Starting phenix.real_space_refine (version: 1.21rc1) on Wed May 3 02:36:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbb_40303/05_2023/8sbb_40303_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbb_40303/05_2023/8sbb_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_40303/05_2023/8sbb_40303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbb_40303/05_2023/8sbb_40303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbb_40303/05_2023/8sbb_40303_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbb_40303/05_2023/8sbb_40303_updated.pdb" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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-1.21rc1-4953/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: 2.82, per 1000 atoms: 0.70 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: 1.76 Conformation dependent library (CDL) restraints added in 709.1 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: 0.48 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: 0.89 Time building geometry restraints manager: 1.91 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.580 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.610 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.520 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.541 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 3 residues processed: 106 average time/residue: 0.2229 time to fit residues: 28.3459 Evaluate side-chains 57 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0543 time to fit residues: 0.9710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7752 moved from start: 0.2857 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= 0.241 Angle : 0.743 6.164 5693 Z= 0.388 Chirality : 0.044 0.154 608 Planarity : 0.008 0.057 717 Dihedral : 5.462 29.741 567 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.45 % Favored : 94.34 % Rotamer Outliers : 3.52 % 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: -4.21 (0.31), residues: 495 helix: -1.98 (0.31), residues: 236 sheet: -3.00 (0.81), residues: 28 loop : -3.72 (0.31), residues: 231 *********************** 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 : 0.455 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 68 average time/residue: 0.1325 time to fit residues: 11.7631 Evaluate side-chains 57 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.498 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0723 time to fit residues: 1.6196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 0.0050 chunk 30 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 39 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 288 GLN A 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 4175 Z= 0.173 Angle : 0.653 6.739 5693 Z= 0.334 Chirality : 0.042 0.200 608 Planarity : 0.006 0.044 717 Dihedral : 5.006 27.862 567 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 3.05 % 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: -3.25 (0.34), residues: 495 helix: -1.42 (0.33), residues: 234 sheet: -1.71 (0.67), residues: 51 loop : -3.12 (0.35), residues: 210 *********************** 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 64 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.517 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 57 average time/residue: 0.1473 time to fit residues: 11.0757 Evaluate side-chains 51 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.493 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0404 time to fit residues: 1.0311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 A 386 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.053 4175 Z= 0.450 Angle : 0.797 8.557 5693 Z= 0.411 Chirality : 0.049 0.204 608 Planarity : 0.006 0.043 717 Dihedral : 5.375 25.494 567 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer Outliers : 3.29 % 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: -3.30 (0.34), residues: 495 helix: -1.49 (0.34), residues: 212 sheet: -1.73 (0.80), residues: 41 loop : -2.97 (0.34), residues: 242 *********************** 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 59 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.499 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 55 average time/residue: 0.1759 time to fit residues: 12.2938 Evaluate side-chains 54 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.480 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0438 time to fit residues: 1.5783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.0370 chunk 27 optimal weight: 0.0670 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 A 386 GLN ** 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: 0.7814 moved from start: 0.4245 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= 0.166 Angle : 0.629 7.284 5693 Z= 0.319 Chirality : 0.041 0.186 608 Planarity : 0.006 0.041 717 Dihedral : 5.031 25.529 567 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 0.94 % 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: -2.61 (0.36), residues: 495 helix: -0.98 (0.36), residues: 209 sheet: -1.10 (0.83), residues: 41 loop : -2.55 (0.35), residues: 245 *********************** 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 45 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.541 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 0.1709 time to fit residues: 9.8028 Evaluate side-chains 40 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0578 time to fit residues: 0.8638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 39 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 0.0030 chunk 34 optimal weight: 0.9980 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4406 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= 0.207 Angle : 0.628 7.393 5693 Z= 0.319 Chirality : 0.042 0.163 608 Planarity : 0.005 0.039 717 Dihedral : 4.912 23.002 567 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.36), residues: 495 helix: -0.92 (0.36), residues: 210 sheet: -0.58 (0.69), residues: 51 loop : -2.45 (0.37), residues: 234 *********************** 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 48 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.512 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 45 average time/residue: 0.1626 time to fit residues: 9.5895 Evaluate side-chains 40 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.511 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0429 time to fit residues: 0.8438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7821 moved from start: 0.4651 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= 0.169 Angle : 0.619 8.333 5693 Z= 0.313 Chirality : 0.041 0.137 608 Planarity : 0.005 0.039 717 Dihedral : 4.765 22.779 567 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 0.94 % 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: -2.23 (0.36), residues: 495 helix: -0.76 (0.37), residues: 208 sheet: -0.32 (0.72), residues: 49 loop : -2.43 (0.37), residues: 238 *********************** 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 42 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.504 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.1817 time to fit residues: 9.5715 Evaluate side-chains 39 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0635 time to fit residues: 0.8193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.0970 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 41 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.0000 overall best weight: 0.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 288 GLN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN B 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 4175 Z= 0.144 Angle : 0.600 7.958 5693 Z= 0.301 Chirality : 0.039 0.131 608 Planarity : 0.005 0.039 717 Dihedral : 4.544 21.803 567 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.47 % 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: -2.01 (0.36), residues: 495 helix: -0.61 (0.37), residues: 209 sheet: 0.01 (0.72), residues: 49 loop : -2.34 (0.37), residues: 237 *********************** 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 40 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.528 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 39 average time/residue: 0.1878 time to fit residues: 9.4026 Evaluate side-chains 38 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0414 time to fit residues: 0.7905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.0370 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 0.0570 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4934 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= 0.185 Angle : 0.616 8.433 5693 Z= 0.309 Chirality : 0.041 0.132 608 Planarity : 0.005 0.040 717 Dihedral : 4.493 20.699 567 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.36), residues: 495 helix: -0.63 (0.37), residues: 209 sheet: 0.17 (0.72), residues: 49 loop : -2.34 (0.37), residues: 237 *********************** 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 46 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.539 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.1945 time to fit residues: 10.2207 Evaluate side-chains 41 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0525 time to fit residues: 0.8617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN B 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4973 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= 0.274 Angle : 0.677 8.659 5693 Z= 0.341 Chirality : 0.043 0.132 608 Planarity : 0.005 0.037 717 Dihedral : 4.664 21.516 567 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 1.17 % 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: -2.17 (0.36), residues: 495 helix: -0.88 (0.37), residues: 212 sheet: -0.02 (0.72), residues: 51 loop : -2.32 (0.37), residues: 232 ********************** 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 46 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.521 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 43 average time/residue: 0.2147 time to fit residues: 11.5641 Evaluate side-chains 45 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.417 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0463 time to fit residues: 1.0702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.167045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130941 restraints weight = 5441.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133565 restraints weight = 3144.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.135067 restraints weight = 2258.553| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4175 Z= 0.164 Angle : 0.641 9.855 5693 Z= 0.316 Chirality : 0.041 0.129 608 Planarity : 0.005 0.038 717 Dihedral : 4.535 22.161 567 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.23 % 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: -2.10 (0.37), residues: 495 helix: -0.75 (0.37), residues: 211 sheet: -0.38 (0.82), residues: 43 loop : -2.20 (0.36), residues: 241 =============================================================================== Job complete usr+sys time: 1118.09 seconds wall clock time: 22 minutes 3.10 seconds (1323.10 seconds total)