Starting phenix.real_space_refine on Wed Mar 5 21:01:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sc6_40339/03_2025/8sc6_40339.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sc6_40339/03_2025/8sc6_40339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sc6_40339/03_2025/8sc6_40339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sc6_40339/03_2025/8sc6_40339.map" model { file = "/net/cci-nas-00/data/ceres_data/8sc6_40339/03_2025/8sc6_40339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sc6_40339/03_2025/8sc6_40339.cif" } resolution = 3.13 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= 0.000 sd= 0.034 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 2293 2.51 5 N 565 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3479 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3461 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'VIB': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.90, per 1000 atoms: 0.83 Number of scatterers: 3479 At special positions: 0 Unit cell: (90.72, 84, 68.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 590 8.00 N 565 7.00 C 2293 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 545.7 milliseconds 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 818 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 80.5% alpha, 1.3% 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 19 through 31 removed outlier: 3.959A pdb=" N LEU A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.727A pdb=" N CYS A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 141 through 147 removed outlier: 4.520A pdb=" N TRP A 146 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 173 removed outlier: 4.333A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.820A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 3.738A pdb=" N VAL A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.612A pdb=" N GLN A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 278 Proline residue: A 271 - end of helix removed outlier: 3.515A pdb=" N LEU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.504A pdb=" N PHE A 338 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 372 Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.508A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 398 removed outlier: 4.072A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 420 removed outlier: 3.542A pdb=" N MET A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 removed outlier: 3.738A pdb=" N ILE A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 491 removed outlier: 3.788A pdb=" N LEU A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) Proline residue: A 481 - end of helix removed outlier: 3.533A pdb=" N LEU A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 removed outlier: 4.019A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 241 hydrogen bonds defined for protein. 696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1071 1.34 - 1.46: 838 1.46 - 1.58: 1616 1.58 - 1.69: 1 1.69 - 1.81: 46 Bond restraints: 3572 Sorted by residual: bond pdb=" CA LEU A 427 " pdb=" C LEU A 427 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.14e-02 7.69e+03 5.00e-01 bond pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta sigma weight residual 1.468 1.461 0.007 1.05e-02 9.07e+03 4.84e-01 bond pdb=" CA THR A 480 " pdb=" C THR A 480 " ideal model delta sigma weight residual 1.520 1.529 -0.008 1.23e-02 6.61e+03 4.75e-01 bond pdb=" C ALA A 257 " pdb=" N LEU A 258 " ideal model delta sigma weight residual 1.327 1.336 -0.009 1.32e-02 5.74e+03 4.45e-01 bond pdb=" C VAL A 461 " pdb=" O VAL A 461 " ideal model delta sigma weight residual 1.226 1.240 -0.013 2.04e-02 2.40e+03 4.30e-01 ... (remaining 3567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 4682 1.06 - 2.12: 147 2.12 - 3.17: 27 3.17 - 4.23: 7 4.23 - 5.29: 7 Bond angle restraints: 4870 Sorted by residual: angle pdb=" C GLU A 386 " pdb=" N ILE A 387 " pdb=" CA ILE A 387 " ideal model delta sigma weight residual 120.33 122.81 -2.48 8.00e-01 1.56e+00 9.59e+00 angle pdb=" C TYR A 72 " pdb=" N THR A 73 " pdb=" CA THR A 73 " ideal model delta sigma weight residual 122.46 117.60 4.86 1.80e+00 3.09e-01 7.30e+00 angle pdb=" CA CYS A 50 " pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " ideal model delta sigma weight residual 114.40 119.23 -4.83 2.30e+00 1.89e-01 4.40e+00 angle pdb=" N THR A 480 " pdb=" CA THR A 480 " pdb=" C THR A 480 " ideal model delta sigma weight residual 112.75 115.58 -2.83 1.36e+00 5.41e-01 4.34e+00 angle pdb=" C VAL A 461 " pdb=" CA VAL A 461 " pdb=" CB VAL A 461 " ideal model delta sigma weight residual 112.36 109.75 2.61 1.37e+00 5.33e-01 3.62e+00 ... (remaining 4865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.01: 1882 11.01 - 22.02: 141 22.02 - 33.03: 34 33.03 - 44.04: 9 44.04 - 55.05: 1 Dihedral angle restraints: 2067 sinusoidal: 788 harmonic: 1279 Sorted by residual: dihedral pdb=" N PHE A 273 " pdb=" CA PHE A 273 " pdb=" CB PHE A 273 " pdb=" CG PHE A 273 " ideal model delta sinusoidal sigma weight residual -60.00 -115.05 55.05 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" N LEU A 150 " pdb=" CA LEU A 150 " pdb=" CB LEU A 150 " pdb=" CG LEU A 150 " ideal model delta sinusoidal sigma weight residual -60.00 -102.93 42.93 3 1.50e+01 4.44e-03 7.71e+00 dihedral pdb=" N MET A 239 " pdb=" CA MET A 239 " pdb=" CB MET A 239 " pdb=" CG MET A 239 " ideal model delta sinusoidal sigma weight residual -180.00 -141.24 -38.76 3 1.50e+01 4.44e-03 6.84e+00 ... (remaining 2064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 313 0.022 - 0.043: 148 0.043 - 0.065: 63 0.065 - 0.087: 18 0.087 - 0.109: 20 Chirality restraints: 562 Sorted by residual: chirality pdb=" CA THR A 480 " pdb=" N THR A 480 " pdb=" C THR A 480 " pdb=" CB THR A 480 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.11 2.00e-01 2.50e+01 2.95e-01 chirality pdb=" CA LEU A 270 " pdb=" N LEU A 270 " pdb=" C LEU A 270 " pdb=" CB LEU A 270 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.88e-01 chirality pdb=" CA PRO A 53 " pdb=" N PRO A 53 " pdb=" C PRO A 53 " pdb=" CB PRO A 53 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.84e-01 ... (remaining 559 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.52e+00 pdb=" N PRO A 271 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 74 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO A 75 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 65 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 66 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.016 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 868 2.80 - 3.32: 3411 3.32 - 3.85: 5504 3.85 - 4.37: 6251 4.37 - 4.90: 11184 Nonbonded interactions: 27218 Sorted by model distance: nonbonded pdb=" O LYS A 147 " pdb=" OH TYR A 199 " model vdw 2.273 3.040 nonbonded pdb=" OE1 GLU A 137 " pdb=" NE1 TRP A 261 " model vdw 2.340 3.120 nonbonded pdb=" NZ LYS A 214 " pdb=" OD1 ASP A 474 " model vdw 2.351 3.120 nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.353 3.040 nonbonded pdb=" O GLN A 209 " pdb=" OG SER A 213 " model vdw 2.363 3.040 ... (remaining 27213 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.170 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 0.003 0.023 3572 Z= 0.166 Angle : 0.502 5.291 4870 Z= 0.288 Chirality : 0.035 0.109 562 Planarity : 0.004 0.031 601 Dihedral : 8.707 55.052 1240 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.81 % Allowed : 2.96 % Favored : 96.23 % 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: 2.80 (0.41), residues: 443 helix: 2.09 (0.31), residues: 302 sheet: None (None), residues: 0 loop : 1.57 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 244 TYR 0.011 0.001 TYR A 168 ARG 0.001 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.348 Fit side-chains REVERT: A 273 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: A 351 MET cc_start: 0.8709 (mtt) cc_final: 0.8385 (mtp) REVERT: A 357 ASP cc_start: 0.7980 (m-30) cc_final: 0.7731 (m-30) outliers start: 3 outliers final: 0 residues processed: 67 average time/residue: 0.1715 time to fit residues: 14.0537 Evaluate side-chains 41 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 39 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS A 447 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.194255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136150 restraints weight = 3532.544| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.47 r_work: 0.3106 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3572 Z= 0.233 Angle : 0.512 6.527 4870 Z= 0.265 Chirality : 0.038 0.135 562 Planarity : 0.004 0.034 601 Dihedral : 4.806 54.486 487 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.16 % Allowed : 9.43 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.42), residues: 443 helix: 2.17 (0.30), residues: 311 sheet: None (None), residues: 0 loop : 1.34 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.011 0.001 PHE A 32 TYR 0.012 0.001 TYR A 168 ARG 0.007 0.001 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.373 Fit side-chains REVERT: A 200 MET cc_start: 0.7472 (mmt) cc_final: 0.7227 (mmp) REVERT: A 273 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7539 (m-80) REVERT: A 351 MET cc_start: 0.8437 (mtt) cc_final: 0.8210 (mtm) REVERT: A 395 ILE cc_start: 0.6638 (OUTLIER) cc_final: 0.6361 (mm) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.1503 time to fit residues: 9.2163 Evaluate side-chains 48 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 0.0870 chunk 25 optimal weight: 0.0060 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.4174 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.194948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.136518 restraints weight = 3550.559| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.14 r_work: 0.3144 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3572 Z= 0.136 Angle : 0.436 4.940 4870 Z= 0.225 Chirality : 0.035 0.128 562 Planarity : 0.004 0.033 601 Dihedral : 4.599 54.500 487 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.16 % Allowed : 8.89 % Favored : 88.95 % 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: 3.14 (0.42), residues: 443 helix: 2.47 (0.30), residues: 306 sheet: None (None), residues: 0 loop : 1.36 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.008 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.003 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.337 Fit side-chains REVERT: A 200 MET cc_start: 0.7460 (mmt) cc_final: 0.7234 (mmp) REVERT: A 273 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7365 (m-80) outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 0.1375 time to fit residues: 9.1791 Evaluate side-chains 50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.194568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.136018 restraints weight = 3530.072| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.14 r_work: 0.3105 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3572 Z= 0.177 Angle : 0.450 4.963 4870 Z= 0.233 Chirality : 0.036 0.128 562 Planarity : 0.004 0.030 601 Dihedral : 4.607 55.957 487 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.43 % Allowed : 9.16 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.41), residues: 443 helix: 2.40 (0.30), residues: 306 sheet: None (None), residues: 0 loop : 1.29 (0.58), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.010 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.003 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.378 Fit side-chains REVERT: A 200 MET cc_start: 0.7468 (mmt) cc_final: 0.7232 (mmp) REVERT: A 273 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7391 (m-80) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 0.1479 time to fit residues: 9.4760 Evaluate side-chains 50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 12 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 8 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.193647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.135312 restraints weight = 3535.612| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.09 r_work: 0.3113 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3572 Z= 0.196 Angle : 0.463 5.068 4870 Z= 0.239 Chirality : 0.037 0.129 562 Planarity : 0.004 0.029 601 Dihedral : 4.653 57.882 487 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.43 % Allowed : 9.70 % Favored : 87.87 % 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: 2.96 (0.41), residues: 443 helix: 2.35 (0.30), residues: 306 sheet: None (None), residues: 0 loop : 1.23 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.002 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 273 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7327 (m-80) outliers start: 9 outliers final: 8 residues processed: 50 average time/residue: 0.1486 time to fit residues: 9.5212 Evaluate side-chains 50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 0.1980 chunk 24 optimal weight: 0.1980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.195544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137263 restraints weight = 3614.519| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.11 r_work: 0.3146 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3572 Z= 0.142 Angle : 0.425 5.080 4870 Z= 0.220 Chirality : 0.035 0.130 562 Planarity : 0.004 0.029 601 Dihedral : 4.547 58.220 487 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.16 % Allowed : 10.51 % Favored : 87.33 % 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: 3.12 (0.41), residues: 443 helix: 2.48 (0.30), residues: 306 sheet: None (None), residues: 0 loop : 1.27 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.008 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.001 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 273 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7241 (m-80) outliers start: 8 outliers final: 6 residues processed: 53 average time/residue: 0.1458 time to fit residues: 9.9347 Evaluate side-chains 54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 0.0270 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.194420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136183 restraints weight = 3512.459| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.11 r_work: 0.3113 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3572 Z= 0.173 Angle : 0.466 9.775 4870 Z= 0.234 Chirality : 0.036 0.128 562 Planarity : 0.004 0.028 601 Dihedral : 4.581 59.323 487 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.16 % Allowed : 11.32 % Favored : 86.52 % 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: 3.05 (0.41), residues: 443 helix: 2.45 (0.30), residues: 305 sheet: None (None), residues: 0 loop : 1.17 (0.57), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.001 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 273 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7276 (m-80) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 0.1494 time to fit residues: 9.7830 Evaluate side-chains 51 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.193078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.134701 restraints weight = 3522.152| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.13 r_work: 0.3127 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3572 Z= 0.204 Angle : 0.479 9.257 4870 Z= 0.243 Chirality : 0.037 0.128 562 Planarity : 0.004 0.028 601 Dihedral : 4.617 59.037 487 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.96 % Allowed : 10.51 % Favored : 86.52 % 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: 2.95 (0.41), residues: 443 helix: 2.38 (0.30), residues: 305 sheet: None (None), residues: 0 loop : 1.13 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.010 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.001 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 273 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7304 (m-80) outliers start: 11 outliers final: 7 residues processed: 52 average time/residue: 0.1438 time to fit residues: 9.5693 Evaluate side-chains 50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 11 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.194712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.136615 restraints weight = 3495.645| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.12 r_work: 0.3126 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3572 Z= 0.150 Angle : 0.449 9.291 4870 Z= 0.227 Chirality : 0.035 0.128 562 Planarity : 0.004 0.028 601 Dihedral : 4.531 58.822 487 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.16 % Allowed : 11.32 % Favored : 86.52 % 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: 3.10 (0.41), residues: 443 helix: 2.49 (0.30), residues: 305 sheet: None (None), residues: 0 loop : 1.19 (0.57), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.008 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.001 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 273 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7201 (m-80) REVERT: A 408 MET cc_start: 0.6506 (OUTLIER) cc_final: 0.6205 (mtt) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 0.1411 time to fit residues: 9.1981 Evaluate side-chains 52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 0.0030 chunk 24 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.196357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.138277 restraints weight = 3524.728| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.11 r_work: 0.3142 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3572 Z= 0.132 Angle : 0.444 9.089 4870 Z= 0.222 Chirality : 0.035 0.127 562 Planarity : 0.004 0.028 601 Dihedral : 4.466 58.538 487 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.16 % Allowed : 11.59 % Favored : 86.25 % 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: 3.10 (0.41), residues: 443 helix: 2.42 (0.30), residues: 311 sheet: None (None), residues: 0 loop : 1.32 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.008 0.001 PHE A 355 TYR 0.010 0.001 TYR A 168 ARG 0.001 0.000 ARG A 344 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.365 Fit side-chains REVERT: A 73 THR cc_start: 0.7859 (m) cc_final: 0.7580 (m) REVERT: A 273 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: A 408 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6178 (mtt) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 0.1386 time to fit residues: 9.0453 Evaluate side-chains 52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 6 optimal weight: 0.0010 chunk 14 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 = 0.187228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133550 restraints weight = 3567.546| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.14 r_work: 0.3133 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3572 Z= 0.152 Angle : 0.464 9.031 4870 Z= 0.234 Chirality : 0.036 0.137 562 Planarity : 0.004 0.028 601 Dihedral : 4.480 57.788 487 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.16 % Allowed : 12.40 % Favored : 85.44 % 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: 3.01 (0.41), residues: 443 helix: 2.38 (0.30), residues: 311 sheet: None (None), residues: 0 loop : 1.22 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.011 0.000 ARG A 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2568.23 seconds wall clock time: 44 minutes 27.62 seconds (2667.62 seconds total)