm) REVERT: A 300 LEU cc_start: 0.9620 (mt) cc_final: 0.9276 (tt) REVERT: A 311 MET cc_start: 0.9244 (tpt) cc_final: 0.8952 (tpt) REVERT: A 321 SER cc_start: 0.9417 (m) cc_final: 0.9203 (p) REVERT: A 337 MET cc_start: 0.8533 (ppp) cc_final: 0.8237 (ppp) REVERT: A 362 LEU cc_start: 0.9329 (tt) cc_final: 0.8892 (mm) REVERT: A 365 GLU cc_start: 0.8748 (tp30) cc_final: 0.8448 (mt-10) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1708 time to fit residues: 15.9277 Evaluate side-chains 61 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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: 1.9990 chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- 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: 0.8104 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3214 Z= 0.227 Angle : 0.628 9.907 4364 Z= 0.326 Chirality : 0.040 0.160 499 Planarity : 0.004 0.024 549 Dihedral : 10.482 61.621 523 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % 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: -0.02 (0.43), residues: 387 helix: 1.08 (0.34), residues: 243 sheet: -1.28 (1.86), residues: 10 loop : -1.98 (0.50), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 49 HIS 0.002 0.001 HIS A 87 PHE 0.009 0.001 PHE A 114 TYR 0.015 0.002 TYR A 258 ARG 0.003 0.001 ARG A 164 *********************** 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 66 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.9656 (mt0) cc_final: 0.9235 (mp10) REVERT: A 76 LEU cc_start: 0.9583 (mt) cc_final: 0.9357 (mt) REVERT: A 103 GLU cc_start: 0.8982 (tt0) cc_final: 0.8554 (pm20) REVERT: A 126 GLN cc_start: 0.9592 (mm-40) cc_final: 0.9362 (pt0) REVERT: A 300 LEU cc_start: 0.9623 (mt) cc_final: 0.9301 (tt) REVERT: A 311 MET cc_start: 0.9398 (tpt) cc_final: 0.9181 (tpt) REVERT: A 321 SER cc_start: 0.9541 (m) cc_final: 0.9292 (p) REVERT: A 326 GLU cc_start: 0.9010 (pm20) cc_final: 0.8797 (pm20) REVERT: A 335 MET cc_start: 0.9429 (mmm) cc_final: 0.8719 (mtp) REVERT: A 337 MET cc_start: 0.8580 (ppp) cc_final: 0.8282 (ppp) REVERT: A 362 LEU cc_start: 0.9326 (tt) cc_final: 0.8874 (mm) REVERT: A 365 GLU cc_start: 0.8793 (tp30) cc_final: 0.8501 (mt-10) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1279 time to fit residues: 10.5661 Evaluate side-chains 51 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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: 0.8072 moved from start: 0.6298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3214 Z= 0.164 Angle : 0.592 8.433 4364 Z= 0.293 Chirality : 0.039 0.188 499 Planarity : 0.003 0.020 549 Dihedral : 10.233 59.151 523 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: 0.24 (0.43), residues: 387 helix: 1.20 (0.34), residues: 247 sheet: -0.94 (2.00), residues: 10 loop : -1.83 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 49 HIS 0.002 0.001 HIS A 80 PHE 0.007 0.001 PHE A 114 TYR 0.009 0.001 TYR A 258 ARG 0.004 0.000 ARG A 17 *********************** 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 64 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9469 (m-30) cc_final: 0.9232 (m-30) REVERT: A 7 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8446 (pt0) REVERT: A 56 LEU cc_start: 0.9784 (tp) cc_final: 0.9206 (pp) REVERT: A 70 GLN cc_start: 0.9679 (mt0) cc_final: 0.9275 (mp10) REVERT: A 76 LEU cc_start: 0.9575 (mt) cc_final: 0.9339 (mt) REVERT: A 103 GLU cc_start: 0.8979 (tt0) cc_final: 0.8546 (pm20) REVERT: A 126 GLN cc_start: 0.9620 (mm-40) cc_final: 0.9362 (pt0) REVERT: A 237 ARG cc_start: 0.8857 (mtp-110) cc_final: 0.8367 (ttm110) REVERT: A 300 LEU cc_start: 0.9625 (mt) cc_final: 0.9335 (tt) REVERT: A 311 MET cc_start: 0.9424 (tpt) cc_final: 0.9216 (tpt) REVERT: A 333 PHE cc_start: 0.9104 (t80) cc_final: 0.8653 (t80) REVERT: A 335 MET cc_start: 0.9414 (mmm) cc_final: 0.8455 (mtp) REVERT: A 337 MET cc_start: 0.8572 (ppp) cc_final: 0.8354 (ppp) REVERT: A 365 GLU cc_start: 0.8848 (tp30) cc_final: 0.8528 (mt-10) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1448 time to fit residues: 11.4942 Evaluate side-chains 50 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.6857 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= 0.292 Angle : 0.685 11.899 4364 Z= 0.352 Chirality : 0.042 0.165 499 Planarity : 0.004 0.035 549 Dihedral : 10.836 65.461 523 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: 0.24 (0.43), residues: 387 helix: 1.26 (0.34), residues: 244 sheet: -0.90 (1.92), residues: 10 loop : -1.88 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 49 HIS 0.005 0.002 HIS A 80 PHE 0.016 0.002 PHE A 359 TYR 0.021 0.002 TYR A 258 ARG 0.005 0.001 ARG A 17 *********************** 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 66 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9527 (m-30) cc_final: 0.9318 (m-30) REVERT: A 26 GLU cc_start: 0.4212 (tp30) cc_final: 0.3338 (pp20) REVERT: A 103 GLU cc_start: 0.8879 (tt0) cc_final: 0.8384 (pm20) REVERT: A 126 GLN cc_start: 0.9645 (mm-40) cc_final: 0.9386 (pt0) REVERT: A 294 MET cc_start: 0.9123 (mmt) cc_final: 0.8836 (mmm) REVERT: A 300 LEU cc_start: 0.9700 (mt) cc_final: 0.9341 (tt) REVERT: A 333 PHE cc_start: 0.9177 (t80) cc_final: 0.8771 (t80) REVERT: A 335 MET cc_start: 0.9358 (mmm) cc_final: 0.8906 (mmm) REVERT: A 365 GLU cc_start: 0.8797 (tp30) cc_final: 0.8523 (mt-10) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1603 time to fit residues: 12.7969 Evaluate side-chains 46 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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: 9.9990 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 0.0020 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.7000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3214 Z= 0.146 Angle : 0.596 8.403 4364 Z= 0.291 Chirality : 0.041 0.176 499 Planarity : 0.003 0.021 549 Dihedral : 10.313 59.257 523 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: 0.50 (0.44), residues: 387 helix: 1.45 (0.34), residues: 246 sheet: -0.75 (1.96), residues: 10 loop : -1.80 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 360 HIS 0.003 0.001 HIS A 87 PHE 0.010 0.001 PHE A 268 TYR 0.007 0.001 TYR A 258 ARG 0.003 0.000 ARG A 127 *********************** 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 65 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9521 (m-30) cc_final: 0.9311 (m-30) REVERT: A 26 GLU cc_start: 0.4037 (tp30) cc_final: 0.3274 (pp20) REVERT: A 56 LEU cc_start: 0.9805 (tp) cc_final: 0.9371 (pp) REVERT: A 70 GLN cc_start: 0.9673 (mt0) cc_final: 0.9082 (mt0) REVERT: A 76 LEU cc_start: 0.9552 (mt) cc_final: 0.9338 (mt) REVERT: A 103 GLU cc_start: 0.8918 (tt0) cc_final: 0.8451 (pm20) REVERT: A 126 GLN cc_start: 0.9630 (mm-40) cc_final: 0.9381 (pt0) REVERT: A 237 ARG cc_start: 0.8882 (mtp-110) cc_final: 0.8193 (ttm110) REVERT: A 300 LEU cc_start: 0.9662 (mt) cc_final: 0.9342 (mt) REVERT: A 333 PHE cc_start: 0.9137 (t80) cc_final: 0.8803 (t80) REVERT: A 335 MET cc_start: 0.9301 (mmm) cc_final: 0.8585 (mtp) REVERT: A 337 MET cc_start: 0.8621 (ppp) cc_final: 0.8363 (ppp) REVERT: A 365 GLU cc_start: 0.8875 (tp30) cc_final: 0.8551 (mt-10) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1406 time to fit residues: 11.3170 Evaluate side-chains 52 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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: 0.9980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.0070 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 31 optimal weight: 0.0060 overall best weight: 0.7616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.7180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3214 Z= 0.136 Angle : 0.607 11.412 4364 Z= 0.289 Chirality : 0.039 0.173 499 Planarity : 0.003 0.021 549 Dihedral : 10.006 59.090 523 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: 0.59 (0.43), residues: 387 helix: 1.56 (0.34), residues: 246 sheet: None (None), residues: 0 loop : -1.82 (0.48), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 173 HIS 0.003 0.001 HIS A 87 PHE 0.012 0.001 PHE A 268 TYR 0.006 0.001 TYR A 258 ARG 0.003 0.000 ARG A 127 *********************** 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 61 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9522 (m-30) cc_final: 0.9307 (m-30) REVERT: A 26 GLU cc_start: 0.4076 (tp30) cc_final: 0.3271 (pp20) REVERT: A 56 LEU cc_start: 0.9799 (tp) cc_final: 0.9372 (pp) REVERT: A 70 GLN cc_start: 0.9666 (mt0) cc_final: 0.9199 (mt0) REVERT: A 76 LEU cc_start: 0.9521 (mt) cc_final: 0.9311 (mt) REVERT: A 103 GLU cc_start: 0.8928 (tt0) cc_final: 0.8458 (pm20) REVERT: A 126 GLN cc_start: 0.9596 (mm-40) cc_final: 0.9369 (pt0) REVERT: A 237 ARG cc_start: 0.8907 (mtp-110) cc_final: 0.8205 (ttm110) REVERT: A 300 LEU cc_start: 0.9676 (mt) cc_final: 0.9338 (tt) REVERT: A 303 MET cc_start: 0.8984 (ppp) cc_final: 0.8703 (ppp) REVERT: A 333 PHE cc_start: 0.9125 (t80) cc_final: 0.8763 (t80) REVERT: A 335 MET cc_start: 0.9390 (mmm) cc_final: 0.8560 (mtp) REVERT: A 337 MET cc_start: 0.8372 (ppp) cc_final: 0.8104 (ppp) REVERT: A 365 GLU cc_start: 0.8849 (tp30) cc_final: 0.8573 (mt-10) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1496 time to fit residues: 11.2625 Evaluate side-chains 51 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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: 9.9990 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 3 optimal weight: 0.1980 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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: 0.8104 moved from start: 0.7252 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= 0.161 Angle : 0.602 8.803 4364 Z= 0.294 Chirality : 0.039 0.162 499 Planarity : 0.003 0.020 549 Dihedral : 10.125 59.007 523 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: 0.80 (0.44), residues: 387 helix: 1.69 (0.34), residues: 246 sheet: -0.53 (1.88), residues: 10 loop : -1.73 (0.51), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 360 HIS 0.003 0.001 HIS A 87 PHE 0.019 0.001 PHE A 54 TYR 0.025 0.001 TYR A 327 ARG 0.002 0.000 ARG A 127 *********************** 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 60 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4224 (tp30) cc_final: 0.3351 (pp20) REVERT: A 70 GLN cc_start: 0.9664 (mt0) cc_final: 0.9177 (mt0) REVERT: A 103 GLU cc_start: 0.8889 (tt0) cc_final: 0.8407 (pm20) REVERT: A 126 GLN cc_start: 0.9597 (mm-40) cc_final: 0.9350 (pt0) REVERT: A 127 ARG cc_start: 0.9551 (ttm-80) cc_final: 0.9318 (tpp80) REVERT: A 300 LEU cc_start: 0.9675 (mt) cc_final: 0.9418 (tt) REVERT: A 306 ASP cc_start: 0.9002 (t0) cc_final: 0.8655 (t70) REVERT: A 333 PHE cc_start: 0.9121 (t80) cc_final: 0.8766 (t80) REVERT: A 335 MET cc_start: 0.9349 (mmm) cc_final: 0.8802 (mtp) REVERT: A 337 MET cc_start: 0.8337 (ppp) cc_final: 0.8054 (ppp) REVERT: A 365 GLU cc_start: 0.8835 (tp30) cc_final: 0.8494 (mt-10) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1456 time to fit residues: 10.8184 Evaluate side-chains 50 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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: 3.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.0170 chunk 30 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- 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: 0.8084 moved from start: 0.7420 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= 0.142 Angle : 0.581 7.866 4364 Z= 0.281 Chirality : 0.039 0.171 499 Planarity : 0.003 0.028 549 Dihedral : 9.987 59.063 523 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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: 0.87 (0.44), residues: 387 helix: 1.77 (0.34), residues: 246 sheet: None (None), residues: 0 loop : -1.68 (0.49), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 360 HIS 0.003 0.001 HIS A 87 PHE 0.012 0.001 PHE A 268 TYR 0.013 0.001 TYR A 327 ARG 0.002 0.000 ARG A 127 ********************** 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 61 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4233 (tp30) cc_final: 0.3489 (pp20) REVERT: A 56 LEU cc_start: 0.9810 (tp) cc_final: 0.9379 (pp) REVERT: A 70 GLN cc_start: 0.9671 (mt0) cc_final: 0.9175 (mt0) REVERT: A 103 GLU cc_start: 0.8882 (tt0) cc_final: 0.8400 (pm20) REVERT: A 126 GLN cc_start: 0.9587 (mm-40) cc_final: 0.9365 (pt0) REVERT: A 127 ARG cc_start: 0.9538 (ttm-80) cc_final: 0.9318 (tpp80) REVERT: A 173 TRP cc_start: 0.9408 (m100) cc_final: 0.9068 (m100) REVERT: A 300 LEU cc_start: 0.9663 (mt) cc_final: 0.9351 (mt) REVERT: A 306 ASP cc_start: 0.8940 (t0) cc_final: 0.8623 (t70) REVERT: A 311 MET cc_start: 0.8819 (tpt) cc_final: 0.8465 (tpt) REVERT: A 333 PHE cc_start: 0.9067 (t80) cc_final: 0.8710 (t80) REVERT: A 335 MET cc_start: 0.9359 (mmm) cc_final: 0.8773 (mtp) REVERT: A 337 MET cc_start: 0.8210 (ppp) cc_final: 0.7918 (ppp) REVERT: A 365 GLU cc_start: 0.8880 (tp30) cc_final: 0.8569 (mt-10) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1402 time to fit residues: 10.6391 Evaluate side-chains 50 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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: 7.9990 chunk 5 optimal weight: 0.0470 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- 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 = 0.3134 r_free = 0.3134 target = 0.067509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.057382 restraints weight = 15405.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.059193 restraints weight = 9199.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.060421 restraints weight = 6219.793| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.7595 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= 0.202 Angle : 0.612 10.082 4364 Z= 0.304 Chirality : 0.040 0.164 499 Planarity : 0.003 0.031 549 Dihedral : 10.354 61.048 523 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 1.76 (0.34), residues: 246 sheet: -0.44 (1.91), residues: 10 loop : -1.74 (0.52), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 360 HIS 0.002 0.001 HIS A 80 PHE 0.009 0.001 PHE A 114 TYR 0.016 0.002 TYR A 258 ARG 0.003 0.000 ARG A 352 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 996.09 seconds wall clock time: 18 minutes 12.63 seconds (1092.63 seconds total)