Starting phenix.real_space_refine on Fri Dec 27 09:25:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qvx_18677/12_2024/8qvx_18677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qvx_18677/12_2024/8qvx_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_18677/12_2024/8qvx_18677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qvx_18677/12_2024/8qvx_18677.map" model { file = "/net/cci-nas-00/data/ceres_data/8qvx_18677/12_2024/8qvx_18677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qvx_18677/12_2024/8qvx_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-5532/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: 0.92 Conformation dependent library (CDL) restraints added in 487.5 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: 0.36 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: 1.05 Time building geometry restraints manager: 1.10 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: 0.260 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: 13.810 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:14.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.720 ------------------------------------------------------------------------------- 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 : 0.421 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: 1.0262 time to fit residues: 54.7013 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 : 0.463 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 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 : 0.405 Fit side-chains revert: symmetry clash REVERT: B 196 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6617 (tpt) REVERT: B 402 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6888 (tt) REVERT: B 426 ILE cc_start: 0.7921 (mp) cc_final: 0.7559 (mp) outliers start: 23 outliers final: 5 residues processed: 62 average time/residue: 0.8422 time to fit residues: 54.9495 Evaluate side-chains 43 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 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 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 14 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.1733 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= 0.191 Angle : 0.579 7.260 5423 Z= 0.300 Chirality : 0.038 0.138 623 Planarity : 0.004 0.046 701 Dihedral : 4.052 17.868 524 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.30 % Favored : 95.49 % Rotamer: Outliers : 4.35 % Allowed : 25.17 % 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: 1.43 (0.39), residues: 488 helix: 1.51 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.70 (0.60), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 161 HIS 0.003 0.001 HIS B 418 PHE 0.013 0.001 PHE B 364 TYR 0.009 0.001 TYR B 143 ARG 0.004 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: 19 poor density : 47 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: B 196 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6591 (tpt) REVERT: B 402 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6873 (tt) REVERT: B 421 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7448 (m-30) REVERT: B 426 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7428 (mp) outliers start: 19 outliers final: 5 residues processed: 58 average time/residue: 0.7789 time to fit residues: 47.8090 Evaluate side-chains 46 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 402 LEU 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 22 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2054 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= 0.197 Angle : 0.564 7.306 5423 Z= 0.291 Chirality : 0.038 0.141 623 Planarity : 0.004 0.047 701 Dihedral : 4.065 20.540 524 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.92 % Favored : 94.88 % Rotamer: Outliers : 4.12 % Allowed : 27.00 % Favored : 68.88 % 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: 1.60 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -0.76 (0.60), 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 0.011 0.001 PHE B 308 TYR 0.010 0.001 TYR B 416 ARG 0.003 0.000 ARG B 93 *********************** 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 60 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: B 192 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6510 (mt) REVERT: B 196 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6721 (tpt) REVERT: B 377 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7978 (mm) REVERT: B 402 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6911 (tt) REVERT: B 421 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7476 (m-30) REVERT: B 426 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7605 (mp) outliers start: 18 outliers final: 7 residues processed: 54 average time/residue: 0.6259 time to fit residues: 36.2075 Evaluate side-chains 49 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 260 VAL Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 377 LEU 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 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** B 354 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2295 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= 0.202 Angle : 0.566 7.174 5423 Z= 0.293 Chirality : 0.038 0.142 623 Planarity : 0.004 0.044 701 Dihedral : 4.032 19.214 524 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.92 % Favored : 94.88 % Rotamer: Outliers : 5.95 % Allowed : 26.32 % Favored : 67.73 % 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: 1.56 (0.39), residues: 488 helix: 1.62 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.75 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 161 HIS 0.004 0.001 HIS B 404 PHE 0.012 0.001 PHE B 308 TYR 0.010 0.001 TYR B 416 ARG 0.001 0.000 ARG A 557 *********************** 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 68 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 42 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: B 192 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6618 (mt) REVERT: B 196 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6696 (tpt) REVERT: B 243 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7166 (mm-30) REVERT: B 402 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7060 (tt) REVERT: B 421 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: B 426 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7580 (mp) outliers start: 26 outliers final: 8 residues processed: 60 average time/residue: 0.6412 time to fit residues: 40.9320 Evaluate side-chains 54 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 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 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 192 LEU Chi-restraints excluded: chain B residue 196 MET 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 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 11 optimal weight: 4.9990 chunk 46 optimal weight: 0.0470 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.2562 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 6.276 5423 Z= 0.298 Chirality : 0.038 0.142 623 Planarity : 0.004 0.046 701 Dihedral : 4.021 18.343 524 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.92 % Favored : 94.88 % Rotamer: Outliers : 5.49 % Allowed : 26.77 % Favored : 67.73 % 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: 1.68 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.80 (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 0.011 0.001 PHE B 308 TYR 0.009 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 65 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 41 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 564 ASP cc_start: 0.8381 (t0) cc_final: 0.8041 (t0) REVERT: B 192 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6599 (mt) REVERT: B 196 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6747 (tpt) REVERT: B 243 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7308 (mm-30) REVERT: B 402 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7047 (tt) REVERT: B 421 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: B 426 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7575 (mp) outliers start: 24 outliers final: 12 residues processed: 56 average time/residue: 0.6881 time to fit residues: 41.0170 Evaluate side-chains 59 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 0.2980 chunk 46 optimal weight: 0.3980 chunk 28 optimal weight: 0.0060 chunk 21 optimal weight: 0.3980 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2673 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= 0.172 Angle : 0.575 6.152 5423 Z= 0.295 Chirality : 0.038 0.143 623 Planarity : 0.004 0.040 701 Dihedral : 3.946 17.409 524 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.49 % Allowed : 27.00 % Favored : 67.51 % 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: 1.70 (0.39), residues: 488 helix: 1.70 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -0.68 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 435 HIS 0.004 0.001 HIS A 576 PHE 0.009 0.001 PHE B 308 TYR 0.006 0.001 TYR B 416 ARG 0.001 0.000 ARG A 557 *********************** 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 73 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 49 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 ASP cc_start: 0.8385 (t0) cc_final: 0.7982 (t0) REVERT: B 196 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6680 (tpt) REVERT: B 222 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6243 (tp-100) REVERT: B 243 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: B 402 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7052 (tt) REVERT: B 421 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: B 426 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7625 (mp) outliers start: 24 outliers final: 8 residues processed: 64 average time/residue: 0.7108 time to fit residues: 48.2639 Evaluate side-chains 55 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 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 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 29 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.0000 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2829 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= 0.204 Angle : 0.609 8.583 5423 Z= 0.309 Chirality : 0.039 0.139 623 Planarity : 0.004 0.043 701 Dihedral : 3.976 18.854 524 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % 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: 1.62 (0.38), residues: 488 helix: 1.64 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -0.71 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 161 HIS 0.004 0.001 HIS A 576 PHE 0.015 0.001 PHE B 364 TYR 0.008 0.001 TYR B 416 ARG 0.004 0.000 ARG A 557 *********************** 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: 22 poor density : 41 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 564 ASP cc_start: 0.8389 (t0) cc_final: 0.7893 (t0) REVERT: B 196 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6700 (tpt) REVERT: B 222 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6281 (tp-100) REVERT: B 243 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7319 (mm-30) REVERT: B 337 HIS cc_start: 0.3778 (OUTLIER) cc_final: 0.3555 (m90) REVERT: B 402 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7013 (tt) REVERT: B 421 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: B 426 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7666 (mp) outliers start: 22 outliers final: 10 residues processed: 55 average time/residue: 0.8467 time to fit residues: 49.0635 Evaluate side-chains 51 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 323 CYS Chi-restraints excluded: chain B residue 337 HIS 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 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 0.0980 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.0670 chunk 31 optimal weight: 0.1980 chunk 47 optimal weight: 5.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2999 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= 0.175 Angle : 0.598 8.354 5423 Z= 0.307 Chirality : 0.038 0.149 623 Planarity : 0.004 0.040 701 Dihedral : 3.928 17.449 524 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.35 % Allowed : 29.52 % 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: 1.68 (0.39), residues: 488 helix: 1.64 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -0.50 (0.62), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 161 HIS 0.005 0.001 HIS A 576 PHE 0.008 0.001 PHE B 308 TYR 0.007 0.001 TYR B 416 ARG 0.002 0.000 ARG B 451 *********************** 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 63 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 ASP cc_start: 0.8200 (t0) cc_final: 0.7880 (t0) REVERT: B 196 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6659 (tpt) REVERT: B 222 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6466 (tp-100) REVERT: B 243 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7417 (mm-30) REVERT: B 401 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7175 (pp20) REVERT: B 402 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6944 (tt) REVERT: B 421 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7405 (m-30) REVERT: B 426 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7649 (mp) outliers start: 19 outliers final: 8 residues processed: 56 average time/residue: 0.6506 time to fit residues: 38.9990 Evaluate side-chains 54 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 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 323 CYS 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 44 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.3101 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= 0.206 Angle : 0.629 8.983 5423 Z= 0.321 Chirality : 0.039 0.141 623 Planarity : 0.004 0.042 701 Dihedral : 3.919 17.783 524 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.92 % Favored : 94.88 % Rotamer: Outliers : 4.12 % Allowed : 30.66 % Favored : 65.22 % 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: 1.64 (0.39), residues: 488 helix: 1.62 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -0.56 (0.61), residues: 116 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 0.011 0.001 PHE B 308 TYR 0.008 0.001 TYR B 86 ARG 0.002 0.000 ARG B 451 ********************** 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 59 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 564 ASP cc_start: 0.8193 (t0) cc_final: 0.7939 (t0) REVERT: B 196 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6506 (tpt) REVERT: B 222 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6299 (tp-100) REVERT: B 243 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7418 (mm-30) REVERT: B 402 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6939 (tt) REVERT: B 421 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7595 (m-30) REVERT: B 426 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7676 (mp) outliers start: 18 outliers final: 11 residues processed: 52 average time/residue: 0.7337 time to fit residues: 40.5096 Evaluate side-chains 57 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 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 38 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.160755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.135416 restraints weight = 6625.163| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 3.14 r_work: 0.3979 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4013 Z= 0.226 Angle : 0.646 8.357 5423 Z= 0.334 Chirality : 0.039 0.137 623 Planarity : 0.004 0.042 701 Dihedral : 3.934 17.838 524 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.51 % Favored : 95.29 % Rotamer: Outliers : 4.58 % Allowed : 30.66 % Favored : 64.76 % 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: 1.66 (0.39), residues: 488 helix: 1.63 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -0.56 (0.61), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 161 HIS 0.004 0.001 HIS B 404 PHE 0.014 0.001 PHE B 364 TYR 0.008 0.001 TYR B 86 ARG 0.002 0.000 ARG B 451 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1591.15 seconds wall clock time: 29 minutes 27.93 seconds (1767.93 seconds total)