Starting phenix.real_space_refine on Thu Mar 6 02:24:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yim_33861/03_2025/7yim_33861.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yim_33861/03_2025/7yim_33861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yim_33861/03_2025/7yim_33861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yim_33861/03_2025/7yim_33861.map" model { file = "/net/cci-nas-00/data/ceres_data/7yim_33861/03_2025/7yim_33861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yim_33861/03_2025/7yim_33861.cif" } resolution = 2.6 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= -0.006 sd= 0.095 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 40 5.16 5 C 2925 2.51 5 N 791 2.21 5 O 901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4657 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4657 Classifications: {'peptide': 592} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 570} Time building chain proxies: 4.06, per 1000 atoms: 0.87 Number of scatterers: 4657 At special positions: 0 Unit cell: (69.5594, 91.3616, 103.82, 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 40 16.00 O 901 8.00 N 791 7.00 C 2925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 114 " distance=2.02 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 124 " distance=2.02 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 270 " distance=2.01 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.00 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 313 " distance=2.04 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 393 " distance=2.02 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 462 " distance=2.01 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 472 " distance=2.01 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 501 " distance=2.01 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 511 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " 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: 1.01 Conformation dependent library (CDL) restraints added in 676.7 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 75.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 removed outlier: 4.209A pdb=" N ASP A 33 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.750A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 75 removed outlier: 3.573A pdb=" N GLU A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 101 through 108 removed outlier: 3.546A pdb=" N LEU A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.613A pdb=" N SER A 115 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 116 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.629A pdb=" N ASP A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 168 Processing helix chain 'A' and resid 174 through 193 Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 197 through 231 removed outlier: 3.915A pdb=" N THR A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 247 Processing helix chain 'A' and resid 251 through 271 Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 301 through 305 removed outlier: 4.018A pdb=" N LEU A 305 " --> pdb=" O CYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 343 through 361 Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.746A pdb=" N PHE A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 removed outlier: 4.181A pdb=" N CYS A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 439 removed outlier: 7.982A pdb=" N GLU A 424 " --> pdb=" O GLN A 420 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N TYR A 425 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 462 Processing helix chain 'A' and resid 467 through 491 removed outlier: 4.204A pdb=" N ALA A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 removed outlier: 3.527A pdb=" N GLY A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 514 Processing helix chain 'A' and resid 527 through 531 removed outlier: 3.999A pdb=" N LYS A 530 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 560 Processing helix chain 'A' and resid 565 through 582 Processing helix chain 'A' and resid 587 through 608 removed outlier: 3.913A pdb=" N CYS A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 924 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: 1.37 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1072 1.33 - 1.46: 1193 1.46 - 1.58: 2428 1.58 - 1.71: 0 1.71 - 1.84: 48 Bond restraints: 4741 Sorted by residual: bond pdb=" CB VAL A 355 " pdb=" CG2 VAL A 355 " ideal model delta sigma weight residual 1.521 1.408 0.113 3.30e-02 9.18e+02 1.17e+01 bond pdb=" C TYR A 174 " pdb=" N ALA A 175 " ideal model delta sigma weight residual 1.332 1.297 0.035 1.09e-02 8.42e+03 1.04e+01 bond pdb=" CG GLN A 245 " pdb=" CD GLN A 245 " ideal model delta sigma weight residual 1.516 1.439 0.077 2.50e-02 1.60e+03 9.56e+00 bond pdb=" CB GLN A 245 " pdb=" CG GLN A 245 " ideal model delta sigma weight residual 1.520 1.427 0.093 3.00e-02 1.11e+03 9.55e+00 bond pdb=" CG1 ILE A 314 " pdb=" CD1 ILE A 314 " ideal model delta sigma weight residual 1.513 1.400 0.113 3.90e-02 6.57e+02 8.40e+00 ... (remaining 4736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 6228 2.87 - 5.74: 147 5.74 - 8.61: 23 8.61 - 11.48: 1 11.48 - 14.36: 1 Bond angle restraints: 6400 Sorted by residual: angle pdb=" CA CYS A 591 " pdb=" CB CYS A 591 " pdb=" SG CYS A 591 " ideal model delta sigma weight residual 114.40 128.76 -14.36 2.30e+00 1.89e-01 3.90e+01 angle pdb=" C CYS A 591 " pdb=" CA CYS A 591 " pdb=" CB CYS A 591 " ideal model delta sigma weight residual 110.88 103.82 7.06 1.57e+00 4.06e-01 2.02e+01 angle pdb=" CA GLU A 81 " pdb=" CB GLU A 81 " pdb=" CG GLU A 81 " ideal model delta sigma weight residual 114.10 122.78 -8.68 2.00e+00 2.50e-01 1.88e+01 angle pdb=" C GLU A 398 " pdb=" N GLU A 399 " pdb=" CA GLU A 399 " ideal model delta sigma weight residual 122.60 116.29 6.31 1.56e+00 4.11e-01 1.64e+01 angle pdb=" C LYS A 581 " pdb=" N CYS A 582 " pdb=" CA CYS A 582 " ideal model delta sigma weight residual 122.54 115.64 6.90 1.82e+00 3.02e-01 1.44e+01 ... (remaining 6395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 2536 17.11 - 34.21: 342 34.21 - 51.31: 60 51.31 - 68.42: 19 68.42 - 85.52: 5 Dihedral angle restraints: 2962 sinusoidal: 1222 harmonic: 1740 Sorted by residual: dihedral pdb=" CB CYS A 582 " pdb=" SG CYS A 582 " pdb=" SG CYS A 591 " pdb=" CB CYS A 591 " ideal model delta sinusoidal sigma weight residual 93.00 173.66 -80.66 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CA LYS A 76 " pdb=" C LYS A 76 " pdb=" N PRO A 77 " pdb=" CA PRO A 77 " ideal model delta harmonic sigma weight residual -180.00 -144.61 -35.39 0 5.00e+00 4.00e-02 5.01e+01 dihedral pdb=" CA SER A 117 " pdb=" C SER A 117 " pdb=" N GLU A 118 " pdb=" CA GLU A 118 " ideal model delta harmonic sigma weight residual -180.00 -146.39 -33.61 0 5.00e+00 4.00e-02 4.52e+01 ... (remaining 2959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 519 0.070 - 0.139: 176 0.139 - 0.209: 19 0.209 - 0.278: 4 0.278 - 0.348: 1 Chirality restraints: 719 Sorted by residual: chirality pdb=" CB ILE A 481 " pdb=" CA ILE A 481 " pdb=" CG1 ILE A 481 " pdb=" CG2 ILE A 481 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB VAL A 355 " pdb=" CA VAL A 355 " pdb=" CG1 VAL A 355 " pdb=" CG2 VAL A 355 " 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 PRO A 510 " pdb=" N PRO A 510 " pdb=" C PRO A 510 " pdb=" CB PRO A 510 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 716 not shown) Planarity restraints: 837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 509 " 0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO A 510 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 592 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C PHE A 592 " 0.047 2.00e-02 2.50e+03 pdb=" O PHE A 592 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 593 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 175 " 0.045 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO A 176 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.038 5.00e-02 4.00e+02 ... (remaining 834 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1194 2.80 - 3.32: 4406 3.32 - 3.85: 7985 3.85 - 4.37: 9276 4.37 - 4.90: 15248 Nonbonded interactions: 38109 Sorted by model distance: nonbonded pdb=" OE1 GLU A 165 " pdb=" NH1 ARG A 169 " model vdw 2.272 3.120 nonbonded pdb=" O ARG A 509 " pdb=" OG SER A 513 " model vdw 2.276 3.040 nonbonded pdb=" OE1 GLU A 62 " pdb=" OH TYR A 108 " model vdw 2.284 3.040 nonbonded pdb=" OG SER A 42 " pdb=" OD2 ASP A 45 " model vdw 2.294 3.040 nonbonded pdb=" O ALA A 44 " pdb=" OG1 THR A 48 " model vdw 2.311 3.040 ... (remaining 38104 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: 15.850 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: 0.730 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.330 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:153.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 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 : 0.013 0.113 4741 Z= 0.829 Angle : 1.136 14.355 6400 Z= 0.635 Chirality : 0.068 0.348 719 Planarity : 0.009 0.089 837 Dihedral : 15.893 85.522 1782 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.78 % Allowed : 6.59 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.25), residues: 590 helix: -2.57 (0.18), residues: 420 sheet: None (None), residues: 0 loop : -2.74 (0.38), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.007 TRP A 181 HIS 0.012 0.003 HIS A 483 PHE 0.031 0.005 PHE A 235 TYR 0.043 0.005 TYR A 185 ARG 0.008 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 519 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6959 (tm-30) outliers start: 4 outliers final: 0 residues processed: 68 average time/residue: 2.4760 time to fit residues: 174.5594 Evaluate side-chains 37 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 220 ASN A 389 ASN A 420 GLN A 534 HIS A 555 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.205396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.161412 restraints weight = 5299.178| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 2.39 r_work: 0.4249 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.4114 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4741 Z= 0.211 Angle : 0.577 7.137 6400 Z= 0.312 Chirality : 0.040 0.158 719 Planarity : 0.005 0.051 837 Dihedral : 5.350 30.476 631 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.97 % Allowed : 13.37 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.62 (0.31), residues: 590 helix: -0.48 (0.23), residues: 429 sheet: None (None), residues: 0 loop : -2.47 (0.41), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 181 HIS 0.008 0.001 HIS A 534 PHE 0.016 0.002 PHE A 235 TYR 0.018 0.001 TYR A 185 ARG 0.001 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7034 (tp) cc_final: 0.6821 (tp) REVERT: A 228 LYS cc_start: 0.7759 (tttt) cc_final: 0.7112 (mppt) REVERT: A 548 MET cc_start: 0.6323 (mtp) cc_final: 0.6022 (tpt) outliers start: 5 outliers final: 1 residues processed: 62 average time/residue: 1.7130 time to fit residues: 110.2061 Evaluate side-chains 46 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.202495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.156459 restraints weight = 5401.122| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 2.42 r_work: 0.4184 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4741 Z= 0.270 Angle : 0.609 8.262 6400 Z= 0.322 Chirality : 0.043 0.150 719 Planarity : 0.005 0.045 837 Dihedral : 5.020 27.460 631 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.33 % Allowed : 15.12 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.32), residues: 590 helix: 0.17 (0.23), residues: 422 sheet: None (None), residues: 0 loop : -2.06 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 181 HIS 0.007 0.001 HIS A 483 PHE 0.025 0.002 PHE A 50 TYR 0.018 0.002 TYR A 164 ARG 0.008 0.001 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7130 (tp) cc_final: 0.6868 (tp) REVERT: A 228 LYS cc_start: 0.7891 (tttt) cc_final: 0.7205 (mppt) outliers start: 12 outliers final: 4 residues processed: 53 average time/residue: 0.9854 time to fit residues: 55.0162 Evaluate side-chains 42 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 0.0570 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 0.0030 chunk 5 optimal weight: 2.9990 overall best weight: 0.5508 ------------------------------------------------------------------------------- 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 = 0.4815 r_free = 0.4815 target = 0.207242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.162133 restraints weight = 5350.066| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 2.38 r_work: 0.4256 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4741 Z= 0.184 Angle : 0.539 7.727 6400 Z= 0.287 Chirality : 0.039 0.129 719 Planarity : 0.004 0.034 837 Dihedral : 4.573 23.632 631 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.91 % Allowed : 16.28 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.33), residues: 590 helix: 0.78 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -2.07 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.005 0.001 HIS A 483 PHE 0.032 0.002 PHE A 50 TYR 0.010 0.001 TYR A 185 ARG 0.004 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7071 (tp) cc_final: 0.6834 (tp) REVERT: A 97 GLU cc_start: 0.6197 (tp30) cc_final: 0.5748 (tp30) REVERT: A 228 LYS cc_start: 0.7731 (tttt) cc_final: 0.7163 (mppt) REVERT: A 448 MET cc_start: 0.6771 (mtp) cc_final: 0.6338 (mtt) outliers start: 15 outliers final: 5 residues processed: 55 average time/residue: 0.9900 time to fit residues: 57.3456 Evaluate side-chains 41 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 58 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.203518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.158076 restraints weight = 5401.509| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 2.42 r_work: 0.4182 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4741 Z= 0.253 Angle : 0.577 7.637 6400 Z= 0.308 Chirality : 0.042 0.138 719 Planarity : 0.004 0.039 837 Dihedral : 4.627 22.578 631 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.71 % Allowed : 16.47 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.33), residues: 590 helix: 0.80 (0.24), residues: 425 sheet: None (None), residues: 0 loop : -1.84 (0.46), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 181 HIS 0.007 0.001 HIS A 483 PHE 0.044 0.002 PHE A 50 TYR 0.013 0.002 TYR A 164 ARG 0.004 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7148 (tp) cc_final: 0.6892 (tp) REVERT: A 228 LYS cc_start: 0.7860 (tttt) cc_final: 0.7193 (mppt) REVERT: A 403 LYS cc_start: 0.6684 (pttt) cc_final: 0.6031 (tptp) REVERT: A 448 MET cc_start: 0.6891 (mtp) cc_final: 0.6360 (mtt) outliers start: 14 outliers final: 4 residues processed: 54 average time/residue: 1.0454 time to fit residues: 59.2896 Evaluate side-chains 42 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 13 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4792 r_free = 0.4792 target = 0.204971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.159977 restraints weight = 5348.984| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 2.42 r_work: 0.4219 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4741 Z= 0.202 Angle : 0.554 8.559 6400 Z= 0.295 Chirality : 0.040 0.129 719 Planarity : 0.004 0.036 837 Dihedral : 4.424 20.913 631 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.16 % Allowed : 19.38 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.34), residues: 590 helix: 1.07 (0.24), residues: 425 sheet: None (None), residues: 0 loop : -1.73 (0.46), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.006 0.001 HIS A 483 PHE 0.034 0.002 PHE A 50 TYR 0.009 0.001 TYR A 185 ARG 0.003 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7108 (tp) cc_final: 0.6841 (tp) REVERT: A 228 LYS cc_start: 0.7806 (tttt) cc_final: 0.7126 (mppt) REVERT: A 403 LYS cc_start: 0.6594 (pttt) cc_final: 0.5936 (tptp) REVERT: A 448 MET cc_start: 0.6944 (mtp) cc_final: 0.6553 (mtt) outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 1.0812 time to fit residues: 54.5848 Evaluate side-chains 43 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.201813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.155750 restraints weight = 5386.055| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 2.44 r_work: 0.4208 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4741 Z= 0.232 Angle : 0.571 9.350 6400 Z= 0.304 Chirality : 0.041 0.128 719 Planarity : 0.004 0.038 837 Dihedral : 4.464 21.190 631 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.13 % Allowed : 20.16 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.34), residues: 590 helix: 1.03 (0.24), residues: 423 sheet: None (None), residues: 0 loop : -1.76 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.009 0.001 HIS A 534 PHE 0.032 0.002 PHE A 50 TYR 0.017 0.002 TYR A 164 ARG 0.003 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7109 (tp) cc_final: 0.6843 (tp) REVERT: A 124 CYS cc_start: 0.6375 (t) cc_final: 0.5924 (t) REVERT: A 228 LYS cc_start: 0.7758 (tttt) cc_final: 0.7100 (mppt) REVERT: A 291 GLN cc_start: 0.5769 (OUTLIER) cc_final: 0.5492 (mt0) REVERT: A 403 LYS cc_start: 0.6510 (pttt) cc_final: 0.6038 (tptp) REVERT: A 534 HIS cc_start: 0.7558 (OUTLIER) cc_final: 0.7244 (p-80) outliers start: 11 outliers final: 6 residues processed: 49 average time/residue: 0.9247 time to fit residues: 47.9960 Evaluate side-chains 42 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.4785 r_free = 0.4785 target = 0.204337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.159206 restraints weight = 5390.508| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 2.41 r_work: 0.4215 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4741 Z= 0.214 Angle : 0.562 9.906 6400 Z= 0.299 Chirality : 0.041 0.133 719 Planarity : 0.004 0.037 837 Dihedral : 4.362 20.671 631 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.94 % Allowed : 19.96 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.34), residues: 590 helix: 1.18 (0.24), residues: 424 sheet: None (None), residues: 0 loop : -1.58 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.008 0.001 HIS A 534 PHE 0.029 0.002 PHE A 50 TYR 0.013 0.001 TYR A 151 ARG 0.003 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7087 (tp) cc_final: 0.6814 (tp) REVERT: A 124 CYS cc_start: 0.6355 (t) cc_final: 0.5896 (t) REVERT: A 228 LYS cc_start: 0.7735 (tttt) cc_final: 0.7089 (mppt) REVERT: A 291 GLN cc_start: 0.5741 (OUTLIER) cc_final: 0.5454 (mt0) REVERT: A 403 LYS cc_start: 0.6436 (pttt) cc_final: 0.6064 (tptp) REVERT: A 448 MET cc_start: 0.6881 (mtm) cc_final: 0.6574 (mtp) REVERT: A 490 MET cc_start: 0.6492 (mpt) cc_final: 0.5549 (mpt) REVERT: A 536 ASP cc_start: 0.5815 (p0) cc_final: 0.5426 (p0) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 0.9743 time to fit residues: 48.5828 Evaluate side-chains 44 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 52 optimal weight: 0.0170 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- 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 = 0.4787 r_free = 0.4787 target = 0.204401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.158674 restraints weight = 5380.405| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 2.44 r_work: 0.4216 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4741 Z= 0.203 Angle : 0.555 10.477 6400 Z= 0.296 Chirality : 0.040 0.138 719 Planarity : 0.004 0.037 837 Dihedral : 4.294 23.348 631 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.74 % Allowed : 20.35 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.34), residues: 590 helix: 1.31 (0.24), residues: 424 sheet: None (None), residues: 0 loop : -1.44 (0.49), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.006 0.001 HIS A 483 PHE 0.025 0.002 PHE A 50 TYR 0.018 0.001 TYR A 164 ARG 0.003 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.468 Fit side-chains REVERT: A 43 LEU cc_start: 0.7116 (tp) cc_final: 0.6861 (tp) REVERT: A 124 CYS cc_start: 0.6386 (t) cc_final: 0.5936 (t) REVERT: A 228 LYS cc_start: 0.7739 (tttt) cc_final: 0.7071 (mppt) REVERT: A 291 GLN cc_start: 0.5670 (OUTLIER) cc_final: 0.5368 (mt0) REVERT: A 403 LYS cc_start: 0.6417 (pttt) cc_final: 0.6062 (tptp) REVERT: A 448 MET cc_start: 0.6848 (mtm) cc_final: 0.6569 (mtp) outliers start: 9 outliers final: 7 residues processed: 47 average time/residue: 0.9221 time to fit residues: 46.0672 Evaluate side-chains 44 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 469 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4794 r_free = 0.4794 target = 0.205376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.160200 restraints weight = 5371.807| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 2.41 r_work: 0.4228 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4741 Z= 0.209 Angle : 0.570 10.545 6400 Z= 0.306 Chirality : 0.041 0.154 719 Planarity : 0.004 0.036 837 Dihedral : 4.291 22.290 631 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.55 % Allowed : 21.32 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.34), residues: 590 helix: 1.27 (0.24), residues: 425 sheet: None (None), residues: 0 loop : -1.36 (0.49), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 181 HIS 0.007 0.001 HIS A 534 PHE 0.025 0.002 PHE A 50 TYR 0.015 0.001 TYR A 151 ARG 0.002 0.000 ARG A 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.521 Fit side-chains REVERT: A 43 LEU cc_start: 0.7111 (tp) cc_final: 0.6856 (tp) REVERT: A 124 CYS cc_start: 0.6379 (t) cc_final: 0.5933 (t) REVERT: A 228 LYS cc_start: 0.7727 (tttt) cc_final: 0.7091 (mppt) REVERT: A 291 GLN cc_start: 0.5658 (OUTLIER) cc_final: 0.5364 (mt0) REVERT: A 403 LYS cc_start: 0.6435 (pttt) cc_final: 0.6115 (tptp) REVERT: A 448 MET cc_start: 0.6806 (mtm) cc_final: 0.6540 (mtp) REVERT: A 490 MET cc_start: 0.6479 (mpt) cc_final: 0.5532 (mpt) outliers start: 8 outliers final: 7 residues processed: 45 average time/residue: 0.9484 time to fit residues: 45.2628 Evaluate side-chains 44 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 469 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 0.0000 chunk 53 optimal weight: 0.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 = 0.4821 r_free = 0.4821 target = 0.207746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.162861 restraints weight = 5435.846| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 2.46 r_work: 0.4262 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4741 Z= 0.177 Angle : 0.544 10.589 6400 Z= 0.291 Chirality : 0.039 0.168 719 Planarity : 0.004 0.033 837 Dihedral : 4.116 22.482 631 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.55 % Allowed : 20.93 % Favored : 77.52 % 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: 1.16 (0.35), residues: 590 helix: 1.51 (0.25), residues: 427 sheet: None (None), residues: 0 loop : -1.22 (0.50), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.005 0.001 HIS A 483 PHE 0.032 0.002 PHE A 252 TYR 0.016 0.001 TYR A 164 ARG 0.002 0.000 ARG A 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5100.17 seconds wall clock time: 89 minutes 5.48 seconds (5345.48 seconds total)