Starting phenix.real_space_refine on Sat Aug 23 15:27:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ugb_64135/08_2025/9ugb_64135.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ugb_64135/08_2025/9ugb_64135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ugb_64135/08_2025/9ugb_64135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ugb_64135/08_2025/9ugb_64135.map" model { file = "/net/cci-nas-00/data/ceres_data/9ugb_64135/08_2025/9ugb_64135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ugb_64135/08_2025/9ugb_64135.cif" } resolution = 3.25 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= 0.001 sd= 0.047 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: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 4144 2.51 5 N 1062 2.21 5 O 1198 1.98 5 H 6509 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s 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: 12942 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 12670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 12670 Classifications: {'peptide': 821} Link IDs: {'PTRANS': 33, 'TRANS': 787} Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 272 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Time building chain proxies: 2.06, per 1000 atoms: 0.16 Number of scatterers: 12942 At special positions: 0 Unit cell: (82.16, 87.36, 132.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 1198 8.00 N 1062 7.00 C 4144 6.00 H 6509 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 385.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1532 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 59.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 76 through 80 Processing helix chain 'B' and resid 89 through 101 Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.902A pdb=" N PHE B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 Processing helix chain 'B' and resid 140 through 172 removed outlier: 3.541A pdb=" N ILE B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 263 through 266 Processing helix chain 'B' and resid 267 through 280 Processing helix chain 'B' and resid 284 through 315 Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 337 through 356 Processing helix chain 'B' and resid 363 through 371 removed outlier: 4.044A pdb=" N GLU B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 371 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 420 through 430 Processing helix chain 'B' and resid 433 through 441 removed outlier: 4.093A pdb=" N THR B 441 " --> pdb=" O LYS B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 488 removed outlier: 3.772A pdb=" N ASP B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 508 Processing helix chain 'B' and resid 540 through 550 removed outlier: 3.524A pdb=" N GLU B 546 " --> pdb=" O GLN B 542 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 573 Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 593 through 604 Processing helix chain 'B' and resid 611 through 625 Processing helix chain 'B' and resid 638 through 645 Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 673 through 714 Processing helix chain 'B' and resid 718 through 734 Processing helix chain 'B' and resid 735 through 739 Processing helix chain 'B' and resid 751 through 776 Processing helix chain 'B' and resid 790 through 811 removed outlier: 4.062A pdb=" N ILE B 807 " --> pdb=" O GLU B 803 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE B 808 " --> pdb=" O ASN B 804 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 809 " --> pdb=" O TRP B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 842 Processing helix chain 'B' and resid 851 through 879 Processing helix chain 'B' and resid 879 through 888 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.818A pdb=" N LEU C 46 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN C 51 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 187 through 192 removed outlier: 5.138A pdb=" N VAL B 181 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE B 201 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 237 through 239 removed outlier: 6.504A pdb=" N GLN B 224 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 358 through 360 removed outlier: 6.254A pdb=" N GLY B 648 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N PHE B 666 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA B 650 " --> pdb=" O PHE B 666 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL B 629 " --> pdb=" O THR B 647 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE B 649 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N MET B 631 " --> pdb=" O ILE B 649 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 628 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU B 373 " --> pdb=" O ARG B 553 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LYS B 555 " --> pdb=" O GLU B 373 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU B 375 " --> pdb=" O LYS B 555 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU B 557 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N SER B 377 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N PHE B 607 " --> pdb=" O VAL B 554 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N MET B 556 " --> pdb=" O PHE B 607 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 389 through 390 Processing sheet with id=AA5, first strand: chain 'B' and resid 394 through 395 removed outlier: 6.742A pdb=" N VAL B 515 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LYS B 457 " --> pdb=" O PRO B 450 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR B 459 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE B 448 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 461 " --> pdb=" O LEU B 446 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1179 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: 2.68 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6500 1.03 - 1.23: 15 1.23 - 1.42: 2664 1.42 - 1.62: 3845 1.62 - 1.81: 49 Bond restraints: 13073 Sorted by residual: bond pdb=" CA THR B 384 " pdb=" HA THR B 384 " ideal model delta sigma weight residual 0.970 0.855 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" N GLY B 284 " pdb=" CA GLY B 284 " ideal model delta sigma weight residual 1.444 1.477 -0.033 1.06e-02 8.90e+03 9.69e+00 bond pdb=" N GLN B 283 " pdb=" CA GLN B 283 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.43e+00 bond pdb=" N MET B 533 " pdb=" H MET B 533 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" N ASP B 378 " pdb=" H ASP B 378 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.52e+00 ... (remaining 13068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.93: 23718 6.93 - 13.85: 3 13.85 - 20.78: 0 20.78 - 27.71: 0 27.71 - 34.64: 3 Bond angle restraints: 23724 Sorted by residual: angle pdb=" C LEU B 172 " pdb=" CA LEU B 172 " pdb=" HA LEU B 172 " ideal model delta sigma weight residual 109.00 74.36 34.64 3.00e+00 1.11e-01 1.33e+02 angle pdb=" N LEU B 172 " pdb=" CA LEU B 172 " pdb=" HA LEU B 172 " ideal model delta sigma weight residual 110.00 75.87 34.13 3.00e+00 1.11e-01 1.29e+02 angle pdb=" CB LEU B 172 " pdb=" CA LEU B 172 " pdb=" HA LEU B 172 " ideal model delta sigma weight residual 109.00 77.25 31.75 3.00e+00 1.11e-01 1.12e+02 angle pdb=" C GLY B 281 " pdb=" N GLY B 282 " pdb=" CA GLY B 282 " ideal model delta sigma weight residual 119.92 124.33 -4.41 9.60e-01 1.09e+00 2.11e+01 angle pdb=" CA GLY B 282 " pdb=" C GLY B 282 " pdb=" O GLY B 282 " ideal model delta sigma weight residual 121.41 117.54 3.87 8.80e-01 1.29e+00 1.93e+01 ... (remaining 23719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 5272 17.04 - 34.07: 542 34.07 - 51.11: 182 51.11 - 68.14: 91 68.14 - 85.18: 19 Dihedral angle restraints: 6106 sinusoidal: 3320 harmonic: 2786 Sorted by residual: dihedral pdb=" C LEU B 172 " pdb=" N LEU B 172 " pdb=" CA LEU B 172 " pdb=" CB LEU B 172 " ideal model delta harmonic sigma weight residual -122.60 -133.29 10.69 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" N LEU B 172 " pdb=" C LEU B 172 " pdb=" CA LEU B 172 " pdb=" CB LEU B 172 " ideal model delta harmonic sigma weight residual 122.80 133.42 -10.62 0 2.50e+00 1.60e-01 1.80e+01 dihedral pdb=" CA ASP C 40 " pdb=" C ASP C 40 " pdb=" N ASP C 41 " pdb=" CA ASP C 41 " ideal model delta harmonic sigma weight residual 180.00 -159.87 -20.13 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 6103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 975 0.091 - 0.181: 64 0.181 - 0.272: 1 0.272 - 0.363: 1 0.363 - 0.453: 1 Chirality restraints: 1042 Sorted by residual: chirality pdb=" CA LEU B 172 " pdb=" N LEU B 172 " pdb=" C LEU B 172 " pdb=" CB LEU B 172 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.14e+00 chirality pdb=" CA THR B 384 " pdb=" N THR B 384 " pdb=" C THR B 384 " pdb=" CB THR B 384 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ILE B 820 " pdb=" N ILE B 820 " pdb=" C ILE B 820 " pdb=" CB ILE B 820 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1039 not shown) Planarity restraints: 1938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 623 " -0.254 2.00e-02 2.50e+03 3.19e-01 1.52e+03 pdb=" CD GLN B 623 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLN B 623 " 0.239 2.00e-02 2.50e+03 pdb=" NE2 GLN B 623 " 0.005 2.00e-02 2.50e+03 pdb="HE21 GLN B 623 " -0.503 2.00e-02 2.50e+03 pdb="HE22 GLN B 623 " 0.483 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 384 " -0.020 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" N LYS B 385 " 0.067 2.00e-02 2.50e+03 pdb=" CA LYS B 385 " -0.017 2.00e-02 2.50e+03 pdb=" H LYS B 385 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 822 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" N TRP B 823 " 0.051 2.00e-02 2.50e+03 pdb=" CA TRP B 823 " -0.013 2.00e-02 2.50e+03 pdb=" H TRP B 823 " -0.023 2.00e-02 2.50e+03 ... (remaining 1935 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 260 2.08 - 2.71: 22061 2.71 - 3.34: 39756 3.34 - 3.97: 48717 3.97 - 4.60: 77610 Nonbonded interactions: 188404 Sorted by model distance: nonbonded pdb=" OE1 GLU B 190 " pdb=" H GLU B 190 " model vdw 1.454 2.450 nonbonded pdb="HE22 GLN B 623 " pdb=" HA ALA B 645 " model vdw 1.530 2.270 nonbonded pdb=" OE1 GLN B 824 " pdb=" H GLN B 824 " model vdw 1.600 2.450 nonbonded pdb=" HE1 TRP B 805 " pdb=" OD2 ASP B 833 " model vdw 1.609 2.450 nonbonded pdb="HH21 ARG B 315 " pdb=" O ALA B 711 " model vdw 1.626 2.450 ... (remaining 188399 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: 1.600 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: 0.080 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.910 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 0.075 6564 Z= 0.231 Angle : 0.721 8.686 8921 Z= 0.437 Chirality : 0.047 0.453 1042 Planarity : 0.005 0.064 1133 Dihedral : 15.663 84.083 2352 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.29 % Allowed : 16.20 % Favored : 83.50 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.28), residues: 836 helix: 1.47 (0.23), residues: 470 sheet: -0.98 (0.49), residues: 101 loop : -0.46 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 324 TYR 0.016 0.001 TYR B 498 PHE 0.023 0.002 PHE B 126 TRP 0.010 0.001 TRP B 141 HIS 0.007 0.001 HIS B 701 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 6564) covalent geometry : angle 0.72122 ( 8921) hydrogen bonds : bond 0.12046 ( 408) hydrogen bonds : angle 6.10535 ( 1179) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 MET cc_start: 0.7176 (mmt) cc_final: 0.6914 (mmt) outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.1631 time to fit residues: 23.7467 Evaluate side-chains 92 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN B 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.178931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145515 restraints weight = 23632.093| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.02 r_work: 0.3539 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6564 Z= 0.199 Angle : 0.579 6.367 8921 Z= 0.307 Chirality : 0.044 0.414 1042 Planarity : 0.005 0.062 1133 Dihedral : 4.304 29.229 893 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.04 % Allowed : 15.77 % Favored : 82.19 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.27), residues: 836 helix: 1.47 (0.22), residues: 472 sheet: -1.55 (0.49), residues: 79 loop : -0.31 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 96 TYR 0.013 0.002 TYR B 694 PHE 0.022 0.002 PHE B 126 TRP 0.008 0.001 TRP B 141 HIS 0.006 0.002 HIS B 701 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 6564) covalent geometry : angle 0.57891 ( 8921) hydrogen bonds : bond 0.04173 ( 408) hydrogen bonds : angle 4.85907 ( 1179) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 247 SER cc_start: 0.7787 (t) cc_final: 0.7575 (m) REVERT: B 533 MET cc_start: 0.8183 (ttp) cc_final: 0.7809 (ttt) REVERT: B 592 MET cc_start: 0.0713 (mtm) cc_final: 0.0497 (mtp) REVERT: B 714 ASP cc_start: 0.8619 (t0) cc_final: 0.8299 (t0) outliers start: 14 outliers final: 9 residues processed: 124 average time/residue: 0.1226 time to fit residues: 22.3962 Evaluate side-chains 107 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 HIS B 577 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.175918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142695 restraints weight = 23618.258| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.08 r_work: 0.3512 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6564 Z= 0.176 Angle : 0.537 5.301 8921 Z= 0.281 Chirality : 0.043 0.412 1042 Planarity : 0.004 0.051 1133 Dihedral : 3.958 19.998 890 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.04 % Allowed : 17.52 % Favored : 80.44 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.27), residues: 836 helix: 1.69 (0.22), residues: 471 sheet: -1.54 (0.52), residues: 76 loop : -0.20 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 324 TYR 0.011 0.001 TYR B 694 PHE 0.011 0.002 PHE B 222 TRP 0.007 0.001 TRP B 750 HIS 0.006 0.001 HIS B 701 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6564) covalent geometry : angle 0.53720 ( 8921) hydrogen bonds : bond 0.04225 ( 408) hydrogen bonds : angle 4.66925 ( 1179) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 LEU cc_start: 0.6187 (pp) cc_final: 0.5444 (mt) REVERT: B 253 ARG cc_start: 0.6934 (mtp85) cc_final: 0.6683 (mtp85) REVERT: B 533 MET cc_start: 0.8185 (ttp) cc_final: 0.7979 (ttt) REVERT: B 714 ASP cc_start: 0.8554 (t0) cc_final: 0.8241 (t0) outliers start: 14 outliers final: 9 residues processed: 116 average time/residue: 0.1245 time to fit residues: 20.5167 Evaluate side-chains 103 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 73 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.175016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.141117 restraints weight = 23437.511| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.14 r_work: 0.3477 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6564 Z= 0.153 Angle : 0.512 5.325 8921 Z= 0.266 Chirality : 0.043 0.409 1042 Planarity : 0.004 0.051 1133 Dihedral : 3.855 19.925 890 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.04 % Allowed : 17.81 % Favored : 80.15 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.28), residues: 836 helix: 1.88 (0.22), residues: 470 sheet: -1.54 (0.52), residues: 76 loop : -0.22 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 253 TYR 0.010 0.001 TYR B 694 PHE 0.008 0.001 PHE B 126 TRP 0.007 0.001 TRP B 771 HIS 0.004 0.001 HIS B 701 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6564) covalent geometry : angle 0.51229 ( 8921) hydrogen bonds : bond 0.03964 ( 408) hydrogen bonds : angle 4.51323 ( 1179) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7637 (tm-30) REVERT: B 235 LEU cc_start: 0.6691 (pp) cc_final: 0.6079 (mp) REVERT: B 253 ARG cc_start: 0.7022 (mtp85) cc_final: 0.6591 (mtp85) REVERT: B 470 ILE cc_start: 0.7228 (mt) cc_final: 0.6907 (mt) REVERT: B 519 ARG cc_start: 0.7518 (mmm-85) cc_final: 0.7249 (mmm-85) REVERT: B 714 ASP cc_start: 0.8539 (t0) cc_final: 0.8216 (t0) outliers start: 14 outliers final: 9 residues processed: 115 average time/residue: 0.1402 time to fit residues: 22.6329 Evaluate side-chains 106 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 2 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 16 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.173455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.139377 restraints weight = 23440.835| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.10 r_work: 0.3452 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6564 Z= 0.158 Angle : 0.515 5.771 8921 Z= 0.267 Chirality : 0.043 0.410 1042 Planarity : 0.004 0.054 1133 Dihedral : 3.787 19.545 890 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.92 % Allowed : 17.81 % Favored : 79.27 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.28), residues: 836 helix: 1.89 (0.23), residues: 470 sheet: -1.52 (0.54), residues: 76 loop : -0.22 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 253 TYR 0.010 0.001 TYR B 694 PHE 0.026 0.001 PHE B 126 TRP 0.008 0.001 TRP B 771 HIS 0.005 0.001 HIS B 523 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6564) covalent geometry : angle 0.51453 ( 8921) hydrogen bonds : bond 0.03917 ( 408) hydrogen bonds : angle 4.44473 ( 1179) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7603 (tm-30) REVERT: B 235 LEU cc_start: 0.7017 (pp) cc_final: 0.6240 (mt) REVERT: B 253 ARG cc_start: 0.7088 (mtp85) cc_final: 0.6704 (mtp85) REVERT: B 405 MET cc_start: 0.7285 (mmt) cc_final: 0.6417 (mmt) REVERT: B 470 ILE cc_start: 0.7258 (mt) cc_final: 0.6939 (mt) REVERT: B 492 GLU cc_start: 0.7028 (tt0) cc_final: 0.6684 (tp30) REVERT: B 519 ARG cc_start: 0.7473 (mmm-85) cc_final: 0.7212 (mmm-85) outliers start: 20 outliers final: 13 residues processed: 112 average time/residue: 0.1306 time to fit residues: 20.4690 Evaluate side-chains 104 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 73 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.172941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.139087 restraints weight = 23394.322| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.07 r_work: 0.3448 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6564 Z= 0.147 Angle : 0.503 5.636 8921 Z= 0.259 Chirality : 0.042 0.416 1042 Planarity : 0.004 0.052 1133 Dihedral : 3.721 18.224 890 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.75 % Allowed : 19.56 % Favored : 78.69 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: 1.37 (0.28), residues: 836 helix: 2.02 (0.23), residues: 470 sheet: -1.49 (0.54), residues: 76 loop : -0.20 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 253 TYR 0.010 0.001 TYR B 694 PHE 0.014 0.001 PHE B 126 TRP 0.007 0.001 TRP B 771 HIS 0.005 0.001 HIS B 391 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6564) covalent geometry : angle 0.50278 ( 8921) hydrogen bonds : bond 0.03832 ( 408) hydrogen bonds : angle 4.36926 ( 1179) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 LEU cc_start: 0.7223 (pp) cc_final: 0.6545 (mt) REVERT: B 253 ARG cc_start: 0.7129 (mtp85) cc_final: 0.6768 (mtp85) REVERT: B 405 MET cc_start: 0.7395 (mmt) cc_final: 0.6464 (mmt) REVERT: B 470 ILE cc_start: 0.7370 (mt) cc_final: 0.7087 (mt) REVERT: B 492 GLU cc_start: 0.7041 (tt0) cc_final: 0.6718 (tp30) REVERT: B 519 ARG cc_start: 0.7305 (mmm-85) cc_final: 0.7059 (mmm-85) outliers start: 12 outliers final: 11 residues processed: 100 average time/residue: 0.1438 time to fit residues: 19.7701 Evaluate side-chains 99 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 76 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.171999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137727 restraints weight = 23395.806| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.11 r_work: 0.3428 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6564 Z= 0.155 Angle : 0.513 5.374 8921 Z= 0.266 Chirality : 0.043 0.415 1042 Planarity : 0.004 0.051 1133 Dihedral : 3.726 18.301 890 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.34 % Allowed : 19.27 % Favored : 78.39 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 836 helix: 2.06 (0.23), residues: 469 sheet: -1.46 (0.54), residues: 76 loop : -0.24 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 414 TYR 0.010 0.001 TYR B 694 PHE 0.021 0.002 PHE B 222 TRP 0.007 0.001 TRP B 771 HIS 0.005 0.001 HIS B 391 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6564) covalent geometry : angle 0.51301 ( 8921) hydrogen bonds : bond 0.03813 ( 408) hydrogen bonds : angle 4.33508 ( 1179) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 LEU cc_start: 0.7217 (pp) cc_final: 0.6846 (mt) REVERT: B 253 ARG cc_start: 0.7188 (mtp85) cc_final: 0.6915 (mtp85) REVERT: B 835 ILE cc_start: 0.8727 (tp) cc_final: 0.8243 (mt) outliers start: 16 outliers final: 12 residues processed: 104 average time/residue: 0.1480 time to fit residues: 21.7988 Evaluate side-chains 100 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 37 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 82 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 67 optimal weight: 0.0970 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.173764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139952 restraints weight = 23045.981| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.11 r_work: 0.3458 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6564 Z= 0.117 Angle : 0.490 5.378 8921 Z= 0.250 Chirality : 0.042 0.411 1042 Planarity : 0.003 0.052 1133 Dihedral : 3.585 17.344 890 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.61 % Allowed : 20.88 % Favored : 77.52 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: 1.65 (0.28), residues: 836 helix: 2.30 (0.23), residues: 469 sheet: -1.38 (0.55), residues: 76 loop : -0.16 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 414 TYR 0.009 0.001 TYR B 694 PHE 0.013 0.001 PHE B 126 TRP 0.007 0.001 TRP B 771 HIS 0.006 0.001 HIS B 391 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6564) covalent geometry : angle 0.48985 ( 8921) hydrogen bonds : bond 0.03625 ( 408) hydrogen bonds : angle 4.23212 ( 1179) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 ASP cc_start: 0.7807 (t0) cc_final: 0.7512 (t70) REVERT: B 235 LEU cc_start: 0.7181 (pp) cc_final: 0.6871 (mp) REVERT: B 253 ARG cc_start: 0.7163 (mtp85) cc_final: 0.6860 (mtp85) REVERT: B 405 MET cc_start: 0.7283 (mmt) cc_final: 0.7028 (mmt) REVERT: B 835 ILE cc_start: 0.8711 (tp) cc_final: 0.8193 (mt) outliers start: 11 outliers final: 10 residues processed: 105 average time/residue: 0.1381 time to fit residues: 20.5134 Evaluate side-chains 107 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 846 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.170185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136085 restraints weight = 23316.563| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.06 r_work: 0.3409 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6564 Z= 0.199 Angle : 0.529 5.771 8921 Z= 0.278 Chirality : 0.044 0.414 1042 Planarity : 0.004 0.052 1133 Dihedral : 3.725 16.812 890 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.04 % Allowed : 20.58 % Favored : 77.37 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 836 helix: 2.07 (0.23), residues: 469 sheet: -1.55 (0.54), residues: 76 loop : -0.24 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 857 TYR 0.011 0.001 TYR B 694 PHE 0.013 0.001 PHE B 126 TRP 0.007 0.001 TRP B 771 HIS 0.005 0.001 HIS B 391 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 6564) covalent geometry : angle 0.52857 ( 8921) hydrogen bonds : bond 0.03917 ( 408) hydrogen bonds : angle 4.36140 ( 1179) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 ASP cc_start: 0.7818 (t0) cc_final: 0.7523 (t70) REVERT: B 253 ARG cc_start: 0.7127 (mtp85) cc_final: 0.6815 (mtp85) REVERT: B 405 MET cc_start: 0.7499 (mmt) cc_final: 0.6869 (mmt) REVERT: B 835 ILE cc_start: 0.8743 (tp) cc_final: 0.8240 (mt) outliers start: 14 outliers final: 12 residues processed: 99 average time/residue: 0.1478 time to fit residues: 20.7692 Evaluate side-chains 102 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain C residue 47 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.170292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136500 restraints weight = 23295.567| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.07 r_work: 0.3409 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6564 Z= 0.176 Angle : 0.521 5.540 8921 Z= 0.273 Chirality : 0.043 0.415 1042 Planarity : 0.004 0.051 1133 Dihedral : 3.735 16.380 890 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.04 % Allowed : 20.44 % Favored : 77.52 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.28), residues: 836 helix: 2.05 (0.23), residues: 469 sheet: -1.53 (0.54), residues: 76 loop : -0.27 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 253 TYR 0.010 0.001 TYR B 694 PHE 0.013 0.001 PHE B 126 TRP 0.007 0.001 TRP B 750 HIS 0.004 0.001 HIS B 701 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 6564) covalent geometry : angle 0.52126 ( 8921) hydrogen bonds : bond 0.03877 ( 408) hydrogen bonds : angle 4.36288 ( 1179) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 ARG cc_start: 0.7228 (mtp85) cc_final: 0.6933 (mtp85) REVERT: B 405 MET cc_start: 0.7515 (mmt) cc_final: 0.6893 (mmt) REVERT: B 423 ASP cc_start: 0.8585 (m-30) cc_final: 0.8261 (m-30) REVERT: B 440 LEU cc_start: 0.9065 (tp) cc_final: 0.8835 (tp) REVERT: B 656 ASP cc_start: 0.7881 (m-30) cc_final: 0.7610 (m-30) REVERT: B 835 ILE cc_start: 0.8737 (tp) cc_final: 0.8240 (mt) outliers start: 14 outliers final: 14 residues processed: 99 average time/residue: 0.1487 time to fit residues: 20.7034 Evaluate side-chains 103 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain C residue 47 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 40 optimal weight: 0.9990 chunk 13 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: B 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.170185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.136287 restraints weight = 23228.264| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.08 r_work: 0.3411 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6564 Z= 0.165 Angle : 0.516 5.541 8921 Z= 0.269 Chirality : 0.043 0.414 1042 Planarity : 0.004 0.050 1133 Dihedral : 3.723 16.184 890 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.90 % Allowed : 20.58 % Favored : 77.52 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: 1.37 (0.28), residues: 836 helix: 2.08 (0.22), residues: 467 sheet: -1.60 (0.54), residues: 76 loop : -0.25 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 253 TYR 0.010 0.001 TYR B 694 PHE 0.012 0.001 PHE B 126 TRP 0.007 0.001 TRP B 750 HIS 0.004 0.001 HIS B 701 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6564) covalent geometry : angle 0.51558 ( 8921) hydrogen bonds : bond 0.03849 ( 408) hydrogen bonds : angle 4.34759 ( 1179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3544.10 seconds wall clock time: 60 minutes 40.02 seconds (3640.02 seconds total)