Starting phenix.real_space_refine on Wed Mar 5 22:23:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qvx_18677/03_2025/8qvx_18677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qvx_18677/03_2025/8qvx_18677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qvx_18677/03_2025/8qvx_18677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qvx_18677/03_2025/8qvx_18677.map" model { file = "/net/cci-nas-00/data/ceres_data/8qvx_18677/03_2025/8qvx_18677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qvx_18677/03_2025/8qvx_18677.cif" } resolution = 2.7 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= 0.002 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 18 5.16 5 C 2501 2.51 5 N 686 2.21 5 O 743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3948 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 468 Classifications: {'peptide': 58} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 48} Chain: "B" Number of atoms: 3480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3480 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 10, 'TRANS': 427} Chain breaks: 2 Time building chain proxies: 2.86, per 1000 atoms: 0.72 Number of scatterers: 3948 At special positions: 0 Unit cell: (114, 76.38, 69.54, 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 18 16.00 O 743 8.00 N 686 7.00 C 2501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.03 Conformation dependent library (CDL) restraints added in 438.6 milliseconds 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 962 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 81.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.673A pdb=" N LEU A 607 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 25 Processing helix chain 'B' and resid 27 through 41 Processing helix chain 'B' and resid 44 through 59 Processing helix chain 'B' and resid 60 through 76 removed outlier: 5.156A pdb=" N LYS B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'B' and resid 93 through 103 removed outlier: 3.613A pdb=" N LYS B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 122 Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 143 through 162 Processing helix chain 'B' and resid 176 through 190 Processing helix chain 'B' and resid 192 through 212 Processing helix chain 'B' and resid 222 through 240 removed outlier: 3.999A pdb=" N ILE B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 235 " --> pdb=" O GLN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 278 through 290 removed outlier: 3.771A pdb=" N LEU B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 removed outlier: 3.512A pdb=" N LYS B 297 " --> pdb=" O GLY B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 317 removed outlier: 3.519A pdb=" N LEU B 312 " --> pdb=" O PHE B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 334 removed outlier: 3.821A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 removed outlier: 4.172A pdb=" N GLN B 344 " --> pdb=" O PRO B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 368 Processing helix chain 'B' and resid 371 through 383 removed outlier: 3.679A pdb=" N ILE B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 379 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 382 " --> pdb=" O THR B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 398 Processing helix chain 'B' and resid 405 through 419 removed outlier: 3.983A pdb=" N GLU B 419 " --> pdb=" O MET B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 443 through 461 removed outlier: 3.544A pdb=" N TYR B 460 " --> pdb=" O PHE B 456 " (cutoff:3.500A) 270 hydrogen bonds defined for protein. 786 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: 1.00 Time building geometry restraints manager: 1.21 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: 1314 1.34 - 1.46: 573 1.46 - 1.58: 2102 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 4013 Sorted by residual: bond pdb=" CA LYS B 256 " pdb=" CB LYS B 256 " ideal model delta sigma weight residual 1.522 1.532 -0.010 7.00e-03 2.04e+04 1.96e+00 bond pdb=" CB GLU A 559 " pdb=" CG GLU A 559 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.17e+00 bond pdb=" CA ILE B 399 " pdb=" CB ILE B 399 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.17e+00 bond pdb=" CG GLU A 559 " pdb=" CD GLU A 559 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.03e+00 bond pdb=" CA VAL B 11 " pdb=" C VAL B 11 " ideal model delta sigma weight residual 1.520 1.528 -0.008 8.80e-03 1.29e+04 9.10e-01 ... (remaining 4008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 5166 1.39 - 2.78: 206 2.78 - 4.17: 33 4.17 - 5.56: 14 5.56 - 6.95: 4 Bond angle restraints: 5423 Sorted by residual: angle pdb=" C SER B 10 " pdb=" N VAL B 11 " pdb=" CA VAL B 11 " ideal model delta sigma weight residual 120.24 122.91 -2.67 6.30e-01 2.52e+00 1.79e+01 angle pdb=" CA GLU B 162 " pdb=" CB GLU B 162 " pdb=" CG GLU B 162 " ideal model delta sigma weight residual 114.10 120.59 -6.49 2.00e+00 2.50e-01 1.05e+01 angle pdb=" C GLN B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 120.58 124.45 -3.87 1.32e+00 5.74e-01 8.62e+00 angle pdb=" CB GLU A 559 " pdb=" CG GLU A 559 " pdb=" CD GLU A 559 " ideal model delta sigma weight residual 112.60 117.09 -4.49 1.70e+00 3.46e-01 6.98e+00 angle pdb=" C VAL B 11 " pdb=" CA VAL B 11 " pdb=" CB VAL B 11 " ideal model delta sigma weight residual 114.35 111.60 2.75 1.06e+00 8.90e-01 6.74e+00 ... (remaining 5418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.25: 2112 18.25 - 36.50: 285 36.50 - 54.74: 75 54.74 - 72.99: 12 72.99 - 91.24: 2 Dihedral angle restraints: 2486 sinusoidal: 1017 harmonic: 1469 Sorted by residual: dihedral pdb=" CA LYS B 383 " pdb=" C LYS B 383 " pdb=" N ILE B 384 " pdb=" CA ILE B 384 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ASN B 388 " pdb=" CB ASN B 388 " pdb=" CG ASN B 388 " pdb=" OD1 ASN B 388 " ideal model delta sinusoidal sigma weight residual -90.00 -162.88 72.88 2 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CB GLU B 177 " pdb=" CG GLU B 177 " pdb=" CD GLU B 177 " pdb=" OE1 GLU B 177 " ideal model delta sinusoidal sigma weight residual 0.00 -91.24 91.24 1 3.00e+01 1.11e-03 1.09e+01 ... (remaining 2483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 364 0.030 - 0.059: 175 0.059 - 0.089: 66 0.089 - 0.119: 13 0.119 - 0.148: 5 Chirality restraints: 623 Sorted by residual: chirality pdb=" CG LEU B 361 " pdb=" CB LEU B 361 " pdb=" CD1 LEU B 361 " pdb=" CD2 LEU B 361 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CB VAL B 118 " pdb=" CA VAL B 118 " pdb=" CG1 VAL B 118 " pdb=" CG2 VAL B 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA VAL B 164 " pdb=" N VAL B 164 " pdb=" C VAL B 164 " pdb=" CB VAL B 164 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 620 not shown) Planarity restraints: 701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 339 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B 340 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 340 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 340 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 373 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C ALA B 373 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA B 373 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU B 374 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 89 " -0.008 2.00e-02 2.50e+03 1.03e-02 2.13e+00 pdb=" CG TYR B 89 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 89 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 89 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B 89 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 89 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 89 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 89 " -0.000 2.00e-02 2.50e+03 ... (remaining 698 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 331 2.74 - 3.28: 4334 3.28 - 3.82: 6778 3.82 - 4.36: 7837 4.36 - 4.90: 13010 Nonbonded interactions: 32290 Sorted by model distance: nonbonded pdb=" O LEU B 246 " pdb=" ND2 ASN B 250 " model vdw 2.195 3.120 nonbonded pdb=" OG SER B 448 " pdb=" OE2 GLU B 452 " model vdw 2.203 3.040 nonbonded pdb=" O ASN B 78 " pdb=" OG SER B 79 " model vdw 2.239 3.040 nonbonded pdb=" OG SER B 159 " pdb=" O VAL B 164 " model vdw 2.261 3.040 nonbonded pdb=" NE2 GLN B 237 " pdb=" OG1 THR B 272 " model vdw 2.279 3.120 ... (remaining 32285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.340 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.950 Find NCS groups from input model: 0.040 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:14.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 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 : 0.004 0.036 4013 Z= 0.243 Angle : 0.679 6.953 5423 Z= 0.377 Chirality : 0.040 0.148 623 Planarity : 0.004 0.050 701 Dihedral : 17.622 91.238 1524 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.71 % Favored : 95.08 % Rotamer: Outliers : 0.46 % Allowed : 28.83 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.30 (0.39), residues: 488 helix: 1.43 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -0.50 (0.60), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 161 HIS 0.007 0.001 HIS B 404 PHE 0.022 0.002 PHE A 558 TYR 0.025 0.002 TYR B 89 ARG 0.003 0.001 ARG B 451 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: B 98 LEU cc_start: 0.7713 (mm) cc_final: 0.7158 (mm) REVERT: B 232 MET cc_start: 0.5365 (mmt) cc_final: 0.5143 (mpt) REVERT: B 419 GLU cc_start: 0.7620 (pm20) cc_final: 0.7398 (pm20) outliers start: 2 outliers final: 0 residues processed: 51 average time/residue: 0.9496 time to fit residues: 50.6885 Evaluate side-chains 40 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.0050 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN B 71 HIS B 96 ASN B 194 GLN B 274 ASN B 304 GLN B 309 ASN B 353 GLN B 368 HIS B 371 ASN B 388 ASN B 434 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.160040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.134729 restraints weight = 6679.985| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 3.18 r_work: 0.3998 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4013 Z= 0.192 Angle : 0.583 7.093 5423 Z= 0.312 Chirality : 0.039 0.142 623 Planarity : 0.004 0.049 701 Dihedral : 4.103 16.747 524 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.92 % Favored : 94.88 % Rotamer: Outliers : 5.26 % Allowed : 24.03 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.39), residues: 488 helix: 1.50 (0.27), residues: 363 sheet: None (None), residues: 0 loop : -0.48 (0.61), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 161 HIS 0.005 0.001 HIS B 368 PHE 0.011 0.001 PHE B 308 TYR 0.014 0.001 TYR B 89 ARG 0.002 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 47 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: B 134 ASP cc_start: 0.6956 (m-30) cc_final: 0.6616 (m-30) REVERT: B 196 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6353 (tpt) REVERT: B 402 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6102 (tt) REVERT: B 405 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6646 (mtpm) REVERT: B 426 ILE cc_start: 0.7507 (mp) cc_final: 0.7211 (mp) outliers start: 23 outliers final: 5 residues processed: 62 average time/residue: 0.8633 time to fit residues: 56.3423 Evaluate side-chains 44 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 405 LYS Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 421 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.158890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.133904 restraints weight = 6744.237| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 3.19 r_work: 0.3987 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4013 Z= 0.204 Angle : 0.583 7.234 5423 Z= 0.303 Chirality : 0.039 0.139 623 Planarity : 0.004 0.046 701 Dihedral : 4.067 17.808 524 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.92 % Favored : 94.88 % Rotamer: Outliers : 5.03 % Allowed : 24.49 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.40 (0.39), residues: 488 helix: 1.47 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -0.67 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 161 HIS 0.003 0.001 HIS B 404 PHE 0.013 0.001 PHE B 364 TYR 0.009 0.001 TYR B 416 ARG 0.002 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: B 134 ASP cc_start: 0.6766 (m-30) cc_final: 0.6492 (m-30) REVERT: B 196 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.6369 (tpt) REVERT: B 401 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: B 402 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6123 (tt) REVERT: B 405 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6607 (mtpm) REVERT: B 421 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7449 (m-30) REVERT: B 426 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7094 (mp) outliers start: 22 outliers final: 6 residues processed: 58 average time/residue: 0.6637 time to fit residues: 41.0919 Evaluate side-chains 49 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 405 LYS Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.157412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.131979 restraints weight = 6704.460| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 3.21 r_work: 0.3964 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4013 Z= 0.218 Angle : 0.583 7.420 5423 Z= 0.301 Chirality : 0.039 0.143 623 Planarity : 0.004 0.048 701 Dihedral : 4.084 17.537 524 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.71 % Favored : 95.08 % Rotamer: Outliers : 5.72 % Allowed : 25.17 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.44 (0.39), residues: 488 helix: 1.52 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -0.72 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 161 HIS 0.005 0.001 HIS B 337 PHE 0.012 0.001 PHE B 308 TYR 0.010 0.001 TYR B 416 ARG 0.002 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 42 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 576 HIS cc_start: 0.8414 (m90) cc_final: 0.8128 (m-70) REVERT: B 192 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6201 (mt) REVERT: B 196 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.6355 (tpt) REVERT: B 243 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6914 (mm-30) REVERT: B 402 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6199 (tt) REVERT: B 421 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7508 (m-30) REVERT: B 426 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7198 (mp) outliers start: 25 outliers final: 10 residues processed: 59 average time/residue: 0.7227 time to fit residues: 45.1836 Evaluate side-chains 54 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 0.1980 chunk 8 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.161462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.136100 restraints weight = 6747.758| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 3.12 r_work: 0.3985 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4013 Z= 0.202 Angle : 0.583 7.826 5423 Z= 0.300 Chirality : 0.038 0.130 623 Planarity : 0.004 0.044 701 Dihedral : 4.083 17.668 524 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.71 % Favored : 95.08 % Rotamer: Outliers : 7.09 % Allowed : 24.71 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.52 (0.39), residues: 488 helix: 1.58 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.73 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 161 HIS 0.004 0.001 HIS B 404 PHE 0.013 0.001 PHE B 364 TYR 0.009 0.001 TYR B 416 ARG 0.001 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 47 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 576 HIS cc_start: 0.8377 (m90) cc_final: 0.8079 (m-70) REVERT: B 110 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7257 (ptpt) REVERT: B 192 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6357 (mt) REVERT: B 196 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6543 (tpt) REVERT: B 243 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6896 (mm-30) REVERT: B 402 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6239 (tt) REVERT: B 421 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: B 426 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7252 (mp) outliers start: 31 outliers final: 12 residues processed: 69 average time/residue: 0.7193 time to fit residues: 52.5043 Evaluate side-chains 60 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN B 290 ASN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 HIS B 371 ASN B 439 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.158795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.133196 restraints weight = 6636.291| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.13 r_work: 0.3948 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4013 Z= 0.247 Angle : 0.617 7.590 5423 Z= 0.314 Chirality : 0.040 0.170 623 Planarity : 0.004 0.048 701 Dihedral : 4.218 20.280 524 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.92 % Favored : 94.88 % Rotamer: Outliers : 6.41 % Allowed : 26.77 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.39 (0.38), residues: 488 helix: 1.51 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.88 (0.59), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 161 HIS 0.006 0.001 HIS B 404 PHE 0.014 0.001 PHE B 308 TYR 0.010 0.001 TYR B 416 ARG 0.001 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 40 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 564 ASP cc_start: 0.8287 (t0) cc_final: 0.7833 (t0) REVERT: A 576 HIS cc_start: 0.8411 (m90) cc_final: 0.8084 (m-70) REVERT: B 110 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7248 (mttp) REVERT: B 196 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6513 (tpt) REVERT: B 243 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7122 (mm-30) REVERT: B 402 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6185 (tt) REVERT: B 421 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: B 426 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7251 (mp) outliers start: 28 outliers final: 12 residues processed: 57 average time/residue: 0.6742 time to fit residues: 40.9835 Evaluate side-chains 55 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN B 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.160591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.135260 restraints weight = 6639.124| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 3.10 r_work: 0.3973 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4013 Z= 0.212 Angle : 0.605 8.273 5423 Z= 0.308 Chirality : 0.038 0.137 623 Planarity : 0.004 0.043 701 Dihedral : 4.113 19.193 524 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.51 % Favored : 95.29 % Rotamer: Outliers : 5.03 % Allowed : 28.38 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.49 (0.39), residues: 488 helix: 1.59 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.85 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 161 HIS 0.004 0.001 HIS B 404 PHE 0.010 0.001 PHE B 308 TYR 0.007 0.001 TYR B 86 ARG 0.001 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 41 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 564 ASP cc_start: 0.8270 (t0) cc_final: 0.7778 (t0) REVERT: A 576 HIS cc_start: 0.8393 (m90) cc_final: 0.8076 (m-70) REVERT: B 196 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6699 (tpt) REVERT: B 222 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6248 (tp-100) REVERT: B 243 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7049 (mm-30) REVERT: B 402 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6245 (tt) REVERT: B 421 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: B 426 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7313 (mp) outliers start: 22 outliers final: 10 residues processed: 55 average time/residue: 0.6856 time to fit residues: 40.1756 Evaluate side-chains 53 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 7 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 36 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN B 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.159630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.134058 restraints weight = 6611.747| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 3.12 r_work: 0.3958 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4013 Z= 0.227 Angle : 0.617 8.268 5423 Z= 0.315 Chirality : 0.039 0.134 623 Planarity : 0.004 0.045 701 Dihedral : 4.120 18.210 524 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 6.18 % Allowed : 27.46 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.45 (0.39), residues: 488 helix: 1.56 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.89 (0.59), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 161 HIS 0.005 0.001 HIS B 404 PHE 0.012 0.001 PHE B 308 TYR 0.008 0.001 TYR B 86 ARG 0.001 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 36 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 564 ASP cc_start: 0.8269 (t0) cc_final: 0.7770 (t0) REVERT: A 576 HIS cc_start: 0.8412 (m90) cc_final: 0.8089 (m-70) REVERT: B 196 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6251 (tpt) REVERT: B 222 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.6304 (tp-100) REVERT: B 243 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7019 (mm-30) REVERT: B 402 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6119 (tt) REVERT: B 421 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7553 (m-30) REVERT: B 426 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7294 (mp) outliers start: 27 outliers final: 12 residues processed: 55 average time/residue: 0.7673 time to fit residues: 44.5610 Evaluate side-chains 52 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN B 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.159643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.134463 restraints weight = 6608.970| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.05 r_work: 0.3967 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4013 Z= 0.222 Angle : 0.620 8.437 5423 Z= 0.318 Chirality : 0.039 0.135 623 Planarity : 0.004 0.043 701 Dihedral : 4.114 17.899 524 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.49 % Allowed : 28.38 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.52 (0.39), residues: 488 helix: 1.63 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.90 (0.59), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 161 HIS 0.005 0.001 HIS B 404 PHE 0.011 0.001 PHE B 308 TYR 0.008 0.001 TYR B 86 ARG 0.001 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 37 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 564 ASP cc_start: 0.8351 (t0) cc_final: 0.7844 (t0) REVERT: A 576 HIS cc_start: 0.8396 (m90) cc_final: 0.8085 (m-70) REVERT: B 196 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6344 (tpt) REVERT: B 222 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.6310 (tp-100) REVERT: B 243 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7058 (mm-30) REVERT: B 402 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6262 (tt) REVERT: B 421 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7569 (m-30) REVERT: B 426 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7327 (mp) outliers start: 24 outliers final: 14 residues processed: 52 average time/residue: 0.7335 time to fit residues: 40.5358 Evaluate side-chains 53 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 33 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.0270 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN B 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.160131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.134897 restraints weight = 6681.229| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 3.09 r_work: 0.3974 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4013 Z= 0.207 Angle : 0.611 8.764 5423 Z= 0.313 Chirality : 0.038 0.136 623 Planarity : 0.004 0.044 701 Dihedral : 4.087 17.820 524 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.03 % Allowed : 28.60 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.60 (0.39), residues: 488 helix: 1.69 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.88 (0.59), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 161 HIS 0.004 0.001 HIS B 404 PHE 0.014 0.001 PHE B 364 TYR 0.007 0.001 TYR B 86 ARG 0.001 0.000 ARG B 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 38 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 564 ASP cc_start: 0.8366 (t0) cc_final: 0.7899 (t0) REVERT: A 576 HIS cc_start: 0.8386 (m90) cc_final: 0.8080 (m-70) REVERT: B 196 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6487 (tpt) REVERT: B 222 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6323 (tp-100) REVERT: B 243 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7054 (mm-30) REVERT: B 402 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6258 (tt) REVERT: B 421 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: B 426 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7330 (mp) outliers start: 22 outliers final: 12 residues processed: 52 average time/residue: 0.7056 time to fit residues: 39.1348 Evaluate side-chains 53 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 35 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 0.0050 chunk 36 optimal weight: 0.2980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN B 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.159912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.134540 restraints weight = 6623.710| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 3.13 r_work: 0.3968 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4013 Z= 0.214 Angle : 0.607 8.712 5423 Z= 0.314 Chirality : 0.038 0.135 623 Planarity : 0.004 0.043 701 Dihedral : 4.076 17.835 524 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.58 % Allowed : 29.29 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.62 (0.39), residues: 488 helix: 1.71 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.89 (0.59), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 161 HIS 0.004 0.001 HIS B 404 PHE 0.010 0.001 PHE B 308 TYR 0.008 0.001 TYR B 86 ARG 0.001 0.000 ARG B 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3326.85 seconds wall clock time: 57 minutes 44.60 seconds (3464.60 seconds total)