Starting phenix.real_space_refine on Wed Mar 5 23:50:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sbb_40303/03_2025/8sbb_40303.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sbb_40303/03_2025/8sbb_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/cci-nas-00/data/ceres_data/8sbb_40303/03_2025/8sbb_40303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sbb_40303/03_2025/8sbb_40303.map" model { file = "/net/cci-nas-00/data/ceres_data/8sbb_40303/03_2025/8sbb_40303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sbb_40303/03_2025/8sbb_40303.cif" } 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. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.18, per 1000 atoms: 0.79 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 491.9 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... Secondary structure from input PDB file: 22 helices and 2 sheets defined 52.3% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 26 through 29 removed outlier: 3.650A pdb=" N TRP A 29 " --> pdb=" O ARG A 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 26 through 29' Processing helix chain 'A' and resid 30 through 35 Processing helix chain 'A' and resid 37 through 49 Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.748A pdb=" N PHE A 55 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 64 removed outlier: 3.553A pdb=" N TYR A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 removed outlier: 3.835A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 92 through 100 removed outlier: 4.516A pdb=" N THR A 98 " --> pdb=" O TYR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 119 removed outlier: 4.060A pdb=" N ILE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 147 removed outlier: 3.882A pdb=" N ILE A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.938A pdb=" N ARG A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 199 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 240 through 256 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 259 through 282 removed outlier: 3.543A pdb=" N LEU A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.636A pdb=" N ASN A 312 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.543A pdb=" N HIS A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.671A pdb=" N MET A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 374 removed outlier: 3.546A pdb=" N TRP A 361 " --> pdb=" O PHE A 357 " (cutoff:3.500A) 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 386 through 393 Processing sheet with id=AA1, 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=AA2, first strand: chain 'B' and resid 48 through 54 removed outlier: 6.128A pdb=" N TRP B 38 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY B 52 " --> pdb=" O MET B 36 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET B 36 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 94 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 95 " --> pdb=" O GLY B 117 " (cutoff:3.500A) 165 hydrogen bonds defined for protein. 483 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: 0.96 Time building geometry restraints manager: 1.32 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: 0.00 - 2.11: 5112 2.11 - 4.22: 497 4.22 - 6.33: 68 6.33 - 8.44: 13 8.44 - 10.55: 3 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: 351 2.70 - 3.25: 4125 3.25 - 3.80: 6375 3.80 - 4.35: 7734 4.35 - 4.90: 12694 Nonbonded interactions: 31279 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 3.120 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 3.040 nonbonded pdb=" NE2 HIS A 324 " pdb="FE FE A 402 " model vdw 2.227 2.340 ... (remaining 31274 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.670 Find NCS groups from input model: 0.040 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:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.180 ------------------------------------------------------------------------------- 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= 1.048 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 to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.408 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: 0.2040 time to fit residues: 25.7605 Evaluate side-chains 58 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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: 6.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.184194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141893 restraints weight = 5547.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.145640 restraints weight = 2756.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.147937 restraints weight = 1821.018| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4175 Z= 0.246 Angle : 0.771 6.671 5693 Z= 0.402 Chirality : 0.045 0.158 608 Planarity : 0.007 0.057 717 Dihedral : 5.858 36.362 574 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.06 % Favored : 93.74 % Rotamer: Outliers : 3.05 % Allowed : 17.37 % Favored : 79.58 % 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: -3.52 (0.33), residues: 495 helix: -0.98 (0.34), residues: 230 sheet: -2.59 (0.65), residues: 39 loop : -3.85 (0.29), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 125 HIS 0.006 0.001 HIS A 147 PHE 0.018 0.002 PHE A 262 TYR 0.019 0.002 TYR B 61 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 73 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.485 Fit side-chains REVERT: A 64 LEU cc_start: 0.8697 (tp) cc_final: 0.8443 (mp) REVERT: A 176 GLU cc_start: 0.8019 (tp30) cc_final: 0.7702 (tm-30) REVERT: A 288 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7049 (mm-40) REVERT: B 23 SER cc_start: 0.7916 (p) cc_final: 0.7516 (m) REVERT: B 54 SER cc_start: 0.7876 (t) cc_final: 0.7461 (m) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.1418 time to fit residues: 13.3355 Evaluate side-chains 61 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 249 VAL 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 35 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.177425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.133359 restraints weight = 5659.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.136761 restraints weight = 2952.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.138929 restraints weight = 2026.974| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4175 Z= 0.312 Angle : 0.742 6.792 5693 Z= 0.388 Chirality : 0.046 0.151 608 Planarity : 0.006 0.048 717 Dihedral : 5.413 27.551 568 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 4.69 % Allowed : 16.90 % Favored : 78.40 % 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: -2.66 (0.35), residues: 495 helix: -0.29 (0.36), residues: 230 sheet: -2.27 (0.65), residues: 39 loop : -3.36 (0.32), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 125 HIS 0.005 0.001 HIS A 147 PHE 0.012 0.002 PHE A 262 TYR 0.016 0.002 TYR A 21 ARG 0.003 0.000 ARG A 387 *********************** 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 69 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.7950 (mmm) cc_final: 0.7622 (mmm) outliers start: 20 outliers final: 13 residues processed: 61 average time/residue: 0.1460 time to fit residues: 11.7840 Evaluate side-chains 58 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 B residue 35 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 chunk 37 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 HIS A 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.170517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.135308 restraints weight = 5327.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134657 restraints weight = 3598.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.136372 restraints weight = 2770.777| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4214 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= 0.161 Angle : 0.639 6.126 5693 Z= 0.329 Chirality : 0.041 0.128 608 Planarity : 0.005 0.042 717 Dihedral : 5.099 27.220 568 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.88 % Allowed : 19.95 % Favored : 78.17 % 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: -1.95 (0.37), residues: 495 helix: 0.24 (0.37), residues: 227 sheet: -1.32 (0.72), residues: 39 loop : -3.01 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 125 HIS 0.002 0.001 HIS A 321 PHE 0.015 0.001 PHE A 262 TYR 0.012 0.001 TYR B 61 ARG 0.003 0.000 ARG A 387 *********************** 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 55 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.444 Fit side-chains REVERT: A 176 GLU cc_start: 0.7967 (tp30) cc_final: 0.7553 (tm-30) REVERT: A 379 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7660 (mtpt) outliers start: 8 outliers final: 6 residues processed: 53 average time/residue: 0.1496 time to fit residues: 10.4787 Evaluate side-chains 51 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 THR 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 380 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 48 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.166538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130054 restraints weight = 5515.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.130992 restraints weight = 3900.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132192 restraints weight = 2755.555| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4175 Z= 0.233 Angle : 0.677 10.008 5693 Z= 0.346 Chirality : 0.043 0.126 608 Planarity : 0.005 0.041 717 Dihedral : 4.963 25.626 567 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.23 % Allowed : 18.08 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.37), residues: 495 helix: 0.32 (0.37), residues: 229 sheet: -1.54 (0.69), residues: 41 loop : -2.85 (0.35), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 34 HIS 0.003 0.001 HIS A 147 PHE 0.013 0.001 PHE A 262 TYR 0.012 0.001 TYR A 93 ARG 0.002 0.000 ARG B 47 *********************** 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 63 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.457 Fit side-chains REVERT: A 176 GLU cc_start: 0.8060 (tp30) cc_final: 0.7702 (tm-30) REVERT: A 379 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7552 (tptp) REVERT: B 114 TRP cc_start: 0.8794 (p90) cc_final: 0.8556 (p90) outliers start: 18 outliers final: 13 residues processed: 56 average time/residue: 0.2056 time to fit residues: 14.5525 Evaluate side-chains 58 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 VAL 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 1 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 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 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.168955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.133333 restraints weight = 5390.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.133494 restraints weight = 3640.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.134692 restraints weight = 2648.931| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4636 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= 0.175 Angle : 0.634 6.910 5693 Z= 0.323 Chirality : 0.042 0.175 608 Planarity : 0.005 0.038 717 Dihedral : 4.857 25.182 567 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.35 % Allowed : 20.66 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.38), residues: 495 helix: 0.53 (0.38), residues: 227 sheet: -0.89 (0.70), residues: 50 loop : -2.72 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 34 HIS 0.003 0.001 HIS A 282 PHE 0.013 0.001 PHE A 262 TYR 0.010 0.001 TYR B 61 ARG 0.002 0.000 ARG A 375 *********************** 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 55 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.470 Fit side-chains REVERT: A 176 GLU cc_start: 0.7834 (tp30) cc_final: 0.7597 (tm-30) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 0.1896 time to fit residues: 13.1388 Evaluate side-chains 48 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 THR 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 315 LEU Chi-restraints excluded: chain A residue 380 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.169431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134205 restraints weight = 5400.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.132729 restraints weight = 3827.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134368 restraints weight = 3362.767| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4832 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= 0.176 Angle : 0.643 10.779 5693 Z= 0.325 Chirality : 0.042 0.148 608 Planarity : 0.005 0.038 717 Dihedral : 4.709 24.258 567 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.58 % Allowed : 20.42 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.38), residues: 495 helix: 0.61 (0.38), residues: 228 sheet: -0.55 (0.73), residues: 50 loop : -2.59 (0.36), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 34 HIS 0.003 0.001 HIS A 282 PHE 0.011 0.001 PHE A 262 TYR 0.010 0.001 TYR B 61 ARG 0.002 0.000 ARG B 21 *********************** 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 57 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.440 Fit side-chains REVERT: B 96 TYR cc_start: 0.6150 (OUTLIER) cc_final: 0.5310 (m-80) outliers start: 11 outliers final: 10 residues processed: 53 average time/residue: 0.1663 time to fit residues: 11.4146 Evaluate side-chains 56 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 THR 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 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 96 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 38 optimal weight: 0.0270 chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.167950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.130268 restraints weight = 5271.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.132523 restraints weight = 3168.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.134199 restraints weight = 2348.091| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4175 Z= 0.211 Angle : 0.654 9.791 5693 Z= 0.332 Chirality : 0.042 0.142 608 Planarity : 0.005 0.038 717 Dihedral : 4.749 25.821 567 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.82 % Allowed : 20.66 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.38), residues: 495 helix: 0.60 (0.38), residues: 228 sheet: -0.91 (0.85), residues: 41 loop : -2.58 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 216 HIS 0.003 0.001 HIS A 182 PHE 0.011 0.001 PHE A 262 TYR 0.010 0.001 TYR A 93 ARG 0.002 0.000 ARG B 73 *********************** 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 61 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.750 Fit side-chains REVERT: A 388 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7297 (mm-30) REVERT: B 96 TYR cc_start: 0.6104 (OUTLIER) cc_final: 0.5241 (m-80) outliers start: 12 outliers final: 11 residues processed: 56 average time/residue: 0.1747 time to fit residues: 12.9669 Evaluate side-chains 58 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 THR 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 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 96 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 46 optimal weight: 0.0020 chunk 19 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 22 optimal weight: 0.0000 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.172263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.135100 restraints weight = 5260.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.137836 restraints weight = 3000.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.139258 restraints weight = 2106.815| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4175 Z= 0.161 Angle : 0.633 9.799 5693 Z= 0.319 Chirality : 0.041 0.125 608 Planarity : 0.005 0.038 717 Dihedral : 4.619 24.126 567 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.88 % Allowed : 23.00 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.38), residues: 495 helix: 0.79 (0.38), residues: 227 sheet: -0.39 (0.72), residues: 50 loop : -2.47 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 125 HIS 0.003 0.001 HIS A 282 PHE 0.012 0.001 PHE A 262 TYR 0.010 0.001 TYR A 44 ARG 0.002 0.000 ARG B 73 *********************** 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 58 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.605 Fit side-chains REVERT: A 97 LEU cc_start: 0.9054 (tp) cc_final: 0.8606 (tt) REVERT: A 388 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7320 (mm-30) REVERT: B 96 TYR cc_start: 0.6090 (OUTLIER) cc_final: 0.5243 (m-80) outliers start: 8 outliers final: 7 residues processed: 56 average time/residue: 0.2178 time to fit residues: 15.2192 Evaluate side-chains 56 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 THR 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 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 96 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 43 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 0.0980 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.170225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.132476 restraints weight = 5324.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.135128 restraints weight = 3018.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.136940 restraints weight = 2121.332| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5154 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= 0.175 Angle : 0.643 9.677 5693 Z= 0.324 Chirality : 0.042 0.128 608 Planarity : 0.005 0.038 717 Dihedral : 4.552 23.128 567 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.11 % Allowed : 22.54 % 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: -1.04 (0.38), residues: 495 helix: 0.85 (0.38), residues: 227 sheet: -0.56 (0.86), residues: 41 loop : -2.43 (0.34), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 125 HIS 0.003 0.001 HIS A 182 PHE 0.010 0.001 PHE A 262 TYR 0.009 0.001 TYR B 61 ARG 0.004 0.000 ARG A 362 ********************** 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 56 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.499 Fit side-chains REVERT: A 97 LEU cc_start: 0.9083 (tp) cc_final: 0.8657 (tt) REVERT: A 388 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7302 (mm-30) REVERT: B 96 TYR cc_start: 0.6042 (OUTLIER) cc_final: 0.5191 (m-80) outliers start: 9 outliers final: 8 residues processed: 53 average time/residue: 0.2603 time to fit residues: 18.4470 Evaluate side-chains 53 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 THR 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 315 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 96 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 20.0000 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 0.0980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.167382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129054 restraints weight = 5292.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.131800 restraints weight = 2988.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133597 restraints weight = 2099.338| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5169 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= 0.200 Angle : 0.656 9.609 5693 Z= 0.330 Chirality : 0.042 0.128 608 Planarity : 0.005 0.038 717 Dihedral : 4.605 25.871 567 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.11 % Allowed : 22.54 % 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: -1.04 (0.38), residues: 495 helix: 0.82 (0.38), residues: 227 sheet: -0.39 (0.87), residues: 41 loop : -2.43 (0.35), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 216 HIS 0.003 0.001 HIS A 182 PHE 0.011 0.001 PHE A 262 TYR 0.009 0.001 TYR A 93 ARG 0.005 0.000 ARG A 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1828.60 seconds wall clock time: 33 minutes 55.19 seconds (2035.19 seconds total)