Starting phenix.real_space_refine on Fri Apr 5 16:58:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbb_40303/04_2024/8sbb_40303_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbb_40303/04_2024/8sbb_40303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbb_40303/04_2024/8sbb_40303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbb_40303/04_2024/8sbb_40303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbb_40303/04_2024/8sbb_40303_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbb_40303/04_2024/8sbb_40303_updated.pdb" } resolution = 3.59 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= 0.012 sd= 0.152 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 10 5.16 5 C 2634 2.51 5 N 705 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B ARG 102": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 4049 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3110 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 26, 'TRANS': 353} Chain: "B" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' FE': 2, 'D12': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.70, per 1000 atoms: 0.67 Number of scatterers: 4049 At special positions: 0 Unit cell: (96.9, 88.35, 69.35, 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) Fe 2 26.01 S 10 16.00 O 698 8.00 N 705 7.00 C 2634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 97 " distance=2.04 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: 1.78 Conformation dependent library (CDL) restraints added in 735.1 milliseconds 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 2 sheets defined 47.1% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 26 through 48 removed outlier: 3.650A pdb=" N TRP A 29 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 30 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 31 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TRP A 35 " --> pdb=" O SER A 32 " (cutoff:3.500A) Proline residue: A 36 - end of helix Proline residue: A 39 - end of helix removed outlier: 3.534A pdb=" N LEU A 45 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 58 through 63 removed outlier: 3.553A pdb=" N TYR A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 85 through 88 No H-bonds generated for 'chain 'A' and resid 85 through 88' Processing helix chain 'A' and resid 92 through 118 removed outlier: 4.353A pdb=" N LEU A 97 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU A 100 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Proline residue: A 103 - end of helix removed outlier: 3.531A pdb=" N VAL A 108 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY A 111 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 117 " --> pdb=" O TRP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 125 through 149 removed outlier: 3.905A pdb=" N GLU A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 167 removed outlier: 4.006A pdb=" N VAL A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 removed outlier: 3.766A pdb=" N PHE A 174 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS A 177 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 178 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 179 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 180 " --> pdb=" O HIS A 177 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N HIS A 181 " --> pdb=" O ASN A 178 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS A 182 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 225 Proline residue: A 209 - end of helix removed outlier: 3.895A pdb=" N ILE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 257 through 281 Proline residue: A 261 - end of helix removed outlier: 4.955A pdb=" N LEU A 264 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 265 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 266 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 278 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 348 through 355 Processing helix chain 'A' and resid 358 through 373 removed outlier: 3.906A pdb=" N ASP A 366 " --> pdb=" O ARG A 362 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ARG A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 392 Processing sheet with id= A, first strand: chain 'B' and resid 6 through 9 removed outlier: 3.623A pdb=" N GLN B 7 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 23 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR B 70 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 93 through 99 removed outlier: 3.543A pdb=" N VAL B 94 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARG B 40 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) 140 hydrogen bonds defined for protein. 285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 1.94 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: 681 1.32 - 1.44: 1229 1.44 - 1.56: 2249 1.56 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 4175 Sorted by residual: bond pdb=" CA TYR A 21 " pdb=" C TYR A 21 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.34e-02 5.57e+03 2.67e+01 bond pdb=" N ARG B 73 " pdb=" CA ARG B 73 " ideal model delta sigma weight residual 1.458 1.488 -0.030 6.30e-03 2.52e+04 2.22e+01 bond pdb=" N ARG B 32 " pdb=" CA ARG B 32 " ideal model delta sigma weight residual 1.459 1.490 -0.031 9.10e-03 1.21e+04 1.16e+01 bond pdb=" CA ALA A 142 " pdb=" CB ALA A 142 " ideal model delta sigma weight residual 1.530 1.478 0.052 1.57e-02 4.06e+03 1.10e+01 bond pdb=" C LEU A 141 " pdb=" O LEU A 141 " ideal model delta sigma weight residual 1.236 1.195 0.042 1.26e-02 6.30e+03 1.09e+01 ... (remaining 4170 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.60: 114 105.60 - 112.77: 2167 112.77 - 119.93: 1622 119.93 - 127.10: 1710 127.10 - 134.26: 80 Bond angle restraints: 5693 Sorted by residual: angle pdb=" N LEU A 318 " pdb=" CA LEU A 318 " pdb=" C LEU A 318 " ideal model delta sigma weight residual 114.31 104.74 9.57 1.29e+00 6.01e-01 5.50e+01 angle pdb=" N GLY A 140 " pdb=" CA GLY A 140 " pdb=" C GLY A 140 " ideal model delta sigma weight residual 112.73 105.63 7.10 1.20e+00 6.94e-01 3.50e+01 angle pdb=" N ILE B 30 " pdb=" CA ILE B 30 " pdb=" C ILE B 30 " ideal model delta sigma weight residual 112.90 107.36 5.54 9.60e-01 1.09e+00 3.32e+01 angle pdb=" N THR A 145 " pdb=" CA THR A 145 " pdb=" C THR A 145 " ideal model delta sigma weight residual 113.50 106.73 6.77 1.23e+00 6.61e-01 3.03e+01 angle pdb=" CA GLY A 256 " pdb=" C GLY A 256 " pdb=" O GLY A 256 " ideal model delta sigma weight residual 122.29 118.00 4.29 8.10e-01 1.52e+00 2.81e+01 ... (remaining 5688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.29: 2071 15.29 - 30.58: 242 30.58 - 45.86: 69 45.86 - 61.15: 25 61.15 - 76.44: 8 Dihedral angle restraints: 2415 sinusoidal: 971 harmonic: 1444 Sorted by residual: dihedral pdb=" CA PHE A 316 " pdb=" C PHE A 316 " pdb=" N HIS A 317 " pdb=" CA HIS A 317 " ideal model delta harmonic sigma weight residual -180.00 -152.27 -27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ARG A 320 " pdb=" C ARG A 320 " pdb=" N HIS A 321 " pdb=" CA HIS A 321 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA GLY A 374 " pdb=" C GLY A 374 " pdb=" N ARG A 375 " pdb=" CA ARG A 375 " ideal model delta harmonic sigma weight residual 180.00 156.08 23.92 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 2412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 325 0.053 - 0.105: 212 0.105 - 0.157: 51 0.157 - 0.210: 15 0.210 - 0.262: 5 Chirality restraints: 608 Sorted by residual: chirality pdb=" CB VAL A 37 " pdb=" CA VAL A 37 " pdb=" CG1 VAL A 37 " pdb=" CG2 VAL A 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA TYR A 21 " pdb=" N TYR A 21 " pdb=" C TYR A 21 " pdb=" CB TYR A 21 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA TYR A 348 " pdb=" N TYR A 348 " pdb=" C TYR A 348 " pdb=" CB TYR A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 605 not shown) Planarity restraints: 717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 344 " 0.050 5.00e-02 4.00e+02 7.66e-02 9.39e+00 pdb=" N PRO A 345 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 80 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO A 81 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 180 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C GLY A 180 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY A 180 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS A 181 " 0.016 2.00e-02 2.50e+03 ... (remaining 714 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 349 2.70 - 3.25: 4163 3.25 - 3.80: 6345 3.80 - 4.35: 7817 4.35 - 4.90: 12705 Nonbonded interactions: 31379 Sorted by model distance: nonbonded pdb=" NE2 HIS A 325 " pdb="FE FE A 401 " model vdw 2.146 2.340 nonbonded pdb=" O GLY B 44 " pdb=" NZ LYS B 45 " model vdw 2.147 2.520 nonbonded pdb=" NE2 HIS A 282 " pdb="FE FE A 401 " model vdw 2.156 2.340 nonbonded pdb=" OG SER B 19 " pdb=" O MET B 84 " model vdw 2.210 2.440 nonbonded pdb=" NE2 HIS A 324 " pdb="FE FE A 402 " model vdw 2.227 2.340 ... (remaining 31374 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.480 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.070 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.016 0.108 4175 Z= 1.023 Angle : 1.326 10.553 5693 Z= 0.830 Chirality : 0.071 0.262 608 Planarity : 0.009 0.077 717 Dihedral : 15.679 76.438 1494 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.95 % Favored : 85.05 % Rotamer: Outliers : 3.99 % Allowed : 12.68 % Favored : 83.33 % 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: -5.32 (0.28), residues: 495 helix: -2.80 (0.28), residues: 230 sheet: -3.34 (0.71), residues: 34 loop : -4.42 (0.28), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP A 125 HIS 0.010 0.002 HIS A 151 PHE 0.022 0.004 PHE A 173 TYR 0.032 0.004 TYR A 93 ARG 0.007 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8790 (tp) cc_final: 0.8464 (mt) REVERT: B 35 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7734 (t) REVERT: B 54 SER cc_start: 0.8234 (t) cc_final: 0.7888 (m) outliers start: 17 outliers final: 3 residues processed: 106 average time/residue: 0.2021 time to fit residues: 25.4678 Evaluate side-chains 58 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 72 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 119 HIS A 144 ASN A 266 GLN A 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4175 Z= 0.246 Angle : 0.737 6.179 5693 Z= 0.387 Chirality : 0.044 0.157 608 Planarity : 0.008 0.058 717 Dihedral : 5.801 37.246 574 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.45 % Favored : 94.34 % Rotamer: Outliers : 3.52 % Allowed : 17.37 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.22 (0.31), residues: 495 helix: -1.95 (0.31), residues: 236 sheet: -3.07 (0.80), residues: 28 loop : -3.75 (0.31), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 125 HIS 0.006 0.001 HIS A 147 PHE 0.015 0.001 PHE A 173 TYR 0.019 0.002 TYR A 126 ARG 0.006 0.001 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 0.516 Fit side-chains REVERT: A 64 LEU cc_start: 0.8779 (tp) cc_final: 0.8475 (mp) REVERT: A 288 GLN cc_start: 0.7190 (mm-40) cc_final: 0.6848 (mm-40) outliers start: 15 outliers final: 11 residues processed: 68 average time/residue: 0.1501 time to fit residues: 13.3458 Evaluate side-chains 59 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 48 optimal weight: 0.0070 chunk 39 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4175 Z= 0.200 Angle : 0.651 6.055 5693 Z= 0.339 Chirality : 0.041 0.125 608 Planarity : 0.006 0.045 717 Dihedral : 5.067 27.226 567 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.23 % Allowed : 16.43 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.34), residues: 495 helix: -1.33 (0.34), residues: 225 sheet: -2.50 (0.86), residues: 28 loop : -3.03 (0.33), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 125 HIS 0.003 0.001 HIS A 147 PHE 0.011 0.001 PHE A 173 TYR 0.017 0.002 TYR A 21 ARG 0.002 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 44 time to evaluate : 0.486 Fit side-chains REVERT: A 187 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8687 (m) REVERT: A 288 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.7001 (mm-40) REVERT: A 365 MET cc_start: 0.7975 (mmm) cc_final: 0.7731 (mmm) outliers start: 18 outliers final: 11 residues processed: 56 average time/residue: 0.1319 time to fit residues: 9.9544 Evaluate side-chains 56 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4175 Z= 0.370 Angle : 0.741 8.676 5693 Z= 0.380 Chirality : 0.046 0.153 608 Planarity : 0.006 0.044 717 Dihedral : 5.266 26.351 567 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.93 % Allowed : 17.61 % Favored : 77.46 % 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: -3.19 (0.34), residues: 495 helix: -1.41 (0.34), residues: 219 sheet: -2.25 (0.93), residues: 28 loop : -2.80 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 216 HIS 0.006 0.001 HIS A 147 PHE 0.021 0.002 PHE A 173 TYR 0.014 0.002 TYR B 61 ARG 0.003 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 43 time to evaluate : 0.448 Fit side-chains REVERT: A 288 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6975 (mm-40) outliers start: 21 outliers final: 17 residues processed: 57 average time/residue: 0.1793 time to fit residues: 12.8239 Evaluate side-chains 60 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 42 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 42 optimal weight: 20.0000 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.0170 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4175 Z= 0.167 Angle : 0.623 7.581 5693 Z= 0.315 Chirality : 0.041 0.178 608 Planarity : 0.005 0.041 717 Dihedral : 5.025 25.144 567 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.05 % Allowed : 20.19 % Favored : 76.76 % 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: -2.50 (0.36), residues: 495 helix: -1.14 (0.35), residues: 217 sheet: -0.86 (0.71), residues: 51 loop : -2.36 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 216 HIS 0.003 0.001 HIS A 321 PHE 0.010 0.001 PHE A 173 TYR 0.014 0.001 TYR B 61 ARG 0.002 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.426 Fit side-chains REVERT: A 288 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.7108 (mm-40) REVERT: A 365 MET cc_start: 0.8043 (mmm) cc_final: 0.7726 (mmm) outliers start: 13 outliers final: 8 residues processed: 50 average time/residue: 0.1747 time to fit residues: 11.0892 Evaluate side-chains 47 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4175 Z= 0.172 Angle : 0.606 6.892 5693 Z= 0.309 Chirality : 0.041 0.135 608 Planarity : 0.005 0.039 717 Dihedral : 4.783 23.060 567 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.76 % Allowed : 19.95 % Favored : 76.29 % 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: -2.30 (0.36), residues: 495 helix: -0.97 (0.36), residues: 215 sheet: -0.69 (0.70), residues: 51 loop : -2.26 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 216 HIS 0.003 0.000 HIS A 321 PHE 0.008 0.001 PHE A 173 TYR 0.012 0.001 TYR B 61 ARG 0.001 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 38 time to evaluate : 0.510 Fit side-chains REVERT: A 288 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7137 (mm-40) REVERT: A 365 MET cc_start: 0.8153 (mmm) cc_final: 0.7850 (mmm) outliers start: 16 outliers final: 11 residues processed: 48 average time/residue: 0.1390 time to fit residues: 9.0115 Evaluate side-chains 49 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4175 Z= 0.225 Angle : 0.637 8.767 5693 Z= 0.322 Chirality : 0.042 0.146 608 Planarity : 0.005 0.039 717 Dihedral : 4.780 23.224 567 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 5.16 % Allowed : 19.48 % Favored : 75.35 % 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: -2.29 (0.36), residues: 495 helix: -0.92 (0.36), residues: 210 sheet: -0.48 (0.69), residues: 51 loop : -2.33 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 216 HIS 0.003 0.001 HIS A 147 PHE 0.014 0.001 PHE A 173 TYR 0.012 0.001 TYR B 61 ARG 0.002 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 39 time to evaluate : 0.435 Fit side-chains REVERT: A 288 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7142 (mm-40) REVERT: A 365 MET cc_start: 0.8171 (mmm) cc_final: 0.7759 (mmm) outliers start: 22 outliers final: 16 residues processed: 51 average time/residue: 0.1276 time to fit residues: 8.7947 Evaluate side-chains 56 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 39 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4175 Z= 0.190 Angle : 0.615 7.974 5693 Z= 0.311 Chirality : 0.041 0.125 608 Planarity : 0.005 0.037 717 Dihedral : 4.700 22.968 567 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.76 % Allowed : 21.36 % Favored : 74.88 % 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: -2.15 (0.37), residues: 495 helix: -0.82 (0.37), residues: 208 sheet: -0.35 (0.69), residues: 51 loop : -2.24 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 216 HIS 0.003 0.001 HIS A 308 PHE 0.010 0.001 PHE A 173 TYR 0.011 0.001 TYR B 61 ARG 0.001 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 37 time to evaluate : 0.466 Fit side-chains REVERT: A 288 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7194 (mm-40) outliers start: 16 outliers final: 15 residues processed: 45 average time/residue: 0.1411 time to fit residues: 8.6350 Evaluate side-chains 54 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 38 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 0.0000 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 HIS ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4175 Z= 0.263 Angle : 0.656 8.410 5693 Z= 0.332 Chirality : 0.043 0.142 608 Planarity : 0.005 0.037 717 Dihedral : 4.806 25.766 567 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.69 % Allowed : 20.66 % Favored : 74.65 % 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: -2.31 (0.36), residues: 495 helix: -0.93 (0.36), residues: 208 sheet: -0.61 (0.83), residues: 41 loop : -2.25 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 216 HIS 0.003 0.001 HIS A 321 PHE 0.016 0.001 PHE A 173 TYR 0.010 0.001 TYR A 93 ARG 0.002 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 41 time to evaluate : 0.457 Fit side-chains REVERT: A 288 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7189 (mm-40) outliers start: 20 outliers final: 17 residues processed: 52 average time/residue: 0.1873 time to fit residues: 12.4075 Evaluate side-chains 56 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 38 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 38 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4175 Z= 0.283 Angle : 0.673 8.681 5693 Z= 0.341 Chirality : 0.043 0.131 608 Planarity : 0.005 0.038 717 Dihedral : 4.958 32.995 567 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.23 % Allowed : 21.36 % Favored : 74.41 % 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: -2.34 (0.36), residues: 495 helix: -0.99 (0.36), residues: 208 sheet: -0.59 (0.83), residues: 41 loop : -2.24 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 216 HIS 0.003 0.001 HIS A 147 PHE 0.013 0.001 PHE A 173 TYR 0.011 0.001 TYR A 93 ARG 0.003 0.000 ARG A 375 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 39 time to evaluate : 0.456 Fit side-chains REVERT: A 288 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7231 (mm-40) outliers start: 18 outliers final: 17 residues processed: 48 average time/residue: 0.1373 time to fit residues: 8.8776 Evaluate side-chains 57 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 39 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.164929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.128586 restraints weight = 5477.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.131297 restraints weight = 3120.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133022 restraints weight = 2218.785| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4175 Z= 0.169 Angle : 0.614 8.896 5693 Z= 0.308 Chirality : 0.040 0.113 608 Planarity : 0.005 0.036 717 Dihedral : 4.693 29.047 567 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.52 % Allowed : 22.77 % Favored : 73.71 % 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: -2.12 (0.37), residues: 495 helix: -0.86 (0.37), residues: 211 sheet: -0.45 (0.83), residues: 41 loop : -2.08 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 216 HIS 0.002 0.001 HIS A 147 PHE 0.007 0.001 PHE A 173 TYR 0.009 0.001 TYR B 61 ARG 0.002 0.000 ARG A 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1189.37 seconds wall clock time: 22 minutes 21.34 seconds (1341.34 seconds total)