Starting phenix.real_space_refine on Wed Feb 12 02:29:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vyi_21461/02_2025/6vyi_21461.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vyi_21461/02_2025/6vyi_21461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vyi_21461/02_2025/6vyi_21461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vyi_21461/02_2025/6vyi_21461.map" model { file = "/net/cci-nas-00/data/ceres_data/6vyi_21461/02_2025/6vyi_21461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vyi_21461/02_2025/6vyi_21461.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 P 4 5.49 5 S 42 5.16 5 C 4620 2.51 5 N 1136 2.21 5 O 1114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6916 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3360 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 18, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3360 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 18, 'TRANS': 387} Chain breaks: 1 Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 147 Unusual residues: {'6OU': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.56, per 1000 atoms: 0.66 Number of scatterers: 6916 At special positions: 0 Unit cell: (109.725, 91.575, 81.675, 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 42 16.00 P 4 15.00 O 1114 8.00 N 1136 7.00 C 4620 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 958.3 milliseconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 78.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.627A pdb=" N GLY A 81 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 113 removed outlier: 3.505A pdb=" N CYS A 92 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ARG A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 removed outlier: 3.607A pdb=" N GLN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 155 removed outlier: 4.299A pdb=" N ASN A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 185 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 190 through 226 removed outlier: 3.693A pdb=" N ARG A 222 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 removed outlier: 3.785A pdb=" N PHE A 257 " --> pdb=" O TYR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 300 Processing helix chain 'A' and resid 300 through 307 removed outlier: 4.089A pdb=" N SER A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.838A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'A' and resid 399 through 420 Processing helix chain 'A' and resid 428 through 448 removed outlier: 3.700A pdb=" N THR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 438 " --> pdb=" O MET A 434 " (cutoff:3.500A) Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 449 through 463 Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.717A pdb=" N VAL A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.626A pdb=" N GLY B 81 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 113 removed outlier: 3.505A pdb=" N CYS B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ARG B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 127 removed outlier: 3.606A pdb=" N GLN B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 155 removed outlier: 4.298A pdb=" N ASN B 141 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 185 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 190 through 226 removed outlier: 3.693A pdb=" N ARG B 222 " --> pdb=" O CYS B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 removed outlier: 3.786A pdb=" N PHE B 257 " --> pdb=" O TYR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 300 Processing helix chain 'B' and resid 300 through 307 removed outlier: 4.089A pdb=" N SER B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 343 removed outlier: 3.838A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 369 through 375 Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 390 through 396 Processing helix chain 'B' and resid 399 through 420 Processing helix chain 'B' and resid 428 through 448 removed outlier: 3.699A pdb=" N THR B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE B 438 " --> pdb=" O MET B 434 " (cutoff:3.500A) Proline residue: B 439 - end of helix Processing helix chain 'B' and resid 449 through 463 Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.718A pdb=" N VAL B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1018 1.32 - 1.44: 2138 1.44 - 1.56: 3894 1.56 - 1.68: 8 1.68 - 1.80: 68 Bond restraints: 7126 Sorted by residual: bond pdb=" O22 6OU A 502 " pdb=" P23 6OU A 502 " ideal model delta sigma weight residual 1.643 1.557 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" O22 6OU B 501 " pdb=" P23 6OU B 501 " ideal model delta sigma weight residual 1.643 1.566 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " ideal model delta sigma weight residual 1.643 1.568 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O22 6OU A 503 " pdb=" P23 6OU A 503 " ideal model delta sigma weight residual 1.643 1.573 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C27 6OU A 503 " pdb=" C28 6OU A 503 " ideal model delta sigma weight residual 1.512 1.563 -0.051 2.00e-02 2.50e+03 6.57e+00 ... (remaining 7121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 9555 3.49 - 6.98: 79 6.98 - 10.46: 3 10.46 - 13.95: 6 13.95 - 17.44: 5 Bond angle restraints: 9648 Sorted by residual: angle pdb=" C21 6OU A 502 " pdb=" O22 6OU A 502 " pdb=" P23 6OU A 502 " ideal model delta sigma weight residual 117.17 134.61 -17.44 3.00e+00 1.11e-01 3.38e+01 angle pdb=" C21 6OU A 501 " pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " ideal model delta sigma weight residual 117.17 134.50 -17.33 3.00e+00 1.11e-01 3.34e+01 angle pdb=" O22 6OU A 503 " pdb=" P23 6OU A 503 " pdb=" O26 6OU A 503 " ideal model delta sigma weight residual 93.95 110.09 -16.14 3.00e+00 1.11e-01 2.89e+01 angle pdb=" C21 6OU B 501 " pdb=" O22 6OU B 501 " pdb=" P23 6OU B 501 " ideal model delta sigma weight residual 117.17 131.43 -14.26 3.00e+00 1.11e-01 2.26e+01 angle pdb=" O22 6OU B 501 " pdb=" P23 6OU B 501 " pdb=" O26 6OU B 501 " ideal model delta sigma weight residual 93.95 108.05 -14.10 3.00e+00 1.11e-01 2.21e+01 ... (remaining 9643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 4045 34.83 - 69.66: 109 69.66 - 104.49: 21 104.49 - 139.31: 11 139.31 - 174.14: 4 Dihedral angle restraints: 4190 sinusoidal: 1778 harmonic: 2412 Sorted by residual: dihedral pdb=" CA GLY A 87 " pdb=" C GLY A 87 " pdb=" N ILE A 88 " pdb=" CA ILE A 88 " ideal model delta harmonic sigma weight residual 180.00 156.65 23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA GLY B 87 " pdb=" C GLY B 87 " pdb=" N ILE B 88 " pdb=" CA ILE B 88 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" C19 6OU B 501 " pdb=" C20 6OU B 501 " pdb=" C21 6OU B 501 " pdb=" O22 6OU B 501 " ideal model delta sinusoidal sigma weight residual -59.00 115.14 -174.14 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 751 0.051 - 0.102: 242 0.102 - 0.153: 35 0.153 - 0.204: 1 0.204 - 0.255: 3 Chirality restraints: 1032 Sorted by residual: chirality pdb=" C20 6OU A 503 " pdb=" C19 6OU A 503 " pdb=" C21 6OU A 503 " pdb=" O30 6OU A 503 " both_signs ideal model delta sigma weight residual False 2.35 2.60 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C20 6OU B 501 " pdb=" C19 6OU B 501 " pdb=" C21 6OU B 501 " pdb=" O30 6OU B 501 " both_signs ideal model delta sigma weight residual False 2.35 2.57 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C20 6OU A 502 " pdb=" C19 6OU A 502 " pdb=" C21 6OU A 502 " pdb=" O30 6OU A 502 " both_signs ideal model delta sigma weight residual False 2.35 2.56 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1029 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 296 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C ILE A 296 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE A 296 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN A 297 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 296 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C ILE B 296 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE B 296 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN B 297 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 243 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO B 244 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 244 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 244 " 0.022 5.00e-02 4.00e+02 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 284 2.71 - 3.25: 7272 3.25 - 3.80: 11658 3.80 - 4.35: 14141 4.35 - 4.90: 24318 Nonbonded interactions: 57673 Sorted by model distance: nonbonded pdb=" OE1 GLU A 351 " pdb=" NH2 ARG A 358 " model vdw 2.157 3.120 nonbonded pdb=" OE1 GLU B 351 " pdb=" NH2 ARG B 358 " model vdw 2.158 3.120 nonbonded pdb=" O GLU B 416 " pdb=" OG SER B 420 " model vdw 2.193 3.040 nonbonded pdb=" O GLU A 416 " pdb=" OG SER A 420 " model vdw 2.194 3.040 nonbonded pdb=" ND2 ASN A 366 " pdb=" O ASN B 84 " model vdw 2.218 3.120 ... (remaining 57668 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 66 through 481 or resid 501)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.680 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 0.010 0.086 7126 Z= 0.614 Angle : 0.941 17.441 9648 Z= 0.447 Chirality : 0.048 0.255 1032 Planarity : 0.005 0.039 1172 Dihedral : 19.278 174.143 2626 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.26), residues: 804 helix: -1.16 (0.19), residues: 592 sheet: None (None), residues: 0 loop : -4.15 (0.33), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 334 HIS 0.005 0.001 HIS B 382 PHE 0.016 0.002 PHE B 338 TYR 0.015 0.002 TYR B 417 ARG 0.005 0.001 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 306 ASN cc_start: 0.8273 (m-40) cc_final: 0.7945 (m-40) REVERT: A 404 ARG cc_start: 0.7495 (mtt-85) cc_final: 0.6766 (mtm110) REVERT: B 404 ARG cc_start: 0.7480 (mtt-85) cc_final: 0.6777 (mtm110) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 1.3498 time to fit residues: 168.3024 Evaluate side-chains 92 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 119 GLN A 162 GLN A 239 HIS ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 GLN A 465 GLN B 119 GLN B 162 GLN B 239 HIS B 266 ASN B 292 GLN B 465 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.133957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.104768 restraints weight = 9387.745| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.94 r_work: 0.3065 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7126 Z= 0.234 Angle : 0.610 7.201 9648 Z= 0.307 Chirality : 0.040 0.123 1032 Planarity : 0.005 0.033 1172 Dihedral : 18.096 179.506 1082 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.22 % Allowed : 11.20 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.29), residues: 804 helix: 0.43 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -3.30 (0.35), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.004 0.001 HIS A 201 PHE 0.028 0.002 PHE B 443 TYR 0.013 0.001 TYR B 211 ARG 0.002 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.760 Fit side-chains REVERT: A 404 ARG cc_start: 0.7485 (mtt-85) cc_final: 0.6449 (mtm110) REVERT: A 425 MET cc_start: 0.8426 (mtt) cc_final: 0.8206 (mtp) REVERT: B 102 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7520 (tpt90) REVERT: B 316 TYR cc_start: 0.7563 (m-10) cc_final: 0.7337 (m-80) REVERT: B 404 ARG cc_start: 0.7475 (mtt-85) cc_final: 0.6425 (mtm110) outliers start: 23 outliers final: 4 residues processed: 115 average time/residue: 1.0259 time to fit residues: 125.6351 Evaluate side-chains 103 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 248 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.134072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.104559 restraints weight = 9547.017| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.94 r_work: 0.3074 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7126 Z= 0.254 Angle : 0.595 7.448 9648 Z= 0.298 Chirality : 0.039 0.121 1032 Planarity : 0.005 0.031 1172 Dihedral : 16.804 179.251 1082 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 4.48 % Allowed : 13.31 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.30), residues: 804 helix: 1.02 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -3.10 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 340 HIS 0.004 0.001 HIS A 474 PHE 0.012 0.001 PHE B 338 TYR 0.013 0.001 TYR B 417 ARG 0.002 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.862 Fit side-chains REVERT: A 176 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8895 (tp) REVERT: A 318 ARG cc_start: 0.7611 (mmp-170) cc_final: 0.7189 (ttm170) REVERT: A 363 ASP cc_start: 0.8939 (p0) cc_final: 0.8522 (p0) REVERT: A 400 LYS cc_start: 0.7840 (ttmt) cc_final: 0.7447 (ttmt) REVERT: A 404 ARG cc_start: 0.7480 (mtt-85) cc_final: 0.6488 (mtm110) REVERT: B 176 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8893 (tp) REVERT: B 316 TYR cc_start: 0.7602 (m-10) cc_final: 0.7374 (m-80) REVERT: B 363 ASP cc_start: 0.8971 (p0) cc_final: 0.8543 (p0) REVERT: B 404 ARG cc_start: 0.7525 (mtt-85) cc_final: 0.6502 (mtm110) outliers start: 32 outliers final: 7 residues processed: 138 average time/residue: 1.0348 time to fit residues: 151.8631 Evaluate side-chains 106 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 402 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 28 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.139745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.107036 restraints weight = 9261.022| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.15 r_work: 0.3123 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7126 Z= 0.207 Angle : 0.575 7.400 9648 Z= 0.287 Chirality : 0.038 0.120 1032 Planarity : 0.004 0.041 1172 Dihedral : 16.129 178.396 1082 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.50 % Allowed : 16.11 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.31), residues: 804 helix: 1.29 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -2.96 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 340 HIS 0.004 0.001 HIS A 474 PHE 0.028 0.001 PHE A 443 TYR 0.011 0.001 TYR B 417 ARG 0.003 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.733 Fit side-chains REVERT: A 318 ARG cc_start: 0.7472 (mmp-170) cc_final: 0.7032 (ttm170) REVERT: A 400 LYS cc_start: 0.7366 (ttmt) cc_final: 0.7033 (ttmt) REVERT: A 404 ARG cc_start: 0.7137 (mtt-85) cc_final: 0.6121 (mtm110) REVERT: B 73 ASP cc_start: 0.8284 (m-30) cc_final: 0.7990 (t0) REVERT: B 400 LYS cc_start: 0.7473 (ttmt) cc_final: 0.7144 (ttmt) REVERT: B 404 ARG cc_start: 0.7142 (mtt-85) cc_final: 0.6137 (mtm110) REVERT: B 425 MET cc_start: 0.8324 (mtt) cc_final: 0.8069 (mtp) outliers start: 25 outliers final: 7 residues processed: 125 average time/residue: 1.0569 time to fit residues: 140.2654 Evaluate side-chains 105 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 377 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 18 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.136917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.104422 restraints weight = 9222.462| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.12 r_work: 0.3103 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7126 Z= 0.341 Angle : 0.625 7.822 9648 Z= 0.311 Chirality : 0.041 0.123 1032 Planarity : 0.005 0.038 1172 Dihedral : 16.150 170.583 1082 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 4.34 % Allowed : 17.79 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.31), residues: 804 helix: 1.28 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -2.84 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 340 HIS 0.004 0.001 HIS A 382 PHE 0.015 0.002 PHE B 338 TYR 0.014 0.001 TYR A 417 ARG 0.003 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.683 Fit side-chains REVERT: A 318 ARG cc_start: 0.7520 (mmp-170) cc_final: 0.7045 (ttm170) REVERT: A 400 LYS cc_start: 0.7417 (ttmt) cc_final: 0.7101 (ttmt) REVERT: A 404 ARG cc_start: 0.7221 (mtt-85) cc_final: 0.6256 (mtm110) REVERT: B 400 LYS cc_start: 0.7518 (ttmt) cc_final: 0.7160 (ttmt) REVERT: B 404 ARG cc_start: 0.7174 (mtt-85) cc_final: 0.6173 (mtm110) outliers start: 31 outliers final: 9 residues processed: 121 average time/residue: 1.0886 time to fit residues: 139.5604 Evaluate side-chains 99 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 76 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.141138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109006 restraints weight = 9154.150| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.12 r_work: 0.3169 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7126 Z= 0.172 Angle : 0.574 7.703 9648 Z= 0.287 Chirality : 0.038 0.121 1032 Planarity : 0.004 0.032 1172 Dihedral : 15.561 172.252 1082 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.36 % Allowed : 18.77 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.31), residues: 804 helix: 1.55 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.83 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 340 HIS 0.004 0.001 HIS B 474 PHE 0.029 0.001 PHE A 443 TYR 0.010 0.001 TYR A 211 ARG 0.003 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.740 Fit side-chains REVERT: A 73 ASP cc_start: 0.8313 (m-30) cc_final: 0.8057 (t0) REVERT: A 224 LYS cc_start: 0.8645 (ttpp) cc_final: 0.7880 (tmmt) REVERT: A 400 LYS cc_start: 0.7308 (ttmt) cc_final: 0.7010 (ttmt) REVERT: A 404 ARG cc_start: 0.7167 (mtt-85) cc_final: 0.6199 (mtm110) REVERT: A 467 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8312 (mp) REVERT: B 73 ASP cc_start: 0.8277 (m-30) cc_final: 0.8005 (t0) REVERT: B 224 LYS cc_start: 0.8651 (ttpp) cc_final: 0.7850 (tmmt) REVERT: B 400 LYS cc_start: 0.7445 (ttmt) cc_final: 0.7137 (ttmt) REVERT: B 404 ARG cc_start: 0.7198 (mtt-85) cc_final: 0.6207 (mtm110) REVERT: B 425 MET cc_start: 0.8351 (mtt) cc_final: 0.8144 (mtp) REVERT: B 467 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8313 (mp) outliers start: 24 outliers final: 6 residues processed: 131 average time/residue: 1.0930 time to fit residues: 151.6444 Evaluate side-chains 108 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 5 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.139034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106503 restraints weight = 9110.078| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.12 r_work: 0.3130 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7126 Z= 0.275 Angle : 0.607 7.541 9648 Z= 0.301 Chirality : 0.040 0.122 1032 Planarity : 0.004 0.035 1172 Dihedral : 15.565 168.096 1082 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 3.78 % Allowed : 19.47 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.31), residues: 804 helix: 1.53 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.83 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 340 HIS 0.004 0.001 HIS A 474 PHE 0.017 0.002 PHE B 443 TYR 0.012 0.001 TYR A 417 ARG 0.003 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.772 Fit side-chains REVERT: A 73 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8049 (t0) REVERT: A 224 LYS cc_start: 0.8626 (ttpp) cc_final: 0.7866 (tmmt) REVERT: A 368 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8389 (pt0) REVERT: A 400 LYS cc_start: 0.7339 (ttmt) cc_final: 0.7038 (ttmt) REVERT: A 404 ARG cc_start: 0.7188 (mtt-85) cc_final: 0.6223 (mtm110) REVERT: B 224 LYS cc_start: 0.8630 (ttpp) cc_final: 0.7875 (tmmt) REVERT: B 400 LYS cc_start: 0.7438 (ttmt) cc_final: 0.7110 (ttmt) REVERT: B 404 ARG cc_start: 0.7216 (mtt-85) cc_final: 0.6220 (mtm110) REVERT: B 425 MET cc_start: 0.8384 (mtt) cc_final: 0.8161 (mtp) outliers start: 27 outliers final: 11 residues processed: 122 average time/residue: 1.1047 time to fit residues: 142.7947 Evaluate side-chains 115 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.141110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108622 restraints weight = 9122.481| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.13 r_work: 0.3164 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7126 Z= 0.181 Angle : 0.585 8.180 9648 Z= 0.292 Chirality : 0.038 0.120 1032 Planarity : 0.004 0.033 1172 Dihedral : 15.164 167.871 1082 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.50 % Allowed : 20.45 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.31), residues: 804 helix: 1.66 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.75 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 340 HIS 0.004 0.001 HIS A 474 PHE 0.032 0.002 PHE A 443 TYR 0.010 0.001 TYR A 417 ARG 0.004 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.771 Fit side-chains REVERT: A 73 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8046 (t0) REVERT: A 224 LYS cc_start: 0.8633 (ttpp) cc_final: 0.7830 (tmmt) REVERT: A 368 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8334 (pt0) REVERT: A 400 LYS cc_start: 0.7352 (ttmt) cc_final: 0.7051 (ttmt) REVERT: A 404 ARG cc_start: 0.7219 (mtt-85) cc_final: 0.6251 (mtm110) REVERT: B 73 ASP cc_start: 0.8281 (m-30) cc_final: 0.8013 (t0) REVERT: B 224 LYS cc_start: 0.8621 (ttpp) cc_final: 0.7817 (tmmt) REVERT: B 368 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8333 (pt0) REVERT: B 400 LYS cc_start: 0.7441 (ttmt) cc_final: 0.7112 (ttmt) REVERT: B 404 ARG cc_start: 0.7206 (mtt-85) cc_final: 0.6228 (mtm110) REVERT: B 425 MET cc_start: 0.8375 (mtt) cc_final: 0.8174 (mtp) REVERT: B 467 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8348 (mp) outliers start: 25 outliers final: 10 residues processed: 122 average time/residue: 1.1097 time to fit residues: 143.4071 Evaluate side-chains 115 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.142438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109485 restraints weight = 9310.225| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.21 r_work: 0.3159 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7126 Z= 0.188 Angle : 0.581 7.881 9648 Z= 0.290 Chirality : 0.039 0.119 1032 Planarity : 0.004 0.031 1172 Dihedral : 14.955 166.412 1082 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.08 % Allowed : 21.99 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.31), residues: 804 helix: 1.74 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -2.71 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 340 HIS 0.004 0.001 HIS B 474 PHE 0.031 0.002 PHE B 443 TYR 0.010 0.001 TYR A 417 ARG 0.003 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.711 Fit side-chains REVERT: A 73 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7823 (t0) REVERT: A 224 LYS cc_start: 0.8624 (ttpp) cc_final: 0.7829 (tmmt) REVERT: A 318 ARG cc_start: 0.7485 (mmp-170) cc_final: 0.7168 (ttm170) REVERT: A 368 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8184 (pt0) REVERT: A 400 LYS cc_start: 0.7414 (ttmt) cc_final: 0.7119 (ttmt) REVERT: A 404 ARG cc_start: 0.7239 (mtt-85) cc_final: 0.6268 (mtm110) REVERT: B 73 ASP cc_start: 0.8081 (m-30) cc_final: 0.7789 (t0) REVERT: B 368 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8180 (pt0) REVERT: B 400 LYS cc_start: 0.7457 (ttmt) cc_final: 0.7136 (ttmt) REVERT: B 404 ARG cc_start: 0.7192 (mtt-85) cc_final: 0.6219 (mtm110) outliers start: 22 outliers final: 10 residues processed: 125 average time/residue: 1.1674 time to fit residues: 153.9344 Evaluate side-chains 120 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 266 ASN A 292 GLN B 162 GLN B 266 ASN B 292 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.143795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.111219 restraints weight = 9407.125| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.21 r_work: 0.3193 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7126 Z= 0.166 Angle : 0.570 7.750 9648 Z= 0.284 Chirality : 0.038 0.159 1032 Planarity : 0.004 0.032 1172 Dihedral : 14.641 163.826 1082 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.94 % Allowed : 21.57 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.31), residues: 804 helix: 1.85 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -2.69 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 340 HIS 0.004 0.001 HIS B 474 PHE 0.018 0.001 PHE B 443 TYR 0.010 0.001 TYR B 211 ARG 0.002 0.000 ARG B 358 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.667 Fit side-chains REVERT: A 73 ASP cc_start: 0.8131 (m-30) cc_final: 0.7847 (t0) REVERT: A 368 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8177 (pt0) REVERT: A 400 LYS cc_start: 0.7480 (ttmt) cc_final: 0.7201 (ttmt) REVERT: A 404 ARG cc_start: 0.7290 (mtt-85) cc_final: 0.6318 (mtm110) REVERT: B 73 ASP cc_start: 0.8073 (m-30) cc_final: 0.7787 (t0) REVERT: B 404 ARG cc_start: 0.7300 (mtt-85) cc_final: 0.6948 (mtt90) REVERT: B 467 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8110 (mp) outliers start: 21 outliers final: 9 residues processed: 136 average time/residue: 1.0777 time to fit residues: 155.3028 Evaluate side-chains 121 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 19 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 292 GLN B 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110935 restraints weight = 9173.540| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.13 r_work: 0.3189 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7126 Z= 0.240 Angle : 1.265 59.193 9648 Z= 0.761 Chirality : 0.042 0.267 1032 Planarity : 0.004 0.032 1172 Dihedral : 14.644 163.801 1082 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.96 % Allowed : 22.83 % Favored : 75.21 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.31), residues: 804 helix: 1.87 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -2.69 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 340 HIS 0.004 0.001 HIS B 474 PHE 0.019 0.002 PHE B 443 TYR 0.010 0.001 TYR B 211 ARG 0.011 0.000 ARG A 427 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4733.74 seconds wall clock time: 84 minutes 8.26 seconds (5048.26 seconds total)