Starting phenix.real_space_refine on Tue Feb 13 08:35:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uac_26420/02_2024/7uac_26420.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uac_26420/02_2024/7uac_26420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uac_26420/02_2024/7uac_26420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uac_26420/02_2024/7uac_26420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uac_26420/02_2024/7uac_26420.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uac_26420/02_2024/7uac_26420.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.045 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 S 21 5.16 5 C 2860 2.51 5 N 759 2.21 5 O 897 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 39": "OE1" <-> "OE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H GLU 154": "OE1" <-> "OE2" Residue "H GLU 156": "OE1" <-> "OE2" Residue "H TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 234": "OE1" <-> "OE2" Residue "H GLU 272": "OE1" <-> "OE2" Residue "H GLU 299": "OE1" <-> "OE2" Residue "H GLU 325": "OE1" <-> "OE2" Residue "H GLU 326": "OE1" <-> "OE2" Residue "H GLU 331": "OE1" <-> "OE2" Residue "H ARG 372": "NH1" <-> "NH2" Residue "H GLU 397": "OE1" <-> "OE2" Residue "H GLU 398": "OE1" <-> "OE2" Residue "H GLU 446": "OE1" <-> "OE2" Residue "H GLU 492": "OE1" <-> "OE2" Residue "H GLU 498": "OE1" <-> "OE2" Residue "H ASP 512": "OD1" <-> "OD2" Residue "H GLU 514": "OE1" <-> "OE2" Residue "H GLU 594": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4540 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 4404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4404 Classifications: {'peptide': 546} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 528} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.03, per 1000 atoms: 0.67 Number of scatterers: 4540 At special positions: 0 Unit cell: (94.34, 77.38, 92.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 2 19.99 S 21 16.00 O 897 8.00 N 759 7.00 C 2860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 107 " - pdb=" SG CYS H 259 " distance=2.03 Simple disulfide: pdb=" SG CYS H 128 " - pdb=" SG CYS H 147 " distance=2.02 Simple disulfide: pdb=" SG CYS H 269 " - pdb=" SG CYS H 277 " distance=2.03 Simple disulfide: pdb=" SG CYS H 343 " - pdb=" SG CYS H 431 " distance=2.05 Simple disulfide: pdb=" SG CYS H 557 " - pdb=" SG CYS H 559 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " BETA1-6 " NAG C 1 " - " FUC C 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN H 140 " " NAG B 1 " - " ASN H 222 " " NAG C 1 " - " ASN H 414 " " NAG D 1 " - " ASN H 440 " Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 830.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 702 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 159 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 165 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 155 " 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1016 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 9 sheets defined 21.8% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'H' and resid 42 through 51 Processing helix chain 'H' and resid 88 through 106 Processing helix chain 'H' and resid 149 through 161 Processing helix chain 'H' and resid 165 through 169 removed outlier: 3.606A pdb=" N SER H 168 " --> pdb=" O HIS H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 174 Processing helix chain 'H' and resid 180 through 183 Processing helix chain 'H' and resid 187 through 192 Processing helix chain 'H' and resid 232 through 238 Processing helix chain 'H' and resid 246 through 258 Processing helix chain 'H' and resid 275 through 279 Processing helix chain 'H' and resid 440 through 448 Processing helix chain 'H' and resid 516 through 520 Processing helix chain 'H' and resid 546 through 550 Processing helix chain 'H' and resid 573 through 577 Processing helix chain 'H' and resid 582 through 586 Processing helix chain 'H' and resid 597 through 600 Processing sheet with id=AA1, first strand: chain 'H' and resid 110 through 112 removed outlier: 7.939A pdb=" N PHE H 122 " --> pdb=" O PRO H 80 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE H 82 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 176 through 178 Processing sheet with id=AA3, first strand: chain 'H' and resid 265 through 269 Processing sheet with id=AA4, first strand: chain 'H' and resid 265 through 269 removed outlier: 5.664A pdb=" N LEU H 421 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LYS H 349 " --> pdb=" O LEU H 421 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP H 423 " --> pdb=" O PHE H 347 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE H 347 " --> pdb=" O ASP H 423 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 280 through 281 removed outlier: 6.826A pdb=" N LEU H 358 " --> pdb=" O THR H 379 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR H 379 " --> pdb=" O LEU H 358 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL H 360 " --> pdb=" O VAL H 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 434 through 438 Processing sheet with id=AA7, first strand: chain 'H' and resid 454 through 455 Processing sheet with id=AA8, first strand: chain 'H' and resid 454 through 455 removed outlier: 3.961A pdb=" N GLY H 466 " --> pdb=" O CYS H 489 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU H 482 " --> pdb=" O GLY H 569 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU H 484 " --> pdb=" O TRP H 567 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 551 through 554 156 hydrogen bonds defined for protein. 375 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: 1.27 Time building geometry restraints manager: 2.14 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: 861 1.32 - 1.45: 1258 1.45 - 1.57: 2495 1.57 - 1.69: 0 1.69 - 1.82: 30 Bond restraints: 4644 Sorted by residual: bond pdb=" N PRO H 412 " pdb=" CA PRO H 412 " ideal model delta sigma weight residual 1.471 1.410 0.061 1.29e-02 6.01e+03 2.26e+01 bond pdb=" C GLN H 40 " pdb=" N LYS H 41 " ideal model delta sigma weight residual 1.331 1.403 -0.072 1.51e-02 4.39e+03 2.26e+01 bond pdb=" C GLU H 39 " pdb=" N GLN H 40 " ideal model delta sigma weight residual 1.330 1.385 -0.055 1.32e-02 5.74e+03 1.75e+01 bond pdb=" N ILE H 276 " pdb=" CA ILE H 276 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.43e+01 bond pdb=" CA SER H 168 " pdb=" CB SER H 168 " ideal model delta sigma weight residual 1.530 1.472 0.058 1.54e-02 4.22e+03 1.40e+01 ... (remaining 4639 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.72: 97 105.72 - 112.99: 2201 112.99 - 120.25: 2162 120.25 - 127.52: 1783 127.52 - 134.78: 49 Bond angle restraints: 6292 Sorted by residual: angle pdb=" CA PHE H 590 " pdb=" CB PHE H 590 " pdb=" CG PHE H 590 " ideal model delta sigma weight residual 113.80 120.35 -6.55 1.00e+00 1.00e+00 4.28e+01 angle pdb=" N GLN H 135 " pdb=" CA GLN H 135 " pdb=" C GLN H 135 " ideal model delta sigma weight residual 113.30 104.70 8.60 1.34e+00 5.57e-01 4.12e+01 angle pdb=" C PRO H 412 " pdb=" CA PRO H 412 " pdb=" CB PRO H 412 " ideal model delta sigma weight residual 112.55 121.90 -9.35 1.50e+00 4.44e-01 3.88e+01 angle pdb=" CA GLY H 138 " pdb=" C GLY H 138 " pdb=" O GLY H 138 " ideal model delta sigma weight residual 122.23 118.25 3.98 6.90e-01 2.10e+00 3.32e+01 angle pdb=" CA ASP H 134 " pdb=" CB ASP H 134 " pdb=" CG ASP H 134 " ideal model delta sigma weight residual 112.60 118.31 -5.71 1.00e+00 1.00e+00 3.26e+01 ... (remaining 6287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.46: 2693 22.46 - 44.92: 116 44.92 - 67.38: 22 67.38 - 89.84: 7 89.84 - 112.30: 22 Dihedral angle restraints: 2860 sinusoidal: 1279 harmonic: 1581 Sorted by residual: dihedral pdb=" CB CYS H 128 " pdb=" SG CYS H 128 " pdb=" SG CYS H 147 " pdb=" CB CYS H 147 " ideal model delta sinusoidal sigma weight residual 93.00 151.89 -58.89 1 1.00e+01 1.00e-02 4.64e+01 dihedral pdb=" C PRO H 412 " pdb=" N PRO H 412 " pdb=" CA PRO H 412 " pdb=" CB PRO H 412 " ideal model delta harmonic sigma weight residual -120.70 -134.70 14.00 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" CA ILE H 424 " pdb=" C ILE H 424 " pdb=" N THR H 425 " pdb=" CA THR H 425 " ideal model delta harmonic sigma weight residual 180.00 153.34 26.66 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 2857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 571 0.128 - 0.256: 109 0.256 - 0.384: 18 0.384 - 0.511: 2 0.511 - 0.639: 1 Chirality restraints: 701 Sorted by residual: chirality pdb=" C1 FUC C 4 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 4 " pdb=" O5 FUC C 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.54e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.76e+01 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.09e+01 ... (remaining 698 not shown) Planarity restraints: 809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.228 2.00e-02 2.50e+03 1.93e-01 4.64e+02 pdb=" C7 NAG A 1 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.155 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.326 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.218 2.00e-02 2.50e+03 1.82e-01 4.12e+02 pdb=" C7 NAG D 1 " 0.059 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.154 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.300 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.115 2.00e-02 2.50e+03 9.51e-02 1.13e+02 pdb=" C7 NAG C 1 " -0.033 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.087 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.151 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.018 2.00e-02 2.50e+03 ... (remaining 806 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 3 2.28 - 2.94: 1967 2.94 - 3.59: 5970 3.59 - 4.25: 11163 4.25 - 4.90: 18169 Nonbonded interactions: 37272 Sorted by model distance: nonbonded pdb=" OD1 ASP H 58 " pdb="ZN ZN H 702 " model vdw 1.626 2.230 nonbonded pdb=" CG ASP H 58 " pdb="ZN ZN H 702 " model vdw 2.169 2.460 nonbonded pdb=" OD2 ASP H 58 " pdb="ZN ZN H 702 " model vdw 2.250 2.230 nonbonded pdb=" OD1 ASP H 288 " pdb="CA CA H 701 " model vdw 2.332 2.510 nonbonded pdb=" OD1 ASP H 285 " pdb="CA CA H 701 " model vdw 2.343 2.510 ... (remaining 37267 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.460 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.050 Find NCS groups from input model: 0.120 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:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.012 0.072 4644 Z= 0.766 Angle : 1.786 9.345 6292 Z= 1.201 Chirality : 0.109 0.639 701 Planarity : 0.015 0.193 805 Dihedral : 17.447 112.300 1829 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.98 % Peptide Plane: Cis-proline : 11.76 % 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: -0.63 (0.33), residues: 538 helix: -0.90 (0.48), residues: 78 sheet: 0.08 (0.43), residues: 127 loop : -0.44 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.012 TRP H 180 HIS 0.013 0.003 HIS H 159 PHE 0.060 0.011 PHE H 593 TYR 0.081 0.014 TYR H 119 ARG 0.007 0.001 ARG H 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: H 130 SER cc_start: 0.8444 (t) cc_final: 0.8059 (m) REVERT: H 150 LYS cc_start: 0.8035 (ttpp) cc_final: 0.7761 (ttmt) REVERT: H 154 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7768 (mt-10) REVERT: H 156 GLU cc_start: 0.8764 (mm-30) cc_final: 0.7882 (mm-30) REVERT: H 183 ILE cc_start: 0.9047 (mt) cc_final: 0.8817 (mt) REVERT: H 192 ASP cc_start: 0.7554 (m-30) cc_final: 0.7349 (m-30) REVERT: H 207 ASP cc_start: 0.7777 (t0) cc_final: 0.7274 (t0) REVERT: H 212 MET cc_start: 0.8763 (mmm) cc_final: 0.8176 (mmp) REVERT: H 225 VAL cc_start: 0.8804 (t) cc_final: 0.8522 (p) REVERT: H 244 ASP cc_start: 0.7817 (t70) cc_final: 0.7600 (t0) REVERT: H 249 ASP cc_start: 0.7589 (m-30) cc_final: 0.7367 (m-30) REVERT: H 251 GLU cc_start: 0.7637 (tt0) cc_final: 0.7378 (tt0) REVERT: H 256 MET cc_start: 0.8696 (ttp) cc_final: 0.8272 (ttt) REVERT: H 323 SER cc_start: 0.8765 (t) cc_final: 0.8346 (p) REVERT: H 326 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7084 (mt-10) REVERT: H 423 ASP cc_start: 0.8088 (m-30) cc_final: 0.7654 (m-30) REVERT: H 492 GLU cc_start: 0.7887 (pt0) cc_final: 0.7250 (tm-30) REVERT: H 525 MET cc_start: 0.7589 (mmt) cc_final: 0.7310 (mmm) REVERT: H 527 PHE cc_start: 0.8466 (p90) cc_final: 0.8030 (p90) REVERT: H 543 ILE cc_start: 0.9345 (mt) cc_final: 0.9120 (mm) REVERT: H 565 LEU cc_start: 0.9180 (tt) cc_final: 0.8928 (tm) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 1.2940 time to fit residues: 217.8405 Evaluate side-chains 98 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 40 GLN H 124 GLN H 203 ASN H 370 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4644 Z= 0.250 Angle : 0.707 8.515 6292 Z= 0.368 Chirality : 0.048 0.192 701 Planarity : 0.004 0.034 805 Dihedral : 14.796 109.464 796 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.48 % Allowed : 10.95 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.04 (0.33), residues: 538 helix: 0.92 (0.63), residues: 71 sheet: 0.42 (0.43), residues: 133 loop : -0.30 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 129 HIS 0.004 0.001 HIS H 155 PHE 0.015 0.002 PHE H 593 TYR 0.016 0.002 TYR H 113 ARG 0.007 0.001 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: H 39 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7705 (pp20) REVERT: H 130 SER cc_start: 0.8665 (t) cc_final: 0.8100 (m) REVERT: H 192 ASP cc_start: 0.7638 (m-30) cc_final: 0.7265 (m-30) REVERT: H 206 TYR cc_start: 0.8726 (t80) cc_final: 0.8404 (t80) REVERT: H 207 ASP cc_start: 0.7737 (t0) cc_final: 0.7450 (t0) REVERT: H 212 MET cc_start: 0.8569 (mmm) cc_final: 0.8239 (mmp) REVERT: H 228 ILE cc_start: 0.8741 (mt) cc_final: 0.8514 (mm) REVERT: H 238 ILE cc_start: 0.8982 (mp) cc_final: 0.8733 (mp) REVERT: H 249 ASP cc_start: 0.7633 (m-30) cc_final: 0.7258 (m-30) REVERT: H 251 GLU cc_start: 0.7710 (tt0) cc_final: 0.7447 (tt0) REVERT: H 284 ARG cc_start: 0.4400 (ttt180) cc_final: 0.0501 (tmt170) REVERT: H 304 LEU cc_start: 0.9227 (mt) cc_final: 0.8776 (mm) REVERT: H 329 LEU cc_start: 0.8984 (mt) cc_final: 0.8733 (mt) REVERT: H 331 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: H 385 ASP cc_start: 0.8481 (t0) cc_final: 0.8215 (t0) REVERT: H 415 SER cc_start: 0.8749 (t) cc_final: 0.8326 (p) REVERT: H 525 MET cc_start: 0.7460 (mmt) cc_final: 0.7231 (mmm) REVERT: H 543 ILE cc_start: 0.9347 (mt) cc_final: 0.9098 (mm) REVERT: H 565 LEU cc_start: 0.9163 (tt) cc_final: 0.8961 (tm) outliers start: 12 outliers final: 3 residues processed: 112 average time/residue: 1.1252 time to fit residues: 130.9904 Evaluate side-chains 97 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 552 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.0050 chunk 15 optimal weight: 0.0980 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 90 ASN H 190 ASN H 203 ASN H 386 HIS H 455 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4644 Z= 0.187 Angle : 0.614 6.623 6292 Z= 0.320 Chirality : 0.045 0.176 701 Planarity : 0.004 0.032 805 Dihedral : 10.503 109.087 796 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.27 % Allowed : 13.22 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.17 (0.34), residues: 538 helix: 1.15 (0.61), residues: 77 sheet: 0.43 (0.43), residues: 141 loop : -0.24 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 129 HIS 0.005 0.001 HIS H 155 PHE 0.024 0.002 PHE H 527 TYR 0.011 0.001 TYR H 403 ARG 0.008 0.001 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.521 Fit side-chains REVERT: H 116 GLU cc_start: 0.6704 (mp0) cc_final: 0.6487 (mp0) REVERT: H 130 SER cc_start: 0.8661 (t) cc_final: 0.8113 (m) REVERT: H 192 ASP cc_start: 0.7635 (m-30) cc_final: 0.7252 (m-30) REVERT: H 207 ASP cc_start: 0.7716 (t0) cc_final: 0.7335 (t0) REVERT: H 212 MET cc_start: 0.8549 (mmm) cc_final: 0.8244 (mmp) REVERT: H 228 ILE cc_start: 0.8756 (mt) cc_final: 0.8524 (mm) REVERT: H 249 ASP cc_start: 0.7589 (m-30) cc_final: 0.6796 (m-30) REVERT: H 251 GLU cc_start: 0.7742 (tt0) cc_final: 0.7522 (tt0) REVERT: H 284 ARG cc_start: 0.4262 (ttt180) cc_final: 0.0531 (tmt170) REVERT: H 331 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: H 415 SER cc_start: 0.8844 (t) cc_final: 0.8394 (p) REVERT: H 489 CYS cc_start: 0.7711 (m) cc_final: 0.7481 (m) REVERT: H 525 MET cc_start: 0.7470 (mmt) cc_final: 0.7199 (mmm) REVERT: H 543 ILE cc_start: 0.9309 (mt) cc_final: 0.8996 (mm) REVERT: H 578 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7898 (ptp90) REVERT: H 586 ASP cc_start: 0.7037 (m-30) cc_final: 0.6734 (m-30) outliers start: 11 outliers final: 5 residues processed: 106 average time/residue: 1.0388 time to fit residues: 114.8274 Evaluate side-chains 102 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 552 THR Chi-restraints excluded: chain H residue 578 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN H 203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4644 Z= 0.259 Angle : 0.604 7.253 6292 Z= 0.316 Chirality : 0.045 0.170 701 Planarity : 0.004 0.034 805 Dihedral : 8.651 97.127 796 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.31 % Allowed : 15.08 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.07 (0.35), residues: 538 helix: 1.22 (0.61), residues: 77 sheet: 0.26 (0.42), residues: 147 loop : -0.31 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 289 HIS 0.005 0.001 HIS H 155 PHE 0.027 0.002 PHE H 527 TYR 0.009 0.001 TYR H 81 ARG 0.008 0.001 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.446 Fit side-chains REVERT: H 130 SER cc_start: 0.8658 (t) cc_final: 0.8097 (m) REVERT: H 192 ASP cc_start: 0.7639 (m-30) cc_final: 0.7262 (m-30) REVERT: H 207 ASP cc_start: 0.7699 (t0) cc_final: 0.7318 (t0) REVERT: H 212 MET cc_start: 0.8632 (mmm) cc_final: 0.8201 (mmp) REVERT: H 228 ILE cc_start: 0.8757 (mt) cc_final: 0.8527 (mm) REVERT: H 238 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8867 (mp) REVERT: H 249 ASP cc_start: 0.7598 (m-30) cc_final: 0.6843 (m-30) REVERT: H 251 GLU cc_start: 0.7782 (tt0) cc_final: 0.7572 (tt0) REVERT: H 252 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.7978 (mtm-85) REVERT: H 284 ARG cc_start: 0.4477 (ttt180) cc_final: 0.0755 (tmt170) REVERT: H 331 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: H 415 SER cc_start: 0.8852 (t) cc_final: 0.8413 (p) REVERT: H 425 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8212 (p) REVERT: H 454 LEU cc_start: 0.7903 (mp) cc_final: 0.7424 (mt) REVERT: H 531 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8840 (mmmm) REVERT: H 543 ILE cc_start: 0.9279 (mt) cc_final: 0.8898 (mm) REVERT: H 586 ASP cc_start: 0.7030 (m-30) cc_final: 0.6763 (m-30) outliers start: 16 outliers final: 6 residues processed: 108 average time/residue: 0.9505 time to fit residues: 107.3987 Evaluate side-chains 98 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 531 LYS Chi-restraints excluded: chain H residue 552 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN H 203 ASN H 392 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4644 Z= 0.302 Angle : 0.617 8.782 6292 Z= 0.323 Chirality : 0.045 0.163 701 Planarity : 0.004 0.037 805 Dihedral : 7.288 73.278 796 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.51 % Allowed : 16.32 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.03 (0.35), residues: 538 helix: 1.26 (0.61), residues: 77 sheet: 0.40 (0.42), residues: 145 loop : -0.44 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 289 HIS 0.005 0.001 HIS H 159 PHE 0.027 0.002 PHE H 527 TYR 0.011 0.001 TYR H 81 ARG 0.009 0.001 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: H 130 SER cc_start: 0.8647 (t) cc_final: 0.8062 (m) REVERT: H 192 ASP cc_start: 0.7658 (m-30) cc_final: 0.7254 (m-30) REVERT: H 207 ASP cc_start: 0.7694 (t0) cc_final: 0.7319 (t0) REVERT: H 212 MET cc_start: 0.8628 (mmm) cc_final: 0.8269 (mmp) REVERT: H 228 ILE cc_start: 0.8789 (mt) cc_final: 0.8563 (mm) REVERT: H 238 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8780 (mp) REVERT: H 249 ASP cc_start: 0.7657 (m-30) cc_final: 0.6922 (m-30) REVERT: H 252 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.8023 (mtm-85) REVERT: H 284 ARG cc_start: 0.4482 (ttt180) cc_final: 0.0766 (tmt170) REVERT: H 301 ASP cc_start: 0.7387 (p0) cc_final: 0.7056 (p0) REVERT: H 331 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: H 415 SER cc_start: 0.8873 (t) cc_final: 0.8432 (p) REVERT: H 525 MET cc_start: 0.7498 (mmm) cc_final: 0.6962 (mmm) REVERT: H 543 ILE cc_start: 0.9265 (mt) cc_final: 0.8878 (mm) REVERT: H 584 ASN cc_start: 0.8560 (t0) cc_final: 0.7893 (t160) REVERT: H 586 ASP cc_start: 0.6953 (m-30) cc_final: 0.6637 (m-30) outliers start: 17 outliers final: 5 residues processed: 108 average time/residue: 1.0955 time to fit residues: 123.3526 Evaluate side-chains 96 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 552 THR Chi-restraints excluded: chain H residue 576 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN H 203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4644 Z= 0.289 Angle : 0.626 7.898 6292 Z= 0.329 Chirality : 0.045 0.172 701 Planarity : 0.004 0.046 805 Dihedral : 5.876 51.043 796 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.69 % Allowed : 17.36 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.04 (0.35), residues: 538 helix: 1.32 (0.61), residues: 77 sheet: 0.22 (0.42), residues: 150 loop : -0.46 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 289 HIS 0.005 0.001 HIS H 155 PHE 0.030 0.002 PHE H 37 TYR 0.010 0.001 TYR H 81 ARG 0.010 0.001 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: H 130 SER cc_start: 0.8645 (t) cc_final: 0.8065 (m) REVERT: H 166 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7652 (mm-30) REVERT: H 192 ASP cc_start: 0.7644 (m-30) cc_final: 0.7228 (m-30) REVERT: H 207 ASP cc_start: 0.7700 (t0) cc_final: 0.7250 (t0) REVERT: H 212 MET cc_start: 0.8625 (mmm) cc_final: 0.8296 (mmp) REVERT: H 228 ILE cc_start: 0.8781 (mt) cc_final: 0.8547 (mm) REVERT: H 238 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8787 (mp) REVERT: H 249 ASP cc_start: 0.7676 (m-30) cc_final: 0.6952 (m-30) REVERT: H 252 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.7970 (mtm-85) REVERT: H 284 ARG cc_start: 0.4468 (ttt180) cc_final: 0.3801 (mtp180) REVERT: H 301 ASP cc_start: 0.7504 (p0) cc_final: 0.7125 (p0) REVERT: H 415 SER cc_start: 0.8854 (t) cc_final: 0.8413 (p) REVERT: H 512 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.8055 (m-30) REVERT: H 525 MET cc_start: 0.7465 (mmm) cc_final: 0.6928 (mmm) REVERT: H 543 ILE cc_start: 0.9217 (mt) cc_final: 0.8834 (mm) REVERT: H 584 ASN cc_start: 0.8618 (t0) cc_final: 0.7987 (t160) REVERT: H 586 ASP cc_start: 0.6949 (m-30) cc_final: 0.6635 (m-30) REVERT: H 592 ASP cc_start: 0.6743 (p0) cc_final: 0.6482 (p0) outliers start: 13 outliers final: 7 residues processed: 104 average time/residue: 1.0662 time to fit residues: 115.5794 Evaluate side-chains 101 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 512 ASP Chi-restraints excluded: chain H residue 552 THR Chi-restraints excluded: chain H residue 576 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN H 203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4644 Z= 0.220 Angle : 0.619 8.514 6292 Z= 0.327 Chirality : 0.044 0.183 701 Planarity : 0.004 0.040 805 Dihedral : 5.298 51.056 796 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.10 % Allowed : 19.01 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.04 (0.35), residues: 538 helix: 1.35 (0.62), residues: 77 sheet: 0.27 (0.42), residues: 150 loop : -0.39 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.032 0.001 PHE H 527 TYR 0.008 0.001 TYR H 81 ARG 0.008 0.000 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 130 SER cc_start: 0.8645 (t) cc_final: 0.8077 (m) REVERT: H 192 ASP cc_start: 0.7595 (m-30) cc_final: 0.7169 (m-30) REVERT: H 207 ASP cc_start: 0.7680 (t0) cc_final: 0.7272 (t0) REVERT: H 238 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8703 (mp) REVERT: H 249 ASP cc_start: 0.7690 (m-30) cc_final: 0.6972 (m-30) REVERT: H 252 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.7967 (mtm-85) REVERT: H 284 ARG cc_start: 0.4436 (ttt180) cc_final: 0.0775 (tmt170) REVERT: H 301 ASP cc_start: 0.7516 (p0) cc_final: 0.7089 (p0) REVERT: H 339 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7992 (mtt90) REVERT: H 415 SER cc_start: 0.8810 (t) cc_final: 0.8372 (p) REVERT: H 512 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: H 525 MET cc_start: 0.7437 (mmm) cc_final: 0.6951 (mmm) REVERT: H 543 ILE cc_start: 0.9180 (mt) cc_final: 0.8800 (mm) REVERT: H 584 ASN cc_start: 0.8586 (t0) cc_final: 0.8336 (t160) outliers start: 15 outliers final: 9 residues processed: 107 average time/residue: 1.0931 time to fit residues: 121.7960 Evaluate side-chains 107 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain H residue 234 GLU Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 339 ARG Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 512 ASP Chi-restraints excluded: chain H residue 552 THR Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 585 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4644 Z= 0.214 Angle : 0.632 9.740 6292 Z= 0.332 Chirality : 0.044 0.166 701 Planarity : 0.004 0.043 805 Dihedral : 5.172 51.532 796 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.53 % Favored : 96.28 % Rotamer: Outliers : 2.27 % Allowed : 21.69 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.10 (0.35), residues: 538 helix: 0.96 (0.60), residues: 83 sheet: 0.31 (0.42), residues: 150 loop : -0.50 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.033 0.002 PHE H 527 TYR 0.008 0.001 TYR H 81 ARG 0.008 0.000 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 130 SER cc_start: 0.8640 (t) cc_final: 0.8077 (m) REVERT: H 192 ASP cc_start: 0.7608 (m-30) cc_final: 0.7161 (m-30) REVERT: H 207 ASP cc_start: 0.7689 (t0) cc_final: 0.7252 (t0) REVERT: H 238 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8707 (mp) REVERT: H 249 ASP cc_start: 0.7653 (m-30) cc_final: 0.6967 (m-30) REVERT: H 252 ARG cc_start: 0.8414 (mtm-85) cc_final: 0.7875 (mtm-85) REVERT: H 284 ARG cc_start: 0.4488 (ttt180) cc_final: 0.0867 (tmt170) REVERT: H 301 ASP cc_start: 0.7433 (p0) cc_final: 0.7068 (p0) REVERT: H 331 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: H 368 THR cc_start: 0.8998 (p) cc_final: 0.8768 (t) REVERT: H 415 SER cc_start: 0.8748 (t) cc_final: 0.8354 (p) REVERT: H 478 SER cc_start: 0.7608 (m) cc_final: 0.7032 (p) REVERT: H 525 MET cc_start: 0.7450 (mmm) cc_final: 0.6917 (mmm) REVERT: H 543 ILE cc_start: 0.9161 (mt) cc_final: 0.8808 (mm) REVERT: H 574 GLN cc_start: 0.7895 (tt0) cc_final: 0.7611 (tt0) REVERT: H 584 ASN cc_start: 0.8801 (t0) cc_final: 0.7686 (t0) REVERT: H 586 ASP cc_start: 0.6894 (m-30) cc_final: 0.6028 (m-30) outliers start: 11 outliers final: 7 residues processed: 107 average time/residue: 1.1075 time to fit residues: 123.8307 Evaluate side-chains 101 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 552 THR Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 585 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.0970 chunk 42 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4644 Z= 0.215 Angle : 0.638 10.171 6292 Z= 0.335 Chirality : 0.044 0.175 701 Planarity : 0.004 0.047 805 Dihedral : 5.064 51.845 796 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.35 % Favored : 96.47 % Rotamer: Outliers : 1.86 % Allowed : 22.52 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.07 (0.36), residues: 538 helix: 0.91 (0.60), residues: 83 sheet: 0.30 (0.43), residues: 150 loop : -0.45 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.037 0.002 PHE H 527 TYR 0.008 0.001 TYR H 81 ARG 0.009 0.000 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 104 LEU cc_start: 0.8979 (tp) cc_final: 0.8739 (tm) REVERT: H 130 SER cc_start: 0.8648 (t) cc_final: 0.8098 (m) REVERT: H 192 ASP cc_start: 0.7605 (m-30) cc_final: 0.7139 (m-30) REVERT: H 207 ASP cc_start: 0.7652 (t0) cc_final: 0.7240 (t0) REVERT: H 238 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8584 (mp) REVERT: H 249 ASP cc_start: 0.7634 (m-30) cc_final: 0.6968 (m-30) REVERT: H 252 ARG cc_start: 0.8349 (mtm-85) cc_final: 0.7908 (mtm-85) REVERT: H 284 ARG cc_start: 0.4565 (ttt180) cc_final: 0.0939 (tmt170) REVERT: H 301 ASP cc_start: 0.7446 (p0) cc_final: 0.7077 (p0) REVERT: H 331 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: H 415 SER cc_start: 0.8729 (t) cc_final: 0.8332 (p) REVERT: H 428 GLU cc_start: 0.7484 (tt0) cc_final: 0.7260 (tt0) REVERT: H 478 SER cc_start: 0.7646 (m) cc_final: 0.7048 (p) REVERT: H 525 MET cc_start: 0.7454 (mmm) cc_final: 0.6910 (mmm) REVERT: H 543 ILE cc_start: 0.9149 (mt) cc_final: 0.8758 (mm) REVERT: H 574 GLN cc_start: 0.7851 (tt0) cc_final: 0.7566 (tt0) REVERT: H 584 ASN cc_start: 0.8625 (t0) cc_final: 0.7955 (t0) outliers start: 9 outliers final: 8 residues processed: 104 average time/residue: 0.9753 time to fit residues: 106.1663 Evaluate side-chains 102 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 552 THR Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 585 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4644 Z= 0.238 Angle : 0.667 11.224 6292 Z= 0.346 Chirality : 0.044 0.174 701 Planarity : 0.004 0.047 805 Dihedral : 5.068 51.788 796 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.72 % Favored : 96.10 % Rotamer: Outliers : 2.27 % Allowed : 22.73 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.05 (0.36), residues: 538 helix: 0.93 (0.60), residues: 83 sheet: 0.30 (0.43), residues: 150 loop : -0.44 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.036 0.002 PHE H 527 TYR 0.008 0.001 TYR H 81 ARG 0.008 0.000 ARG H 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 104 LEU cc_start: 0.8977 (tp) cc_final: 0.8750 (tm) REVERT: H 130 SER cc_start: 0.8648 (t) cc_final: 0.8095 (m) REVERT: H 192 ASP cc_start: 0.7605 (m-30) cc_final: 0.7140 (m-30) REVERT: H 207 ASP cc_start: 0.7642 (t0) cc_final: 0.7238 (t0) REVERT: H 238 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8595 (mp) REVERT: H 249 ASP cc_start: 0.7628 (m-30) cc_final: 0.6975 (m-30) REVERT: H 252 ARG cc_start: 0.8362 (mtm-85) cc_final: 0.7935 (mtm-85) REVERT: H 284 ARG cc_start: 0.4412 (ttt180) cc_final: 0.0865 (tmt170) REVERT: H 301 ASP cc_start: 0.7467 (p0) cc_final: 0.7098 (p0) REVERT: H 331 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: H 415 SER cc_start: 0.8737 (t) cc_final: 0.8319 (p) REVERT: H 478 SER cc_start: 0.7672 (m) cc_final: 0.7078 (p) REVERT: H 525 MET cc_start: 0.7480 (mmm) cc_final: 0.6935 (mmm) REVERT: H 543 ILE cc_start: 0.9151 (mt) cc_final: 0.8762 (mm) REVERT: H 574 GLN cc_start: 0.7855 (tt0) cc_final: 0.7564 (tt0) REVERT: H 584 ASN cc_start: 0.8771 (t0) cc_final: 0.8122 (t0) outliers start: 11 outliers final: 9 residues processed: 104 average time/residue: 1.0803 time to fit residues: 117.1659 Evaluate side-chains 104 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 552 THR Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 585 ASP Chi-restraints excluded: chain H residue 592 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.090223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.080738 restraints weight = 8468.786| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.37 r_work: 0.3133 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4644 Z= 0.234 Angle : 0.670 11.649 6292 Z= 0.346 Chirality : 0.044 0.169 701 Planarity : 0.004 0.050 805 Dihedral : 5.062 51.704 796 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.53 % Favored : 96.28 % Rotamer: Outliers : 2.27 % Allowed : 22.73 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.05 (0.36), residues: 538 helix: 0.92 (0.60), residues: 83 sheet: 0.32 (0.43), residues: 150 loop : -0.43 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.036 0.002 PHE H 527 TYR 0.008 0.001 TYR H 81 ARG 0.008 0.000 ARG H 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2564.76 seconds wall clock time: 46 minutes 8.18 seconds (2768.18 seconds total)