Starting phenix.real_space_refine on Fri Aug 22 14:10:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qvx_18677/08_2025/8qvx_18677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qvx_18677/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8qvx_18677/08_2025/8qvx_18677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qvx_18677/08_2025/8qvx_18677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qvx_18677/08_2025/8qvx_18677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qvx_18677/08_2025/8qvx_18677.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.28, per 1000 atoms: 0.32 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: 0.33 Conformation dependent library (CDL) restraints added in 154.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.12 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: 0.63 Time building geometry restraints manager: 0.48 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.180 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:7.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.750 ------------------------------------------------------------------------------- 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= 0.166 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.001 ARG B 451 TYR 0.025 0.002 TYR B 89 PHE 0.022 0.002 PHE A 558 TRP 0.009 0.001 TRP B 161 HIS 0.007 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4013) covalent geometry : angle 0.67916 ( 5423) hydrogen bonds : bond 0.16122 ( 270) hydrogen bonds : angle 5.74020 ( 786) *********************** 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 : 0.156 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: 0.4543 time to fit residues: 24.0527 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 : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.0050 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN B 368 HIS B 371 ASN B 388 ASN B 434 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.158899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.133599 restraints weight = 6754.894| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 3.20 r_work: 0.3981 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.1338 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= 0.143 Angle : 0.586 6.819 5423 Z= 0.313 Chirality : 0.040 0.138 623 Planarity : 0.004 0.050 701 Dihedral : 4.148 16.964 524 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.92 % Favored : 94.88 % Rotamer: Outliers : 5.49 % Allowed : 23.57 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.39), residues: 488 helix: 1.50 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -0.58 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 20 TYR 0.015 0.001 TYR B 89 PHE 0.011 0.001 PHE B 308 TRP 0.007 0.001 TRP B 161 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4013) covalent geometry : angle 0.58648 ( 5423) hydrogen bonds : bond 0.04360 ( 270) hydrogen bonds : angle 4.31163 ( 786) *********************** 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 74 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: B 134 ASP cc_start: 0.6777 (m-30) cc_final: 0.6496 (m-30) REVERT: B 196 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6374 (tpt) REVERT: B 243 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7133 (tp30) REVERT: B 401 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6987 (tm-30) REVERT: B 402 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6144 (tt) REVERT: B 405 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6669 (ttpt) REVERT: B 426 ILE cc_start: 0.7497 (mp) cc_final: 0.7194 (mp) outliers start: 24 outliers final: 4 residues processed: 66 average time/residue: 0.4167 time to fit residues: 28.7564 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 : 0.155 ------------------------------------------------------------------------------- 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 243 GLU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN ** B 309 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 = 0.4383 r_free = 0.4383 target = 0.158065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.132826 restraints weight = 6740.729| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 3.19 r_work: 0.3977 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.1675 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= 0.139 Angle : 0.579 7.004 5423 Z= 0.301 Chirality : 0.039 0.139 623 Planarity : 0.004 0.046 701 Dihedral : 4.085 17.959 524 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.12 % Favored : 94.67 % Rotamer: Outliers : 5.26 % Allowed : 24.94 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.39), residues: 488 helix: 1.47 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -0.74 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.009 0.001 TYR B 416 PHE 0.013 0.001 PHE B 364 TRP 0.006 0.001 TRP B 161 HIS 0.004 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4013) covalent geometry : angle 0.57932 ( 5423) hydrogen bonds : bond 0.03948 ( 270) hydrogen bonds : angle 4.09585 ( 786) *********************** 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: 23 poor density : 43 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: B 196 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6389 (tpt) REVERT: B 243 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7016 (tp30) REVERT: B 401 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.7000 (tm-30) REVERT: B 402 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6117 (tt) REVERT: B 405 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6626 (mtpm) REVERT: B 426 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7184 (mp) outliers start: 23 outliers final: 6 residues processed: 58 average time/residue: 0.3271 time to fit residues: 20.0224 Evaluate side-chains 47 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 243 GLU 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 426 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS B 290 ASN ** B 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.156843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.131248 restraints weight = 6749.389| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 3.20 r_work: 0.3946 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 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 : 0.004 0.037 4013 Z= 0.147 Angle : 0.581 7.255 5423 Z= 0.300 Chirality : 0.039 0.142 623 Planarity : 0.004 0.049 701 Dihedral : 4.115 17.743 524 Min Nonbonded Distance : 2.535 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.39), residues: 488 helix: 1.50 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -0.79 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 147 TYR 0.010 0.001 TYR B 416 PHE 0.013 0.001 PHE B 308 TRP 0.005 0.001 TRP B 161 HIS 0.005 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4013) covalent geometry : angle 0.58132 ( 5423) hydrogen bonds : bond 0.03797 ( 270) hydrogen bonds : angle 4.01728 ( 786) *********************** 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 68 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 43 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 576 HIS cc_start: 0.8304 (m90) cc_final: 0.8006 (m-70) REVERT: B 192 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.6245 (mt) REVERT: B 196 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.6384 (tpt) REVERT: B 243 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7098 (mm-30) REVERT: B 402 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6147 (tt) REVERT: B 426 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7292 (mp) outliers start: 25 outliers final: 11 residues processed: 60 average time/residue: 0.3311 time to fit residues: 20.9985 Evaluate side-chains 57 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 415 MET 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 39 optimal weight: 6.9990 chunk 37 optimal weight: 0.0060 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 309 ASN B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.160771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.135479 restraints weight = 6569.539| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 3.06 r_work: 0.3977 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2344 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= 0.135 Angle : 0.581 7.325 5423 Z= 0.297 Chirality : 0.038 0.133 623 Planarity : 0.004 0.045 701 Dihedral : 4.061 17.775 524 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.92 % Favored : 94.88 % Rotamer: Outliers : 6.41 % Allowed : 26.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.39), residues: 488 helix: 1.59 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.78 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 20 TYR 0.008 0.001 TYR B 416 PHE 0.011 0.001 PHE B 308 TRP 0.006 0.001 TRP B 161 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4013) covalent geometry : angle 0.58109 ( 5423) hydrogen bonds : bond 0.03600 ( 270) hydrogen bonds : angle 3.92673 ( 786) *********************** 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 72 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 44 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 564 ASP cc_start: 0.8306 (t0) cc_final: 0.7840 (t0) REVERT: A 576 HIS cc_start: 0.8371 (m90) cc_final: 0.8085 (m-70) REVERT: B 110 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7225 (ptpt) REVERT: B 192 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6327 (mt) REVERT: B 243 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6903 (mm-30) REVERT: B 402 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6293 (tt) REVERT: B 426 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7251 (mp) outliers start: 28 outliers final: 13 residues processed: 63 average time/residue: 0.3701 time to fit residues: 24.4094 Evaluate side-chains 56 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 192 LEU 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 415 MET 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 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 0.0570 chunk 36 optimal weight: 0.0170 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 = 0.4452 r_free = 0.4452 target = 0.162691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.137164 restraints weight = 6658.904| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 3.15 r_work: 0.3993 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2554 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= 0.124 Angle : 0.573 6.589 5423 Z= 0.294 Chirality : 0.038 0.135 623 Planarity : 0.004 0.043 701 Dihedral : 4.048 19.904 524 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.71 % Favored : 95.08 % Rotamer: Outliers : 4.58 % Allowed : 27.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.39), residues: 488 helix: 1.64 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.78 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 20 TYR 0.007 0.001 TYR B 416 PHE 0.009 0.001 PHE B 308 TRP 0.005 0.001 TRP B 161 HIS 0.003 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 4013) covalent geometry : angle 0.57327 ( 5423) hydrogen bonds : bond 0.03442 ( 270) hydrogen bonds : angle 3.86449 ( 786) *********************** 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 63 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 564 ASP cc_start: 0.8297 (t0) cc_final: 0.7858 (t0) REVERT: A 576 HIS cc_start: 0.8375 (m90) cc_final: 0.8045 (m-70) REVERT: B 192 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6187 (mt) REVERT: B 402 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6213 (tt) REVERT: B 426 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7275 (mp) outliers start: 20 outliers final: 7 residues processed: 55 average time/residue: 0.2680 time to fit residues: 15.7654 Evaluate side-chains 48 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 402 LEU 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 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4434 r_free = 0.4434 target = 0.161051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.135421 restraints weight = 6725.077| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 3.12 r_work: 0.3973 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2664 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= 0.136 Angle : 0.582 8.208 5423 Z= 0.298 Chirality : 0.038 0.134 623 Planarity : 0.004 0.044 701 Dihedral : 4.034 18.610 524 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.71 % Favored : 95.08 % Rotamer: Outliers : 5.26 % Allowed : 27.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.39), residues: 488 helix: 1.64 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.83 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 20 TYR 0.008 0.001 TYR B 416 PHE 0.011 0.001 PHE B 308 TRP 0.006 0.001 TRP B 161 HIS 0.004 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4013) covalent geometry : angle 0.58215 ( 5423) hydrogen bonds : bond 0.03524 ( 270) hydrogen bonds : angle 3.85357 ( 786) *********************** 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 64 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 564 ASP cc_start: 0.8323 (t0) cc_final: 0.7892 (t0) REVERT: A 576 HIS cc_start: 0.8385 (m90) cc_final: 0.8073 (m-70) REVERT: B 192 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6383 (mt) REVERT: B 196 MET cc_start: 0.6420 (tpt) cc_final: 0.6176 (tpt) REVERT: B 222 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.6264 (tp-100) REVERT: B 243 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7160 (mm-30) REVERT: B 402 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6300 (tt) REVERT: B 426 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7323 (mp) outliers start: 23 outliers final: 10 residues processed: 57 average time/residue: 0.2620 time to fit residues: 16.0142 Evaluate side-chains 52 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 192 LEU 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 47 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.160382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.134821 restraints weight = 6653.237| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 3.15 r_work: 0.3964 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.2781 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= 0.139 Angle : 0.585 8.183 5423 Z= 0.299 Chirality : 0.038 0.134 623 Planarity : 0.004 0.044 701 Dihedral : 4.026 18.171 524 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.03 % Allowed : 29.06 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.39), residues: 488 helix: 1.64 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.87 (0.59), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 20 TYR 0.007 0.001 TYR B 86 PHE 0.011 0.001 PHE B 308 TRP 0.006 0.001 TRP B 161 HIS 0.004 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4013) covalent geometry : angle 0.58462 ( 5423) hydrogen bonds : bond 0.03520 ( 270) hydrogen bonds : angle 3.85493 ( 786) *********************** 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 61 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 39 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 564 ASP cc_start: 0.8306 (t0) cc_final: 0.7857 (t0) REVERT: A 576 HIS cc_start: 0.8401 (m90) cc_final: 0.8086 (m-70) REVERT: B 192 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6229 (mt) REVERT: B 196 MET cc_start: 0.6323 (tpt) cc_final: 0.6123 (tpt) REVERT: B 222 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.6250 (tp-100) REVERT: B 243 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7127 (mm-30) REVERT: B 402 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6246 (tt) REVERT: B 426 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7308 (mp) outliers start: 22 outliers final: 11 residues processed: 54 average time/residue: 0.3556 time to fit residues: 20.2623 Evaluate side-chains 51 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 192 LEU 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 394 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 18 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: A 551 ASN B 250 ASN B 290 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.159951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.134442 restraints weight = 6756.811| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 3.12 r_work: 0.3966 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4013 Z= 0.137 Angle : 0.597 8.014 5423 Z= 0.308 Chirality : 0.038 0.134 623 Planarity : 0.004 0.043 701 Dihedral : 3.998 17.682 524 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.81 % Allowed : 29.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.39), residues: 488 helix: 1.67 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -0.79 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 451 TYR 0.007 0.001 TYR B 86 PHE 0.010 0.001 PHE B 308 TRP 0.007 0.001 TRP B 161 HIS 0.004 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4013) covalent geometry : angle 0.59699 ( 5423) hydrogen bonds : bond 0.03491 ( 270) hydrogen bonds : angle 3.80734 ( 786) *********************** 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 60 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 564 ASP cc_start: 0.8310 (t0) cc_final: 0.7872 (t0) REVERT: A 576 HIS cc_start: 0.8390 (m90) cc_final: 0.8076 (m-70) REVERT: B 192 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6316 (mt) REVERT: B 222 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.6287 (tp-100) REVERT: B 243 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7253 (mm-30) REVERT: B 402 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6340 (tt) REVERT: B 426 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7346 (mp) outliers start: 21 outliers final: 14 residues processed: 53 average time/residue: 0.2967 time to fit residues: 16.6587 Evaluate side-chains 55 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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 192 LEU 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 3 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.159996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.134750 restraints weight = 6643.404| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 3.10 r_work: 0.3971 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 4013 Z= 0.195 Angle : 1.183 59.200 5423 Z= 0.698 Chirality : 0.043 0.498 623 Planarity : 0.005 0.067 701 Dihedral : 4.267 34.776 524 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.35 % Allowed : 29.75 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.39), residues: 488 helix: 1.68 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -0.79 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 451 TYR 0.007 0.001 TYR B 86 PHE 0.010 0.001 PHE B 308 TRP 0.006 0.001 TRP B 161 HIS 0.004 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 4013) covalent geometry : angle 1.18304 ( 5423) hydrogen bonds : bond 0.03490 ( 270) hydrogen bonds : angle 3.80618 ( 786) ********************** 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 56 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 564 ASP cc_start: 0.8292 (t0) cc_final: 0.7844 (t0) REVERT: A 576 HIS cc_start: 0.8398 (m90) cc_final: 0.8077 (m-70) REVERT: B 192 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.6292 (mt) REVERT: B 222 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.6284 (tp-100) REVERT: B 243 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7227 (mm-30) REVERT: B 402 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6283 (tt) REVERT: B 426 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7328 (mp) outliers start: 19 outliers final: 13 residues processed: 50 average time/residue: 0.3195 time to fit residues: 16.9340 Evaluate side-chains 54 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 192 LEU 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 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 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 30 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.159829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.134473 restraints weight = 6664.052| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 3.10 r_work: 0.3970 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 4013 Z= 0.195 Angle : 1.183 59.200 5423 Z= 0.698 Chirality : 0.043 0.498 623 Planarity : 0.005 0.067 701 Dihedral : 4.267 34.776 524 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.12 % Allowed : 29.98 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.39), residues: 488 helix: 1.68 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -0.79 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 451 TYR 0.007 0.001 TYR B 86 PHE 0.010 0.001 PHE B 308 TRP 0.006 0.001 TRP B 161 HIS 0.004 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 4013) covalent geometry : angle 1.18304 ( 5423) hydrogen bonds : bond 0.03490 ( 270) hydrogen bonds : angle 3.80618 ( 786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1570.86 seconds wall clock time: 27 minutes 36.22 seconds (1656.22 seconds total)